Collaboration diagram for BLAST (Basic Local Alignment Search Tool):
Classes | |
| class | CBl2Seq |
| Runs the BLAST algorithm between 2 sequences. More... | |
| class | CBlastAdvancedProteinOptionsHandle |
| Handle to the Advanced BLASTP options. More... | |
| class | CFrameFinder |
| Function object to assist in finding all CSeqLocInfo objects which corresponds to a given frame. More... | |
| struct | CConstRefCSeqId_LessThan |
| class | CAutomaticGenCodeSingleton |
| Initializes and uninitializes the genetic code singleton as if it was an automatic variable (to facilitate use in our unit tests and in the CBlastOptions object). More... | |
| class | CBlastAppDiagHandler |
| Class to capture message from diag handler. More... | |
| class | CBLAST_SequenceBlk |
| Wrapper class for BLAST_SequenceBlk . More... | |
| class | CBlastQueryInfo |
| Wrapper class for BlastQueryInfo . More... | |
| class | CQuerySetUpOptions |
| Wrapper class for QuerySetUpOptions . More... | |
| class | CLookupTableOptions |
| Wrapper class for LookupTableOptions . More... | |
| class | CLookupTableWrap |
| Wrapper class for LookupTableWrap . More... | |
| class | CBlastInitialWordOptions |
| Wrapper class for BlastInitialWordOptions . More... | |
| class | CBlastInitialWordParameters |
| Wrapper class for BlastInitialWordParameters . More... | |
| class | CBlast_ExtendWord |
| Wrapper class for Blast_ExtendWord . More... | |
| class | CBlastExtensionOptions |
| Wrapper class for BlastExtensionOptions . More... | |
| class | CBlastExtensionParameters |
| Wrapper class for BlastExtensionParameters . More... | |
| class | CBlastHitSavingOptions |
| Wrapper class for BlastHitSavingOptions . More... | |
| class | CBlastHitSavingParameters |
| Wrapper class for BlastHitSavingParameters . More... | |
| class | CPSIBlastOptions |
| Wrapper class for PSIBlastOptions . More... | |
| class | CBlastDatabaseOptions |
| Wrapper class for BlastDatabaseOptions . More... | |
| class | CBlastScoreBlk |
| Wrapper class for BlastScoreBlk . More... | |
| class | CBlastScoringOptions |
| Wrapper class for BlastScoringOptions . More... | |
| class | CBlastScoringParameters |
| Wrapper class for BlastScoringParameters . More... | |
| class | CBlastEffectiveLengthsOptions |
| Wrapper class for BlastEffectiveLengthsOptions . More... | |
| class | CBlastEffectiveLengthsParameters |
| Wrapper class for BlastEffectiveLengthsParameters . More... | |
| class | CBlastGapAlignStruct |
| Wrapper class for BlastGapAlignStruct . More... | |
| class | CBlastHSPResults |
| Wrapper class for BlastHSPResults . More... | |
| class | CPSIMsa |
| Wrapper class for PSIMsa . More... | |
| class | CPSIMatrix |
| Wrapper class for PSIMatrix . More... | |
| class | CPSIDiagnosticsRequest |
| Wrapper class for PSIDiagnosticsRequest . More... | |
| class | CPSIDiagnosticsResponse |
| Wrapper class for PSIDiagnosticsResponse . More... | |
| class | CBlastSeqSrc |
| Wrapper class for BlastSeqSrc . More... | |
| class | CBlastSeqSrcIterator |
| Wrapper class for BlastSeqSrcIterator . More... | |
| class | CBlast_Message |
| Wrapper class for Blast_Message . More... | |
| class | CBlastMaskLoc |
| Wrapper class for BlastMaskLoc . More... | |
| class | CBlastSeqLoc |
| Wrapper class for BlastSeqLoc . More... | |
| class | CSBlastProgress |
| Wrapper class for SBlastProgress . More... | |
| class | CBlastSystemException |
| Defines system exceptions occurred while running BLAST. More... | |
| class | CBlastException |
| Defines BLAST error codes (user errors included) More... | |
| class | CBlastNucleotideOptionsHandle |
| Handle to the nucleotide-nucleotide options to the BLAST algorithm. More... | |
| class | CBlastOptions |
| Encapsulates ALL the BLAST algorithm's options. More... | |
| class | CBlastOptionsBuilder |
| Class to build CBlastOptionsHandle from blast4 ASN objects. More... | |
| class | CBlastOptionsBuilder::SOptional< T > |
| Optional-value idiom. More... | |
| class | CBlastOptionsFactory |
| Creates BlastOptionsHandle objects with default values for the programs/tasks requested. More... | |
| class | CBlastOptionsHandle |
| Handle to the options to the BLAST algorithm. More... | |
| class | CBlastProteinOptionsHandle |
| Handle to the protein-protein options to the BLAST algorithm. More... | |
| class | CBlastAncillaryData |
| Class used to return ancillary data from a blast search, i.e. More... | |
| class | CSearchResults |
| Search Results for One Query. More... | |
| class | CSearchResultSet |
| Search Results for All Queries. More... | |
| class | CBlastRPSOptionsHandle |
| Handle to the rpsblast options to the BLAST algorithm. More... | |
| class | IBlastSeqInfoSrc |
| Abstract base class to encapsulate retrieval of sequence identifiers. More... | |
| class | CBlastpKmerOptionsHandle |
| Handle to the KMER BLASTP options. More... | |
| class | CBlastxOptionsHandle |
| Handle to the translated nucleotide-protein options to the BLAST algorithm. More... | |
| class | IPssmInputCdd |
| Interface for strategy to pre-process multiple alignment of conserved domains matches as input data for PSSM engine. More... | |
| class | CCddInputData |
| Strategy for pre-processing RPS-BLAST matches for PSSM computation. More... | |
| class | CCddInputData::CHitSegment |
| Represents one alignment segment of a RPS-BLAST hit. More... | |
| class | CCddInputData::CHit |
| Single RPS-BLAST hit. More... | |
| class | CCddInputData::compare_hitseg_range |
| Class used for sorting hit segments by range. More... | |
| class | CCddInputData::compare_range |
| Class used for sorting ranges. More... | |
| class | CCddInputData::compare_hits_by_seqid_eval |
| Class used for sorting hits by subject seq-id and e-value. More... | |
| class | CDeltaBlast |
| A simple realization of the DELTA-BLAST algorithm: seacrch domain database, compute PSSM, search sequence database. More... | |
| class | CDeltaBlastOptionsHandle |
| Handle to the protein-protein options to the BLAST algorithm. More... | |
| class | CDiscNucleotideOptionsHandle |
| Handle to the nucleotide-nucleotide options to the discontiguous BLAST algorithm. More... | |
| class | CEffectiveSearchSpaceCalculator |
| Auxiliary class to compute the effective search space. More... | |
| class | CBlastHSPListQueueData |
| Data structure for the queue implementation of BlastHSPStream. More... | |
| class | CLocalBlast |
| Class to perform a BLAST search on local BLAST databases Note that PHI-BLAST can be run using this class also, one only need to configure it as a regular blastp or blastn search and set the pattern in the CBlastOptionsHandle object. More... | |
| class | CLocalDbAdapter |
| Interface to create a BlastSeqSrc suitable for use in CORE BLAST from a a variety of BLAST database/subject representations. More... | |
| class | CLocalSeqSearch |
| Local sequence search. More... | |
| class | CLocalPssmSearch |
| class | CLocalSearchFactory |
| Factory for CLocalSearch. More... | |
| class | CMagicBlast |
| BLAST RNA-Seq mapper. More... | |
| class | CMagicBlastResults |
| Magic-BLAST results for a single query/read or a pair of reads. More... | |
| class | CMagicBlastResultSet |
| Results of Magic-BLAST mapping. More... | |
| class | CMagicBlastOptionsHandle |
| Handle to the nucleotide mapping options to the BLAST algorithm. More... | |
| class | CPsiBlastInputClustalW |
| This class is a concrete strategy for IPssmInputData which converts the CLUSTALW-style output containing a multiple sequence alignment into the data structures needed by the PSSM engine. More... | |
| class | CObjMgr_QueryFactory |
| NCBI C++ Object Manager dependant implementation of IQueryFactory. More... | |
| class | CObjMgrFree_QueryFactory |
| NCBI C++ Object Manager free implementation of IQueryFactory. More... | |
| class | CPHIBlastNuclOptionsHandle |
| Handle to the nuclein PHI BLAST options. More... | |
| class | CPHIBlastProtOptionsHandle |
| Handle to the protein PHI BLAST options. More... | |
| class | CBlastPrelimSearch |
| Search class to perform the preliminary stage of the BLAST search. More... | |
| class | CPsiBlastInputFreqRatios |
| Implements the interface to retrieve data for the last 2 stages of the PSSM creation. More... | |
| class | CPsiBlastInputData |
| This class is a concrete strategy for IPssmInputData, and it implements the traditional PSI-BLAST algorithm for building a multiple sequence alignment from a list of pairwise alignments using the C++ object manager. More... | |
| class | CPsiBl2Seq |
| Runs a single iteration of the PSI-BLAST algorithm between 2 sequences. More... | |
| class | CPsiBlast |
| Runs a single iteration of the PSI-BLAST algorithm on a BLAST database. More... | |
| class | CPsiBlastIterationState |
| Represents the iteration state in PSI-BLAST. More... | |
| class | CPSIBlastOptionsHandle |
| Handle to the protein-protein options to the BLAST algorithm. More... | |
| class | CPssmEngineException |
| Exception class for the CPssmEngine class. More... | |
| class | CPssmEngine |
| Computes a PSSM as specified in PSI-BLAST. More... | |
| class | CScorematPssmConverter |
| Auxiliary class to convert data encoded in the PSSM to CNcbiMatrix. More... | |
| struct | IPssmInput_Base |
| Base class for the IPssmInputData and IPssmInputFreqRatios interfaces, provided to avoid duplicating the methods that are common to both interfaces. More... | |
| struct | IPssmInputData |
| Abstract base class to encapsulate the source(s) and pre-processing of PSSM input data as well as options to the PSI-BLAST PSSM engine. More... | |
| struct | IPssmInputFreqRatios |
| Interface used to retrieve the PSSM frequency ratios to allow for "restart" processing in PSI-BLAST: Given a preliminary. More... | |
| class | ILocalQueryData |
| Provides access (not ownership) to the C structures used to configure local BLAST search class implementations. More... | |
| class | IRemoteQueryData |
| class | IQueryFactory |
| Source of query sequence data for BLAST Provides an interface for search classes to retrieve sequence data to be used in local/remote searches without coupling them to the actual means of retrieving the data. More... | |
| class | CRemoteBlastException |
| Exception class for the CRemoteBlast class. More... | |
| class | CRemoteBlast |
| API for Remote Blast Requests. More... | |
| class | CRemoteSeqSearch |
| Remote Sequence Search. More... | |
| class | CRemotePssmSearch |
| Remote Sequence Search. More... | |
| class | CRemoteSearchFactory |
| Factory for CRemoteSearch. More... | |
| class | CBlastRPSInfo |
| Wrapper class to manage the BlastRPSInfo structure, as currently there aren't any allocation or deallocation functions for this structure in the CORE of BLAST. More... | |
| class | CRPSTBlastnOptionsHandle |
| Handle to the options for translated nucleotide-RPS blast. More... | |
| struct | CImportStrategyData |
| This is the "mutable" data for CImportStrategy. More... | |
| class | CImportStrategy |
| Class to return parts of the CBlast4_request, or data associated with a CBlast4_request, such as options. More... | |
| class | CExportStrategy |
| struct | SPatternUnit |
| class | CSeedTop |
| class | CSeqDbSeqInfoSrc |
| Implementation of the IBlastSeqInfoSrc interface to encapsulate retrieval of sequence identifiers and lengths from a BLAST database. More... | |
| class | CSeqVecSeqInfoSrc |
| Implementation of the IBlastSeqInfoSrc interface to encapsulate retrieval of sequence identifiers and lengths from a vector of Seq-locs. More... | |
| class | CStructWrapper< TData > |
| class | CThreadable |
| Class that supports setting the number of threads to use with a given algorithm. More... | |
| class | CSetupFactory |
| Auxiliary class to create the various C structures to set up the preliminary and/or traceback stages of the search. More... | |
| struct | SInternalData |
| Lightweight wrapper to enclose C structures needed for running the preliminary and traceback stages of the BLAST search. More... | |
| struct | SDatabaseScanData |
| Structure to hold results of the preliminary (databases scanning phase) part of the search that are needed for the traceback. More... | |
| class | CTBlastnOptionsHandle |
| Handle to the protein-translated nucleotide options to the BLAST algorithm. More... | |
| class | CTBlastxOptionsHandle |
| Handle to the translated nucleotide-translated nucleotide options to the BLAST algorithm. More... | |
| class | CBlastTracebackSearch |
| class | CSearchException |
| Exception class. More... | |
| class | CSearchDatabase |
| Blast Search Subject. More... | |
| class | ISearch |
| Single Iteration Blast Database Search. More... | |
| class | ISeqSearch |
| Single Iteration Search of Sequence(s) Against Blast Database(s) More... | |
| class | IPssmSearch |
| Experimental interface (since this does not provide a full interface to PSI-BLAST) More... | |
| class | ISearchFactory |
| Factory for ISearch. More... | |
| class | CBlastVersion |
| Keeps track of the version of the BLAST engine in the NCBI C++ toolkit. More... | |
| class | CReference |
| Class to keep track of the various BLAST references. More... | |
| class | CIgBlastVersion |
| Keeps track of the version of IgBLAST in the NCBI C++ toolkit. More... | |
| class | CIgBlastOptions |
| class | CIgAnnotation |
| class | CIgAnnotationInfo |
| class | CIgBlastResults |
| class | CIgBlast |
| class | ScorePositionSort |
| class | CBlastServicesException |
| RemoteServicesException. More... | |
| class | CBlastServices |
| API for Remote Blast Services. More... | |
| class | CBlastSeqVectorFromCSeq_data |
| Implementation of the IBlastSeqVector interface which obtains data from a CSeq_data object. More... | |
| class | CBlastQuerySourceBioseqSet |
| Implements the IBlastQuerySource interface using a CBioseq_set as data source. More... | |
| struct | TQueryMessagesLessComparator |
| struct | TQueryMessagesEqualComparator |
| struct | SBlastSetupData |
| Return type of BlastSetupPreliminarySearch. More... | |
| class | CIndexedDb |
| This class is responsible for loading indices and doing the actual seed search. More... | |
| class | CIndexedDb_Old |
| Index wrapper for old style MegaBLAST indexing functionality. More... | |
| class | CIndexedDb_New |
| Index wrapper for new style MegaBLAST indexing functionality. More... | |
| struct | CIndexedDb_New::SVolumeDescriptor |
| Information about one leaf index volume. More... | |
| struct | CIndexedDb_New::SVolResults |
| Reference count for the volume results. More... | |
| class | CBlastOptionsMemento |
| Class that allows the transfer of data structures from the CBlastOptionsLocal class to either the BLAST preliminary or traceback search classes. More... | |
| class | CEffectiveSearchSpacesMemento |
| Memento class to save, replace out, and restore the effective search space options of the CBlastOptions object passed to its constructor. More... | |
| class | CBlastQuerySourceOM |
| Implements the object manager dependant version of the IBlastQuerySource. More... | |
| class | CBlastSeqVectorOM |
| Implementation of the IBlastSeqVector interface which obtains data from a CSeq_loc and a CScope relying on the CSeqVector class. More... | |
| struct | SBlast4ParamFinder |
| Finder class for matching CBlast4_parameter. More... | |
| class | CBlastOptionsRemote |
| Encapsulates all blast input parameters. More... | |
| class | CBlastOptionsLocal |
| Encapsulates all blast input parameters. More... | |
| struct | SBlastSequence |
| Structure to store sequence data and its length for use in the CORE of BLAST (it's a malloc'ed array of Uint1 and its length) FIXME: do not confuse with blast_seg.c's SSequence. More... | |
| class | IBlastQuerySource |
| Lightweight wrapper around an indexed sequence container. More... | |
| class | IBlastSeqVector |
| Lightweight wrapper around sequence data which provides a CSeqVector-like interface to the data. More... | |
| class | CBlastQueryFilteredFrames |
| Collection of BlastSeqLoc lists for filtering processing. More... | |
| class | CFilteringMemento |
| Memento class to save, null out, and restore the filtering options of the CBlastOptionsMemento object passed to its constructor This prevents side effects (like filtering the query sequence) to occur during calculation of the effective search space. More... | |
| struct | seq_align_pairs_first |
| struct | compare_alignments_fwrev_first |
| struct | compare_alignments_revfw_first |
| class | CObjMgr_LocalQueryData |
| Provides access (not ownership) to the C structures used to configure local BLAST search class implementations. More... | |
| class | CObjMgr_RemoteQueryData |
| class | CObjMgrFree_LocalQueryData |
| class | CObjMgrFree_RemoteQueryData |
| class | CPrelimSearchRunner |
| Functor to run the preliminary stage of the BLAST search. More... | |
| class | CPrelimSearchThread |
| Thread class to run the preliminary stage of the BLAST search. More... | |
| class | CNcbiMatrix< T > |
| class | CPsiBlastAlignmentProcessor |
| Auxiliary class to retrieve sequence identifiers its position in the alignment which are below the inclusion evalue threshold. More... | |
| class | CPsiBlastValidate |
| Auxialiry class containing static methods to validate PSI-BLAST search components. More... | |
| class | CPsiBlastImpl |
| Implementation class for PSI-BLAST (database search and 2 sequences). More... | |
| struct | SNcbiMatrix2DoubleMatrix |
| Auxiliary class to convert from a CNcbiMatrix into a double** as required by the C API. More... | |
| class | CBlastRPSAuxInfo |
| Wrapper class to manage the BlastRPSAuxInfo structure, as currently there aren't any allocation or deallocation functions for this structure in the CORE of BLAST. More... | |
| class | CRpsAuxFile |
| This class represents the .aux file in a RPS-BLAST file, which contains information about the scoring matrix to be used during the RPS-BLAST search, the scaling factor, an array of K statistical values (karlin_k), as well as various fields that are currently unused. More... | |
| class | CRpsMmappedFile |
| Encapsulates logic of mmap'ing and performing sanity checks on RPS-BLAST database files. More... | |
| class | CRpsLookupTblFile |
| This class represents the .loo file in a RPS-BLAST file, which contains the pre-computed lookup table. More... | |
| class | CRpsPssmFile |
| This class represents the .rps file in a RPS-BLAST file, which contains the PSSMs for the database. More... | |
| class | CRpsFreqsFile |
| This class represents the .wcounts file in a RPS-BLAST file, which contains the weighted residue frequencies for the database. More... | |
| class | CRpsObsrFile |
| This class represents the .obsr file in a RPS-BLAST file, which contains the numbers of independent observations for the database. More... | |
| class | CRpsFreqRatiosFile |
| This class represents the .freq file in a RPS-BLAST file, which contains the frequency ratios for the database. More... | |
| class | CBioseqSeqInfoSrc |
| Implementation of the IBlastSeqInfoSrc interface to encapsulate retrieval of sequence identifiers and lengths from a CBioseq/CBioseq_set object. More... | |
| class | CMultiSeqInfo |
| Contains information about all sequences in a set. More... | |
| struct | SMultiSeqSrcNewArgs |
| Encapsulates the arguments needed to initialize multi-sequence source. More... | |
| class | CQueryFactoryInfo |
| Contains information about all sequences in a set. More... | |
| struct | SQueryFactorySrcNewArgs |
| Encapsulates the arguments needed to initialize multi-sequence source. More... | |
| struct | SSeqDB_SeqSrc_Data |
| Simple container to support SeqSrc-local data. More... | |
| class | CSeqDbSrcNewArgs |
| Encapsulates the arguments needed to initialize CSeqDB. More... | |
| class | CQuerySplitter |
| Class responsible for splitting query sequences and providing data to the BLAST search class to search a split query chunk. More... | |
| class | CContextTranslator |
| Auxiliary class to provide convenient and efficient access to conversions between contexts local to query split chunks and the absolute (full, unsplit) query. More... | |
| class | CQueryDataPerChunk |
| Auxiliary class to determine information about the query that was split into chunks. More... | |
| class | CSplitQueryBlk |
| Wrapper class around SSplitQueryBlk structure. More... | |
| class | CAutoNcbiConfigFile |
| Auxiliary class to write temporary NCBI configuration files in the local directory for the purpose of testing the CBlastScopeSource configuration class via this file (and override any other installed NCBI configuration files) More... | |
| class | CBlastScopeSourceWrapper |
| RAII class for the CBlastScopeSource. More... | |
Macros | |
| #define | TYPEDEF_AUTOPTR_CDELETER(type) typedef AutoPtr<type, CDeleter<type> > TAuto ## type ## Ptr |
| Uses C Deleter (free) - used in functions that deal with CORE BLAST. More... | |
| #define | TYPEDEF_AUTOPTR_ARRAYDELETER(type) typedef AutoPtr<type, ArrayDeleter<type> > TAuto ## type ## ArrayPtr |
| Uses delete [] operator - for C++ arrays. More... | |
| #define | DECLARE_AUTO_CLASS_WRAPPER(struct_name, free_func) |
| Declares class to handle deallocating of the structure using the appropriate function. More... | |
| #define | BLAST2NA_SIZE 4 |
| Size of compressed nucleic acid alphabet. More... | |
| #define | BLASTNA_SIZE 16 |
| Size of nucleic acid alphabet. More... | |
| #define | BLASTAA_SIZE 28 |
| Size of aminoacid alphabet. More... | |
| #define | BLASTNA_SEQ_CODE 99 |
| Identifies the blastna alphabet, for use in blast only. More... | |
| #define | BLASTAA_SEQ_CODE 11 |
| == Seq_code_ncbistdaa More... | |
| #define | NCBI4NA_SEQ_CODE 4 |
| == Seq_code_ncbi4na More... | |
| #define | NCBI_MODULE NETBLAST |
| #define | SMALLEST_EVALUE 1.0e-180 |
| Threshold below which e-values are saved as 0. More... | |
| #define | GAP_VALUE -1 |
| Value in the Dense-seg indicating a gap. More... | |
| #define | GAP_IN_ALIGNMENT ((Uint4)-1) |
| Representation of GAP in Seq-align. More... | |
| #define | GAP_IN_ALIGNMENT ((Uint4)-1) |
| Representation of GAP in Seq-align. More... | |
| #define | NCBI_MODULE NETBLAST |
Typedefs | |
| typedef AutoPtr< Uint1, CDeleter< Uint1 > > | TAutoUint1Ptr |
| Declares TAutoUint1Ptr (for Uint1 arrays allocated with malloc/calloc) More... | |
| typedef AutoPtr< Char, CDeleter< Char > > | TAutoCharPtr |
| Declares TAutoCharPtr (for Char arrays allocated with malloc/calloc) More... | |
| typedef AutoPtr< Uint1, ArrayDeleter< Uint1 > > | TAutoUint1ArrayPtr |
| Declares TAutoUint1ArrayPtr (for Uint1 arrays allocated with new[]) More... | |
| typedef CSeqLocInfo::ETranslationFrame | CFrameFinder::ETranslationFrame |
| Convenience typedef. More... | |
| typedef const CRef< CSeqLocInfo > | CFrameFinder::argument_type |
| typedef bool | CFrameFinder::result_type |
| typedef objects::CBlast4_parameters::Tdata | CBlastOptionsBuilder::TValueList |
| List of name/value pairs. More... | |
| typedef list< CRef< objects::CBlast4_mask > > | CBlastOptionsBuilder::TMaskList |
| List of Blast4 masks. More... | |
| typedef CBlastOptions::EAPILocality | CBlastOptionsFactory::EAPILocality |
| Convenience define. More... | |
| typedef CBlastOptions::EAPILocality | CBlastOptionsHandle::EAPILocality |
| Convenience define. More... | |
| typedef CRef< CSearchResults > | CSearchResultSet::value_type |
| data type contained by this container More... | |
| typedef vector< CConstRef< objects::CSeq_id > > | CSearchResultSet::TQueryIdVector |
| List of query ids. More... | |
| typedef vector< value_type >::size_type | CSearchResultSet::size_type |
| size_type type definition More... | |
| typedef vector< CRef< CBlastAncillaryData > > | CSearchResultSet::TAncillaryVector |
| typedef for a vector of CRef<CBlastAncillaryData> More... | |
| typedef vector< value_type >::const_iterator | CSearchResultSet::const_iterator |
| const_iterator type definition More... | |
| typedef vector< value_type >::iterator | CSearchResultSet::iterator |
| iterator type definition More... | |
| typedef Uint4 | CCddInputData::TFreqs |
| Type used for residue frequencies stored in CDD. More... | |
| typedef Uint4 | CCddInputData::TObsr |
| Type used for number of independent observations stored in CDD. More... | |
| typedef CRange< int > | CCddInputData::TRange |
| typedef int | CMagicBlastResults::TResultsInfo |
| typedef CRef< CMagicBlastResults > | CMagicBlastResultSet::value_type |
| data type contained by this container More... | |
| typedef vector< value_type >::size_type | CMagicBlastResultSet::size_type |
| size_type type definition More... | |
| typedef vector< value_type >::const_iterator | CMagicBlastResultSet::const_iterator |
| const_iterator type definition More... | |
| typedef vector< value_type >::iterator | CMagicBlastResultSet::iterator |
| iterator type definition More... | |
| typedef set< objects::CSeq_id_Handle > | CPsiBlastIterationState::TSeqIds |
| List of CSeq_ids. More... | |
| typedef list< CRef< objects::CSeq_loc > > | IRemoteQueryData::TSeqLocs |
| Type definition for CSeq_loc set used as queries in the BLAST remote search class. More... | |
| typedef list< CRef< objects::CSeq_loc > > | CRemoteBlast::TSeqLocList |
| Typedef for a list of Seq-locs. More... | |
| typedef list< CRef< objects::CBlast4_ka_block > > | CRemoteBlast::TKarlinAltschulBlocks |
| Convenience typedef for a list of CRef<CBlast4_ka_block> More... | |
| typedef vector< CRef< objects::CSeq_interval > > | CRemoteBlast::TSeqIntervalVector |
| Defines a std::vector of CRef<CSeq_interval> More... | |
| typedef vector< CRef< objects::CSeq_data > > | CRemoteBlast::TSeqDataVector |
| Defines a std::vector of CRef<CSeq_data> More... | |
| typedef list< CRef< objects::CBlast4_parameter > > | CRemoteBlast::TValueList |
| Value list. More... | |
| typedef objects::CBlast4_get_search_results_reply | CRemoteBlast::TGSRR |
| An alias for the most commonly used part of the Blast4 search results. More... | |
| typedef vector< CConstRef< CSeq_loc > > | CSeedTop::TSeedTopResults |
| typedef TData *() | CStructWrapper< TData >::TDelete(TData *) |
| type definition for a function that deallocated memory associated with an object. More... | |
| typedef CStructWrapper< BlastScoreBlk > | TBlastScoreBlk |
| typedef CStructWrapper< LookupTableWrap > | TLookupTableWrap |
| typedef CStructWrapper< BlastDiagnostics > | TBlastDiagnostics |
| typedef CStructWrapper< BlastHSPStream > | TBlastHSPStream |
| typedef CStructWrapper< BlastSeqSrc > | TBlastSeqSrc |
| typedef CStructWrapper< SPHIPatternSearchBlk > | TSPHIPatternSearchBlk |
| typedef vector< TGi > | CSearchDatabase::TGiList |
| Define a list of gis. More... | |
| typedef vector< CRef< objects::CSeq_id > > | CBlastServices::TSeqIdVector |
| Defines a std::vector of CRef<CSeq_id> More... | |
| typedef vector< CRef< objects::CBioseq > > | CBlastServices::TBioseqVector |
| Defines a std::vector of CRef<CBioseq> More... | |
| typedef vector< CRef< objects::CSeq_interval > > | CBlastServices::TSeqIntervalVector |
| Defines a std::vector of CRef<CSeq_interval> More... | |
| typedef vector< CRef< objects::CSeq_data > > | CBlastServices::TSeqDataVector |
| Defines a std::vector of CRef<CSeq_data> More... | |
| typedef vector< CConstRef< CDbIndex::CSearchResults > > | CIndexedDb_Old::TResultSet |
| Type used to represent collections of search result sets. More... | |
| typedef vector< CDbIndex::TSeqNum > | CIndexedDb_Old::TSeqMap |
| Type used to map loaded indices to subject ids. More... | |
| typedef std::vector< std::string > | CIndexedDb_New::TStrVec |
| Alias for a vector os strings. More... | |
| typedef std::vector< SVolumeDescriptor > | CIndexedDb_New::TVolList |
| List of leaf index volumes. More... | |
| typedef CConstRef< CDbIndex::CSearchResults > | CIndexedDb_New::TVolResults |
| This type captures the seeds found by search of an index volume. More... | |
| typedef std::vector< SVolResults > | CIndexedDb_New::TResultsHolder |
| List of reference counted result holders. More... | |
| typedef ncbi::objects::CBlast4_parameters | CBlastOptionsRemote::TBlast4Opts |
| typedef vector< CConstRef< objects::CSeq_loc > > | CBlastOptionsRemote::TSeqLocVector |
| typedef CSeqLocInfo::ETranslationFrame | CBlastQueryFilteredFrames::ETranslationFrame |
| Data type for frame value, however inputs to methods use "int" instead of this type for readability and brevity. More... | |
| typedef map< ETranslationFrame, BlastSeqLoc * > | CBlastQueryFilteredFrames::TFrameSet |
| Frame and BlastSeqLoc* info type. More... | |
| typedef CPsiBlastIterationState::TSeqIds | CPsiBlastAlignmentProcessor::THitIdentifiers |
| Container of Seq-ids for the subject sequences (hits) aligned with the query. More... | |
| typedef list< CRef< objects::CBlast4_error > > | TErrorList |
| Error value type used by Blast4 ASN.1 objects. More... | |
| typedef SSeqDB_SeqSrc_Data | TSeqDBData |
| typedef vector< CRef< objects::CScope > > | CQuerySplitter::TScopeVector |
| Defines a vector of CScope objects. More... | |
| typedef vector< CRef< CBlastQueryVector > > | CQuerySplitter::TSplitQueryVector |
| Definition of a vector of CBlastQueryVectors, each element corresponds to a query chunk. More... | |
| typedef COpenRange< TSeqPos > | TChunkRange |
| Range describing a query chunk. More... | |
| typedef blast::SDataLoaderConfig::EConfigOpts | CAutoNcbiConfigFile::EConfigOpts |
Detailed Description
Macro Definition Documentation
◆ BLAST2NA_SIZE
| #define BLAST2NA_SIZE 4 |
Size of compressed nucleic acid alphabet.
Definition at line 91 of file blast_encoding.h.
◆ BLASTAA_SEQ_CODE
| #define BLASTAA_SEQ_CODE 11 |
== Seq_code_ncbistdaa
Definition at line 98 of file blast_encoding.h.
◆ BLASTAA_SIZE
| #define BLASTAA_SIZE 28 |
Size of aminoacid alphabet.
Definition at line 93 of file blast_encoding.h.
◆ BLASTNA_SEQ_CODE
| #define BLASTNA_SEQ_CODE 99 |
Identifies the blastna alphabet, for use in blast only.
Definition at line 97 of file blast_encoding.h.
◆ BLASTNA_SIZE
| #define BLASTNA_SIZE 16 |
Size of nucleic acid alphabet.
Definition at line 92 of file blast_encoding.h.
◆ DECLARE_AUTO_CLASS_WRAPPER
| #define DECLARE_AUTO_CLASS_WRAPPER | ( | struct_name, | |
| free_func | |||
| ) |
Declares class to handle deallocating of the structure using the appropriate function.
Definition at line 274 of file blast_aux.hpp.
◆ GAP_IN_ALIGNMENT [1/2]
| #define GAP_IN_ALIGNMENT ((Uint4)-1) |
Representation of GAP in Seq-align.
Definition at line 65 of file cdd_pssm_input.cpp.
◆ GAP_IN_ALIGNMENT [2/2]
| #define GAP_IN_ALIGNMENT ((Uint4)-1) |
Representation of GAP in Seq-align.
Definition at line 72 of file psi_pssm_input.cpp.
◆ GAP_VALUE
| #define GAP_VALUE -1 |
Value in the Dense-seg indicating a gap.
Definition at line 66 of file blast_seqalign.cpp.
◆ NCBI4NA_SEQ_CODE
| #define NCBI4NA_SEQ_CODE 4 |
== Seq_code_ncbi4na
Definition at line 99 of file blast_encoding.h.
◆ NCBI_MODULE [1/2]
| #define NCBI_MODULE NETBLAST |
Definition at line 61 of file blast_services.hpp.
◆ NCBI_MODULE [2/2]
| #define NCBI_MODULE NETBLAST |
Definition at line 57 of file blast_services.cpp.
◆ SMALLEST_EVALUE
| #define SMALLEST_EVALUE 1.0e-180 |
Threshold below which e-values are saved as 0.
Definition at line 62 of file blast_seqalign.cpp.
◆ TYPEDEF_AUTOPTR_ARRAYDELETER
| #define TYPEDEF_AUTOPTR_ARRAYDELETER | ( | type | ) | typedef AutoPtr<type, ArrayDeleter<type> > TAuto ## type ## ArrayPtr |
Uses delete [] operator - for C++ arrays.
Definition at line 93 of file blast_aux.hpp.
◆ TYPEDEF_AUTOPTR_CDELETER
| #define TYPEDEF_AUTOPTR_CDELETER | ( | type | ) | typedef AutoPtr<type, CDeleter<type> > TAuto ## type ## Ptr |
Uses C Deleter (free) - used in functions that deal with CORE BLAST.
Definition at line 89 of file blast_aux.hpp.
Typedef Documentation
◆ argument_type
| typedef const CRef<CSeqLocInfo> CFrameFinder::argument_type |
Definition at line 137 of file blast_aux.hpp.
◆ const_iterator [1/2]
| typedef vector<value_type>::const_iterator CSearchResultSet::const_iterator |
const_iterator type definition
Definition at line 322 of file blast_results.hpp.
◆ const_iterator [2/2]
| typedef vector<value_type>::const_iterator CMagicBlastResultSet::const_iterator |
const_iterator type definition
Definition at line 251 of file magicblast.hpp.
◆ EAPILocality [1/2]
Convenience define.
- See also
- CBlastOptions class
Definition at line 85 of file blast_options_handle.hpp.
◆ EAPILocality [2/2]
Convenience define.
- See also
- CBlastOptions class
Definition at line 146 of file blast_options_handle.hpp.
◆ EConfigOpts
| typedef blast::SDataLoaderConfig::EConfigOpts CAutoNcbiConfigFile::EConfigOpts |
Definition at line 61 of file blast_input_unit_test_aux.hpp.
◆ ETranslationFrame [1/2]
Convenience typedef.
Definition at line 136 of file blast_aux.hpp.
◆ ETranslationFrame [2/2]
Data type for frame value, however inputs to methods use "int" instead of this type for readability and brevity.
Definition at line 432 of file blast_setup.hpp.
◆ iterator [1/2]
| typedef vector<value_type>::iterator CSearchResultSet::iterator |
iterator type definition
Definition at line 325 of file blast_results.hpp.
◆ iterator [2/2]
| typedef vector<value_type>::iterator CMagicBlastResultSet::iterator |
iterator type definition
Definition at line 254 of file magicblast.hpp.
◆ result_type
| typedef bool CFrameFinder::result_type |
Definition at line 138 of file blast_aux.hpp.
◆ size_type [1/2]
| typedef vector<value_type>::size_type CSearchResultSet::size_type |
size_type type definition
Definition at line 316 of file blast_results.hpp.
◆ size_type [2/2]
| typedef vector<value_type>::size_type CMagicBlastResultSet::size_type |
size_type type definition
Definition at line 248 of file magicblast.hpp.
◆ TAncillaryVector
| typedef vector< CRef<CBlastAncillaryData> > CSearchResultSet::TAncillaryVector |
typedef for a vector of CRef<CBlastAncillaryData>
Definition at line 319 of file blast_results.hpp.
◆ TAutoCharPtr
| typedef AutoPtr< Char , CDeleter< Char > > TAutoCharPtr |
Declares TAutoCharPtr (for Char arrays allocated with malloc/calloc)
Definition at line 100 of file blast_aux.hpp.
◆ TAutoUint1ArrayPtr
| typedef AutoPtr< Uint1 , ArrayDeleter< Uint1 > > TAutoUint1ArrayPtr |
Declares TAutoUint1ArrayPtr (for Uint1 arrays allocated with new[])
Definition at line 102 of file blast_aux.hpp.
◆ TAutoUint1Ptr
| typedef AutoPtr< Uint1 , CDeleter< Uint1 > > TAutoUint1Ptr |
Declares TAutoUint1Ptr (for Uint1 arrays allocated with malloc/calloc)
Definition at line 98 of file blast_aux.hpp.
◆ TBioseqVector
| typedef vector< CRef<objects::CBioseq> > CBlastServices::TBioseqVector |
Defines a std::vector of CRef<CBioseq>
Definition at line 161 of file blast_services.hpp.
◆ TBlast4Opts
| typedef ncbi::objects::CBlast4_parameters CBlastOptionsRemote::TBlast4Opts |
Definition at line 88 of file blast_options_cxx.cpp.
◆ TBlastDiagnostics
Definition at line 304 of file setup_factory.hpp.
◆ TBlastHSPStream
| typedef CStructWrapper<BlastHSPStream> TBlastHSPStream |
Definition at line 305 of file setup_factory.hpp.
◆ TBlastScoreBlk
| typedef CStructWrapper<BlastScoreBlk> TBlastScoreBlk |
Definition at line 302 of file setup_factory.hpp.
◆ TBlastSeqSrc
| typedef CStructWrapper<BlastSeqSrc> TBlastSeqSrc |
Definition at line 306 of file setup_factory.hpp.
◆ TChunkRange
| typedef COpenRange<TSeqPos> TChunkRange |
Range describing a query chunk.
Definition at line 50 of file split_query_blk.hpp.
◆ TDelete
| typedef TData*() CStructWrapper< TData >::TDelete(TData *) |
type definition for a function that deallocated memory associated with an object.
This functions return value is ignored; it would be void, except that most existing deletion functions return "NULL".
Definition at line 100 of file setup_factory.hpp.
◆ TErrorList
| typedef list< CRef<objects::CBlast4_error> > TErrorList |
Error value type used by Blast4 ASN.1 objects.
Definition at line 78 of file remote_blast.cpp.
◆ TFrameSet
|
private |
Frame and BlastSeqLoc* info type.
Definition at line 517 of file blast_setup.hpp.
◆ TFreqs
| typedef Uint4 CCddInputData::TFreqs |
Type used for residue frequencies stored in CDD.
Definition at line 100 of file cdd_pssm_input.hpp.
◆ TGiList
| typedef vector<TGi> CSearchDatabase::TGiList |
Define a list of gis.
Definition at line 112 of file uniform_search.hpp.
◆ TGSRR
|
private |
An alias for the most commonly used part of the Blast4 search results.
Definition at line 515 of file remote_blast.hpp.
◆ THitIdentifiers
Container of Seq-ids for the subject sequences (hits) aligned with the query.
Definition at line 108 of file psiblast_aux_priv.hpp.
◆ TKarlinAltschulBlocks
| typedef list< CRef<objects::CBlast4_ka_block > > CRemoteBlast::TKarlinAltschulBlocks |
Convenience typedef for a list of CRef<CBlast4_ka_block>
Definition at line 348 of file remote_blast.hpp.
◆ TLookupTableWrap
Definition at line 303 of file setup_factory.hpp.
◆ TMaskList
| typedef list< CRef<objects::CBlast4_mask> > CBlastOptionsBuilder::TMaskList |
List of Blast4 masks.
Definition at line 63 of file blast_options_builder.hpp.
◆ TObsr
| typedef Uint4 CCddInputData::TObsr |
Type used for number of independent observations stored in CDD.
Definition at line 103 of file cdd_pssm_input.hpp.
◆ TQueryIdVector
| typedef vector< CConstRef<objects::CSeq_id> > CSearchResultSet::TQueryIdVector |
List of query ids.
Definition at line 313 of file blast_results.hpp.
◆ TRange
|
protected |
Definition at line 201 of file cdd_pssm_input.hpp.
◆ TResultSet
|
private |
Type used to represent collections of search result sets.
Definition at line 214 of file blast_dbindex.cpp.
◆ TResultsHolder
|
private |
List of reference counted result holders.
Definition at line 388 of file blast_dbindex.cpp.
◆ TResultsInfo
| typedef int CMagicBlastResults::TResultsInfo |
Definition at line 149 of file magicblast.hpp.
◆ TScopeVector
| typedef vector< CRef<objects::CScope> > CQuerySplitter::TScopeVector |
Defines a vector of CScope objects.
Definition at line 69 of file split_query.hpp.
◆ TSeedTopResults
| typedef vector< CConstRef <CSeq_loc> > CSeedTop::TSeedTopResults |
Definition at line 140 of file seedtop.hpp.
◆ TSeqDataVector [1/2]
| typedef vector< CRef<objects::CSeq_data> > CRemoteBlast::TSeqDataVector |
Defines a std::vector of CRef<CSeq_data>
Definition at line 387 of file remote_blast.hpp.
◆ TSeqDataVector [2/2]
| typedef vector< CRef<objects::CSeq_data> > CBlastServices::TSeqDataVector |
Defines a std::vector of CRef<CSeq_data>
Definition at line 222 of file blast_services.hpp.
◆ TSeqDBData
| typedef SSeqDB_SeqSrc_Data TSeqDBData |
Definition at line 106 of file seqsrc_seqdb.cpp.
◆ TSeqIds
| typedef set<objects::CSeq_id_Handle> CPsiBlastIterationState::TSeqIds |
List of CSeq_ids.
Definition at line 89 of file psiblast_iteration.hpp.
◆ TSeqIdVector
| typedef vector< CRef<objects::CSeq_id> > CBlastServices::TSeqIdVector |
Defines a std::vector of CRef<CSeq_id>
Definition at line 159 of file blast_services.hpp.
◆ TSeqIntervalVector [1/2]
| typedef vector< CRef<objects::CSeq_interval> > CRemoteBlast::TSeqIntervalVector |
Defines a std::vector of CRef<CSeq_interval>
Definition at line 385 of file remote_blast.hpp.
◆ TSeqIntervalVector [2/2]
| typedef vector< CRef<objects::CSeq_interval> > CBlastServices::TSeqIntervalVector |
Defines a std::vector of CRef<CSeq_interval>
Definition at line 220 of file blast_services.hpp.
◆ TSeqLocList
| typedef list< CRef<objects::CSeq_loc> > CRemoteBlast::TSeqLocList |
Typedef for a list of Seq-locs.
Definition at line 193 of file remote_blast.hpp.
◆ TSeqLocs
| typedef list< CRef<objects::CSeq_loc> > IRemoteQueryData::TSeqLocs |
Type definition for CSeq_loc set used as queries in the BLAST remote search class.
Definition at line 123 of file query_data.hpp.
◆ TSeqLocVector
| typedef vector< CConstRef<objects::CSeq_loc> > CBlastOptionsRemote::TSeqLocVector |
Definition at line 94 of file blast_options_cxx.cpp.
◆ TSeqMap
|
private |
Type used to map loaded indices to subject ids.
Definition at line 217 of file blast_dbindex.cpp.
◆ TSPHIPatternSearchBlk
Definition at line 307 of file setup_factory.hpp.
◆ TSplitQueryVector
| typedef vector< CRef<CBlastQueryVector> > CQuerySplitter::TSplitQueryVector |
Definition of a vector of CBlastQueryVectors, each element corresponds to a query chunk.
Definition at line 73 of file split_query.hpp.
◆ TStrVec
|
private |
Alias for a vector os strings.
Definition at line 339 of file blast_dbindex.cpp.
◆ TValueList [1/2]
| typedef objects::CBlast4_parameters::Tdata CBlastOptionsBuilder::TValueList |
List of name/value pairs.
Definition at line 60 of file blast_options_builder.hpp.
◆ TValueList [2/2]
|
private |
Value list.
Definition at line 512 of file remote_blast.hpp.
◆ TVolList
|
private |
List of leaf index volumes.
Definition at line 369 of file blast_dbindex.cpp.
◆ TVolResults
|
private |
This type captures the seeds found by search of an index volume.
Definition at line 372 of file blast_dbindex.cpp.
◆ value_type [1/2]
data type contained by this container
Definition at line 310 of file blast_results.hpp.
◆ value_type [2/2]
data type contained by this container
Definition at line 245 of file magicblast.hpp.
Enumeration Type Documentation
◆ anonymous enum
| anonymous enum |
Never have less than 1 thread.
| Enumerator | |
|---|---|
| kMinNumThreads | |
Definition at line 166 of file setup_factory.hpp.
◆ anonymous enum
|
private |
Initial value of all entries in the above cache.
| Enumerator | |
|---|---|
| kUninitialized | |
Definition at line 250 of file split_query_aux_priv.hpp.
◆ EApplyTo
Master selection for operations involving ranges.
| Enumerator | |
|---|---|
| eQuery | |
| eSubject | |
Definition at line 285 of file cdd_pssm_input.hpp.
◆ EBlastEncoding
| enum EBlastEncoding |
Different types of sequence encodings for sequence retrieval from the BLAST database.
Definition at line 53 of file blast_encoding.h.
◆ EDebugMode
Debugging support can be turned on with eDebug or off with eSilent.
| Enumerator | |
|---|---|
| eDebug | |
| eSilent | |
Definition at line 371 of file remote_blast.hpp.
◆ EErrCode [1/6]
Error types that BLAST can generate.
| Enumerator | |
|---|---|
| eOutOfMemory | Out-of-memory. |
| eNetworkError | Network error. |
Definition at line 51 of file blast_exception.hpp.
◆ EErrCode [2/6]
Error types that BLAST can generate.
| Enumerator | |
|---|---|
| eCoreBlastError | FIXME: need to interpret CORE errors. |
| eInvalidOptions | Invalid algorithm options. |
| eInvalidArgument | Invalid argument to some function/method (could be programmer error - prefer assertions in those cases unless API needs to be "bullet-proof") |
| eNotSupported | Feature not supported. |
| eInvalidCharacter | Invalid character in sequence data. |
| eSeqSrcInit | Initialization error in BlastSeqSrc implementation. |
| eRpsInit | Error while initializing RPS-BLAST. |
| eSetup | Error while setting up BLAST. |
| eSystem | System exception. |
Definition at line 74 of file blast_exception.hpp.
◆ EErrCode [3/6]
Types of exceptions generated by the CPssmEngine class.
| Enumerator | |
|---|---|
| eNullInputData | |
| eInvalidInputData | |
Definition at line 66 of file pssm_engine.hpp.
◆ EErrCode [4/6]
Types of exceptions generated by the CRemoteBlast class.
| Enumerator | |
|---|---|
| eServiceNotAvailable | Service is not available. |
| eIncompleteConfig | Remote BLAST object not fully configured. |
Definition at line 68 of file remote_blast.hpp.
◆ EErrCode [5/6]
Errors are classified into one of two types.
| Enumerator | |
|---|---|
| eConfigErr | Argument validation failed. |
| eMemErr | Memory allocation failed. |
| eInternal | Internal error (e.g. unimplemented methods). |
Definition at line 81 of file uniform_search.hpp.
◆ EErrCode [6/6]
Errors are classified into one of two types.
| Enumerator | |
|---|---|
| eArgErr | Argument validation failed. |
| eFileErr | Files were missing or contents were incorrect. |
| eRequestErr | Request failed. |
| eMemErr | Memory allocation failed. |
Definition at line 70 of file blast_services.hpp.
◆ EImmediacy
|
private |
Indicates whether to use async mode.
| Enumerator | |
|---|---|
| ePollAsync | |
| ePollImmed | |
Definition at line 535 of file remote_blast.hpp.
◆ EMoleculeType
Molecule of the BLAST database.
| Enumerator | |
|---|---|
| eBlastDbIsProtein | protein |
| eBlastDbIsNucleotide | nucleotide |
Definition at line 115 of file uniform_search.hpp.
◆ ENeedConfig
|
private |
This class attempts to verify whether all necessary configuration is complete before attempting to submit the search.
| Enumerator | |
|---|---|
| eNoConfig | |
| eProgram | |
| eService | |
| eQueries | |
| eSubject | |
| eNeedAll | |
Definition at line 542 of file remote_blast.hpp.
◆ EOpenFlags
Flags for opening database files.
Definition at line 72 of file rps_aux.hpp.
◆ EOrdering
Ordering of alignments.
| Enumerator | |
|---|---|
| eFwRevFirst | |
| eRevFwFirst | |
Definition at line 152 of file magicblast.hpp.
◆ EPublication
Enumerates the various BLAST publications.
Definition at line 70 of file version.hpp.
◆ EQueryFactoryType
Enumeration to specify the different uses of the query factory.
| Enumerator | |
|---|---|
| eQFT_Query | |
| eQFT_Subject | |
Definition at line 139 of file psiblast_aux_priv.hpp.
◆ EResultsInfo
Information flags about mapping results.
| Enumerator | |
|---|---|
| fUnaligned | Read is unaligned. |
| fFiltered | Read did not pass quality filtering. |
Definition at line 141 of file magicblast.hpp.
◆ ESearchStatus
Represents the status of previously submitted search/RID.
Definition at line 251 of file remote_blast.hpp.
◆ ESentinelType
| enum ESentinelType |
Allows specification of whether sentinel bytes should be used or not.
| Enumerator | |
|---|---|
| eSentinels | Use sentinel bytes. |
| eNoSentinels | Do not use sentinel bytes. |
Definition at line 93 of file blast_setup.hpp.
◆ EState
|
private |
Various states the search can be in.
eStart Not submitted, can still be configured. eFailed An error was encountered. eWait The search is still running. eDone Results are available.
| Enumerator | |
|---|---|
| eStart | |
| eFailed | |
| eWait | |
| eDone | |
Definition at line 527 of file remote_blast.hpp.
◆ ETaskSets
Sets of tasks for the command line BLAST binaries.
| Enumerator | |
|---|---|
| eNuclNucl | Nucleotide-nucleotide tasks. |
| eProtProt | Protein-protein tasks. |
| eMapping | Mapping tasks. |
| eAll | Retrieve all available tasks. |
Definition at line 111 of file blast_options_handle.hpp.
Function Documentation
◆ AddContextOffsetToChunk()
| void CSplitQueryBlk::AddContextOffsetToChunk | ( | size_t | chunk_num, |
| Int4 | context_offset | ||
| ) |
Adds a context offset (correction) to a given chunk.
- Parameters
-
chunk_num desired chunk [in] context_offset query context offset (correction) to be added [in]
Definition at line 183 of file split_query_blk.cpp.
References CSplitQueryBlk::m_SplitQueryBlk, and SplitQueryBlk_AddContextOffsetToChunk().
Referenced by CQuerySplitter::x_ComputeContextOffsets_NonTranslatedQueries(), and CQuerySplitter::x_ComputeContextOffsets_TranslatedQueries().
◆ AddContextToChunk()
| void CSplitQueryBlk::AddContextToChunk | ( | size_t | chunk_num, |
| Int4 | context_index | ||
| ) |
Adds a query context to a given chunk.
- Parameters
-
chunk_num desired chunk [in] context_index context of the concatenated query to be added [in]
Definition at line 173 of file split_query_blk.cpp.
References CSplitQueryBlk::m_SplitQueryBlk, and SplitQueryBlk_AddContextToChunk().
Referenced by CQuerySplitter::x_ComputeQueryContextsForChunks().
◆ AddGeneticCode()
| void CAutomaticGenCodeSingleton::AddGeneticCode | ( | int | genetic_code | ) |
Add the genetic code to the genetic code singleton.
- Parameters
-
genetic_code Integer representing the genetic code [in]
Definition at line 653 of file blast_aux.cpp.
References FindGeneticCode(), GenCodeSingletonAdd(), GenCodeSingletonFind(), AutoPtr< X, Del >::get(), and NULL.
Referenced by CBlastOptions::SetDbGeneticCode(), and CBlastOptions::SetQueryGeneticCode().
◆ AddIndexInfo()
|
private |
Definition at line 664 of file blast_dbindex.cpp.
References CSeqDB::eNucleotide, ERR_POST, Error(), CIndexSuperHeader_Base::GenerateIndexVolumeName(), GetIdxVolNumOIDs(), GetIndexSuperHeader(), CIndexedDb_New::GetNextUnusedOID(), CSeqDB::GetNumOIDs(), i, Info(), CRef< C, Locker >::Reset(), SeqDB_ResolveDbPath(), string, CIndexedDb_New::volumes_, and CException::what().
Referenced by CIndexedDb_New::CIndexedDb_New().
◆ AddMessageAllQueries()
| void TSearchMessages::AddMessageAllQueries | ( | EBlastSeverity | severity, |
| int | error_id, | ||
| const string & | message | ||
| ) |
Add a message for all queries.
- Parameters
-
severity The severity of this message. [in] error_id A number unique to this error. [in] message A description of the error for the user. [in]
Definition at line 1056 of file blast_aux.cpp.
References eBlastSevWarning, kBlastMessageNoContext, and NON_CONST_ITERATE.
Referenced by CSetupFactory::CreateScoreBlock(), and CBlastPrelimSearch::Run().
◆ AddQueryToChunk()
| void CSplitQueryBlk::AddQueryToChunk | ( | size_t | chunk_num, |
| Int4 | query_index | ||
| ) |
Adds a query index to a given chunk.
- Parameters
-
chunk_num desired chunk [in] query_index index of query to be added [in]
Definition at line 163 of file split_query_blk.cpp.
References CSplitQueryBlk::m_SplitQueryBlk, and SplitQueryBlk_AddQueryToChunk().
Referenced by CQuerySplitter::x_ComputeQueryIndicesForChunks().
◆ AddSeqLoc()
Add a masked interval to the specified frame.
The specified interval of the specified frame is masked. This creates a BlastSeqLoc object inside this container for that frame, which will be freed at destruction time unless the client code calls Release() for that frame.
- Parameters
-
intv The interval to mask. frame The specific frame, expressed as a value from ETranslationFrame, on which this interval falls.
Definition at line 1731 of file blast_setup_cxx.cpp.
References _ASSERT, BlastSeqLocNew(), eBlastTypeBlastn, eBlastTypeMapping, CSeqLocInfo::eFrameMinus1, CSeqLocInfo::eFramePlus1, set< Key, Compare >::empty(), i, CBlastQueryFilteredFrames::m_Frames, CBlastQueryFilteredFrames::m_Program, CBlastQueryFilteredFrames::m_Seqlocs, CBlastQueryFilteredFrames::m_SeqlocTails, and CBlastQueryFilteredFrames::x_VerifyFrame().
Referenced by CBlastQueryFilteredFrames::CBlastQueryFilteredFrames().
◆ AdjustProgram()
|
static |
Adjust the EProgram based on option values.
The blast4 protocol uses a notion of program and service to represent the type of search to do. However, for some values of program and service, it is necessary to look at options values in order to determine the precise EProgram value. This is particularly true when dealing with discontiguous megablast for example. This method adjusts the program value based on the additional information found in these options.
- Parameters
-
L The list of options used for this search. program The EProgram suggested by program+service. program_string The program as a string.
- Returns
- The EProgram value as adjusted by options or the argument program if L is NULL
Definition at line 586 of file blast_options_builder.cpp.
References _TRACE, eBlastn, eBlastOpt_IgnoreMsaMaster, eBlastOpt_MBTemplateLength, eBlastOpt_PHIPattern, eBlastOpt_PseudoCount, eBlastOpt_Web_RunPsiBlast, eBlastOpt_Web_StepNumber, eBlastp, eDiscMegablast, ePHIBlastn, ePHIBlastp, ePSIBlast, CBlast4Field::Get(), CBlast4_value_Base::GetInteger(), CBlast4Field::GetName(), CBlast4_parameter_Base::GetValue(), ITERATE, msg(), and NCBI_THROW.
Referenced by CBlastOptionsBuilder::GetSearchOptions().
◆ AdjustRanges()
Change ranges on query and subject by given values.
- Parameters
-
d_from Change value for the beginning of the segment [in] d_to Change value for the end of the segment [in]
d_from and d_to are added to begining and end of both query and subject ranges. d_from and d_to can be negative.
Definition at line 788 of file cdd_pssm_input.cpp.
Referenced by CCddInputData::CHit::IntersectWith(), and CCddInputData::CHit::Subtract().
◆ Advance()
Advance the iterator by passing it the list of Seq-ids which passed the inclusion criteria for the current iteration.
Definition at line 119 of file psiblast_iteration.cpp.
References CPsiBlastIterationState::m_CurrentData, CPsiBlastIterationState::m_IterationsDone, CPsiBlastIterationState::m_PreviousData, and CPsiBlastIterationState::x_ThrowExceptionOnLogicError().
Referenced by BOOST_AUTO_TEST_CASE(), CDeltaBlastApp::DoPsiBlastIterations(), RunNIterationsWithoutConverging(), and CPsiBlastApp::x_RunLocalPsiBlastIterations().
◆ begin() [1/4]
|
inline |
Returns iterator to beginning of container, provided to facilitate STL-style iteration.
Definition at line 439 of file blast_results.hpp.
References CSearchResultSet::m_Results.
◆ begin() [2/4]
|
inline |
Returns iterator to the beginning of the container.
Definition at line 277 of file magicblast.hpp.
References CMagicBlastResultSet::m_Results.
◆ begin() [3/4]
|
inline |
Returns const_iterator to beginning of container, provided to facilitate STL-style iteration.
Definition at line 431 of file blast_results.hpp.
References CSearchResultSet::m_Results.
Referenced by s_AddNewResultSet().
◆ begin() [4/4]
|
inline |
Returns const iteartor to the beginning of the container, provided to facilitate STL-style iteartion.
Definition at line 271 of file magicblast.hpp.
References CMagicBlastResultSet::m_Results.
◆ Blast_CMT_LOCKInit()
| MT_LOCK Blast_CMT_LOCKInit | ( | void | ) |
Initialize a mutex locking mechanism for BLAST.
Initialize a mutex locking mechanism for BLAST.
Definition at line 72 of file blast_mtlock.cpp.
References BlastLockCleanup(), BlastLockHandler(), and MT_LOCK_Create().
Referenced by BlastSetupPreliminarySearchEx(), CSetupFactory::CreateDiagnosticsStructureMT(), CBlastPrelimSearch::SetNumberOfThreads(), and testHSPStream().
◆ BLAST_FindBestNucleotideWordSize()
Given a minimum amount of identity and the minimum desired length of nucleotide alignments, find the largest blastn word size that will find random instances of those alignments with high probability.
Note that when blast is actually run, it is obviously still possible to find alignments that are shorter and/or have less identity than what is specified here. The returned word size is just a choice that makes it unlikely that ungapped blast will miss alignments that exceed *both* minimums. The algorithm used is described in
Valer Gotea, Vamsi Veeramachaneni, and Wojciech Makalowski "Mastering seeds for genomic size nucleotide BLAST searches" Nucleic Acids Research, 2003, Vol 31, No. 23, pp 6935-6941
- Parameters
-
min_percent_identity How much identity is expected in random alignments. Less identity means the probability of finding such alignments is decreased [in] min_align_length The smallest alignment length desired. Longer length gives blastn more leeway to find seeds and increases the computed probability that alignments will be found [in]
- Returns
- The optimal word size, or zero if the optimization process failed
Definition at line 436 of file blast_tune.c.
References s_FindWordSize(), s_MatrixDataFree(), and s_MatrixDataInit().
◆ Blast_FindDustFilterLoc() [1/3]
| void Blast_FindDustFilterLoc | ( | CBlastQueryVector & | query, |
| Uint4 | level = CSymDustMasker::DEFAULT_LEVEL, |
||
| Uint4 | window = CSymDustMasker::DEFAULT_WINDOW, |
||
| Uint4 | linker = CSymDustMasker::DEFAULT_LINKER |
||
| ) |
Overloaded version of the function above which takes the filtering implementation's arguments directly, CBlastQueryVector version.
- Parameters
-
query Vector of sequence locations. [in] [out] level Dust filtering level argument [in] window Dust filtering window argument [in] linker Dust filtering linker argument [in]
Definition at line 166 of file dust_filter.cpp.
References data, eBlastTypeBlastn, CBioseq_Handle::eCoding_Iupac, CBlastQueryVector::GetMasks(), CBlastQueryVector::GetQuerySeqLoc(), CBlastQueryVector::GetScope(), i, CRef< C, Locker >::NotEmpty(), PackedSeqLocToMaskedQueryRegions(), s_CombineDustMasksWithUserProvidedMasks(), CBlastQueryVector::SetMaskedRegions(), and CBlastQueryVector::Size().
◆ Blast_FindDustFilterLoc() [2/3]
| void Blast_FindDustFilterLoc | ( | TSeqLocVector & | query, |
| const CBlastNucleotideOptionsHandle * | nucl_handle | ||
| ) |
Finds dust locations for a given set of sequences by calling the the symmetric dust lib.
The locations are saved in the respective fields of the SSeqLoc structures. If previous masks exist, they are combined with the new masks.
- Parameters
-
query Vector of sequence locations. [in] [out] nucl_handle options handle for blast search [in]
Definition at line 60 of file dust_filter.cpp.
References CBlastNucleotideOptionsHandle::GetDustFiltering(), CBlastNucleotideOptionsHandle::GetDustFilteringLevel(), CBlastNucleotideOptionsHandle::GetDustFilteringLinker(), CBlastNucleotideOptionsHandle::GetDustFilteringWindow(), and NULL.
Referenced by BOOST_AUTO_TEST_CASE(), CBlastQuerySourceOM::x_CalculateMasks(), and x_TestGetFilteredQueryRegions().
◆ Blast_FindDustFilterLoc() [3/3]
| void Blast_FindDustFilterLoc | ( | TSeqLocVector & | query, |
| Uint4 | level = CSymDustMasker::DEFAULT_LEVEL, |
||
| Uint4 | window = CSymDustMasker::DEFAULT_WINDOW, |
||
| Uint4 | linker = CSymDustMasker::DEFAULT_LINKER |
||
| ) |
Overloaded version of the function above which takes the filtering implementation's arguments directly, TSeqLocVector version.
- Parameters
-
query Vector of sequence locations. [in] [out] level Dust filtering level argument [in] window Dust filtering window argument [in] linker Dust filtering linker argument [in]
Definition at line 147 of file dust_filter.cpp.
References data, CBioseq_Handle::eCoding_Iupac, NON_CONST_ITERATE, query, and s_CombineDustMasksWithUserProvidedMasks().
◆ Blast_FindRepeatFilterLoc() [1/3]
| void Blast_FindRepeatFilterLoc | ( | CBlastQueryVector & | query, |
| const char * | filter_db | ||
| ) |
Overloaded version of the function above which takes the name of the repeats filtering database to use, and a CBlastQueryVector.
- Parameters
-
query Vector of sequence locations. [in] [out] filter_db Name of the BLAST database with repeats to use for filtering [in]
Definition at line 375 of file repeats_filter_cxx.cpp.
References CBlastQueryVector::AddQuery(), CSearchDatabase::eBlastDbIsNucleotide, eBlastTypeBlastn, CBlastQueryVector::GetQuerySeqLoc(), CBlastQueryVector::GetScope(), i, query, results, CLocalBlast::Run(), s_CreateRepeatsSearchOptions(), s_FillMaskLocFromBlastResults(), and CBlastQueryVector::Size().
◆ Blast_FindRepeatFilterLoc() [2/3]
| void Blast_FindRepeatFilterLoc | ( | TSeqLocVector & | query, |
| const char * | filter_db | ||
| ) |
Overloaded version of the function above which takes the name of the repeats filtering database to use, and a TSeqLocVector.
- Parameters
-
query Vector of sequence locations. [in] [out] filter_db Name of the BLAST database with repeats to use for filtering [in]
Definition at line 343 of file repeats_filter_cxx.cpp.
References CSearchDatabase::eBlastDbIsNucleotide, mask, NULL, query, results, CLocalBlast::Run(), s_CreateRepeatsSearchOptions(), and s_FillMaskLocFromBlastResults().
◆ Blast_FindRepeatFilterLoc() [3/3]
| void Blast_FindRepeatFilterLoc | ( | TSeqLocVector & | query_loc, |
| const CBlastOptionsHandle * | opts_handle | ||
| ) |
Finds repeats locations for a given set of sequences.
The locations are saved in the respective fields of the SSeqLoc structures. If previous masks exist, they are combined with the new masks. opts_handle will be downcast to CBlastNucleotideOptionsHandle and if that succeeds and repeat filtering is specified then it will be run, otherwise it just returns.
- Parameters
-
query_loc Vector of sequence locations. [in] [out] opts_handle options handle for blast search [in]
Definition at line 329 of file repeats_filter_cxx.cpp.
References CBlastNucleotideOptionsHandle::GetRepeatFiltering(), CBlastNucleotideOptionsHandle::GetRepeatFilteringDB(), NULL, and query.
Referenced by BOOST_AUTO_TEST_CASE(), and CBlastQuerySourceOM::x_CalculateMasks().
◆ Blast_FindWindowMaskerLoc() [1/6]
| void Blast_FindWindowMaskerLoc | ( | CBlastQueryVector & | query, |
| const CBlastOptions * | opts_handle | ||
| ) |
Find Window Masker filtered locations using a BlastOptions.
- Parameters
-
query These queries will be masked. [in|out] opts_handle This provides the database name or taxid. [in]
Definition at line 245 of file winmask_filter.cpp.
References Blast_FindWindowMaskerLoc_Fwd(), and query.
Referenced by Blast_FindWindowMaskerLoc_Fwd(), Blast_FindWindowMaskerLocTaxId(), BOOST_AUTO_TEST_CASE(), and CBlastQuerySourceOM::x_CalculateMasks().
◆ Blast_FindWindowMaskerLoc() [2/6]
| void Blast_FindWindowMaskerLoc | ( | CBlastQueryVector & | query, |
| const CBlastOptionsHandle * | opts_handle | ||
| ) |
Find Window Masker filtered locations using a BlastOptionsHandle.
- Parameters
-
query These queries will be masked. [in|out] opts_handle This provides the database name or taxid. [in]
Definition at line 259 of file winmask_filter.cpp.
References Blast_FindWindowMaskerLoc_Fwd(), and query.
◆ Blast_FindWindowMaskerLoc() [3/6]
| void Blast_FindWindowMaskerLoc | ( | CBlastQueryVector & | query, |
| const string & | lstat | ||
| ) |
Find Window Masker filtered locations by database name.
- Parameters
-
query These queries will be masked. [in|out] lstat Filename of the WindowMasker database. [in]
Definition at line 280 of file winmask_filter.cpp.
References CSeq_id::Assign(), CBioseq_Handle::eCoding_Iupac, eNa_strand_plus, CBlastQueryVector::GetBlastSearchQuery(), CSeq_loc::GetId(), CBlastQueryVector::GetScope(), query, s_BuildMaskedRanges(), s_BuildSeqMasker(), and CBlastQueryVector::Size().
◆ Blast_FindWindowMaskerLoc() [4/6]
| void Blast_FindWindowMaskerLoc | ( | TSeqLocVector & | query, |
| const CBlastOptions * | opts | ||
| ) |
Find Window Masker filtered locations using BlastOptions.
- Parameters
-
query These queries will be masked. [in|out] opts This provides the database name or taxid. [in]
Definition at line 252 of file winmask_filter.cpp.
References Blast_FindWindowMaskerLoc_Fwd(), and query.
◆ Blast_FindWindowMaskerLoc() [5/6]
| void Blast_FindWindowMaskerLoc | ( | TSeqLocVector & | query, |
| const CBlastOptionsHandle * | opts_handle | ||
| ) |
Find Window Masker filtered locations using a BlastOptionsHandle.
- Parameters
-
query These queries will be masked. [in|out] opts_handle This provides the database name or taxid. [in]
Definition at line 266 of file winmask_filter.cpp.
References Blast_FindWindowMaskerLoc_Fwd(), and query.
◆ Blast_FindWindowMaskerLoc() [6/6]
| void Blast_FindWindowMaskerLoc | ( | TSeqLocVector & | query, |
| const string & | lstat | ||
| ) |
Find Window Masker filtered locations on TSeqLocVector by database name.
- Parameters
-
query These queries will be masked. [in|out] lstat Filename of the WindowMasker database. [in]
Definition at line 316 of file winmask_filter.cpp.
References CSeq_id::Assign(), CBioseq_Handle::eCoding_Iupac, eNa_strand_both, eNa_strand_plus, eNa_strand_unknown, CSeq_loc::GetId(), mask, NON_CONST_ITERATE, s_BuildMaskedRanges(), and s_BuildSeqMasker().
◆ Blast_FindWindowMaskerLoc_Fwd() [1/2]
| void Blast_FindWindowMaskerLoc_Fwd | ( | TQueries & | query, |
| const CBlastOptions * | opts | ||
| ) |
Definition at line 216 of file winmask_filter.cpp.
References Blast_FindWindowMaskerLoc(), Blast_FindWindowMaskerLocTaxId(), CBlastOptions::GetWindowMaskerDatabase(), CBlastOptions::GetWindowMaskerTaxId(), and query.
Referenced by Blast_FindWindowMaskerLoc(), and Blast_FindWindowMaskerLoc_Fwd().
◆ Blast_FindWindowMaskerLoc_Fwd() [2/2]
| void Blast_FindWindowMaskerLoc_Fwd | ( | TQueries & | query, |
| const CBlastOptionsHandle * | opts_handle | ||
| ) |
Definition at line 231 of file winmask_filter.cpp.
References Blast_FindWindowMaskerLoc_Fwd(), CBlastOptionsHandle::GetOptions(), and query.
◆ Blast_FindWindowMaskerLocTaxId() [1/2]
| void Blast_FindWindowMaskerLocTaxId | ( | CBlastQueryVector & | query, |
| int | taxid | ||
| ) |
Find Window Masker filtered locations by taxonomic ID.
- Parameters
-
query These queries will be masked. [in|out] taxid This taxid will be used to find a database. [in]
Definition at line 418 of file winmask_filter.cpp.
References Blast_FindWindowMaskerLoc(), and WindowMaskerTaxidToDb().
Referenced by Blast_FindWindowMaskerLoc_Fwd().
◆ Blast_FindWindowMaskerLocTaxId() [2/2]
| void Blast_FindWindowMaskerLocTaxId | ( | TSeqLocVector & | query, |
| int | taxid | ||
| ) |
Find Window Masker filtered locations on a TSeqLocVector by Taxid.
- Parameters
-
query These queries will be masked. [in|out] taxid This taxid will be used to find a database. [in]
Definition at line 425 of file winmask_filter.cpp.
References Blast_FindWindowMaskerLoc(), and WindowMaskerTaxidToDb().
◆ Blast_GetSeqLocInfoVector()
| void Blast_GetSeqLocInfoVector | ( | EBlastProgramType | program, |
| const objects::CPacked_seqint & | queries, | ||
| const BlastMaskLoc * | mask, | ||
| TSeqLocInfoVector & | mask_v | ||
| ) |
Converts a BlastMaskLoc internal structure into an object returned by the C++ API.
- Parameters
-
program Type of BLAST program [in] queries Container of query ids and start/stop locations [in] mask All masking locations [in] mask_v Vector of per-query lists of mask locations in CSeqLocInfo form. [out]
Definition at line 904 of file blast_aux.cpp.
References _ASSERT, BLAST_ContextToFrame(), Blast_ProgramNameFromType(), eBlastTypeBlastn, eBlastTypeMapping, GetNumberOfContexts(), INT1_MAX, NStr::IntToString(), ITERATE, SSeqRange::left, Map(), mask, msg(), NCBI_THROW, BlastSeqLoc::next, compile_time_bits::range(), SSeqRange::right, s_ConvertBlastnMasks(), CSeq_interval_Base::SetFrom(), CSeq_interval_Base::SetId(), CSeq_interval_Base::SetTo(), NStr::SizetToString(), and BlastSeqLoc::ssr.
Referenced by BOOST_AUTO_TEST_CASE(), CSetupFactory::CreateScoreBlock(), and x_TestGetSeqLocInfoVector().
◆ Blast_HSPListCQueueInit()
| BlastHSPStream* Blast_HSPListCQueueInit | ( | ) |
Function to initialize a queue HSP stream.
◆ Blast_Message2TSearchMessages()
| void Blast_Message2TSearchMessages | ( | const Blast_Message * | blmsg, |
| const BlastQueryInfo * | query_info, | ||
| TSearchMessages & | messages | ||
| ) |
Converts the Blast_Message structure into a TSearchMessages object.
Definition at line 67 of file blast_aux_priv.cpp.
References _ASSERT, Blast_Message::context, BlastQueryInfo::contexts, kBlastMessageNoContext, kQueryIndex, Blast_Message::message, msg(), Blast_Message::next, NON_CONST_ITERATE, BlastQueryInfo::num_queries, BlastContextInfo::query_index, TSearchMessages::RemoveDuplicates(), and Blast_Message::severity.
Referenced by CSetupFactory::CreateLookupTable(), and CSetupFactory::CreateScoreBlock().
◆ Blast_ProgramNameFromType()
| string Blast_ProgramNameFromType | ( | EBlastProgramType | program | ) |
Returns a string program name, given a blast::EBlastProgramType enumeration.
- Parameters
-
program Enumerated program value [in]
- Returns
- String program name.
Definition at line 813 of file blast_aux.cpp.
References BlastNumber2Program(), NcbiEmptyString, and sfree.
Referenced by Blast_GetSeqLocInfoVector(), BOOST_AUTO_TEST_CASE(), CCmdLineBlastXML2ReportData::GetBlastProgramName(), CCmdLineBlastXMLReportData::GetBlastProgramName(), GetNumberOfContexts(), LogBlastOptions(), CBlastFormatterApp::PrintFormattedOutput(), s_ImportPssm(), CCmdLineBlastXML2ReportData::x_FillScoreMatrix(), CCmdLineBlastXMLReportData::x_FillScoreMatrix(), and x_TestGetSeqLocInfoVector().
◆ BLAST_SmithWatermanGetGappedScore()
| Int2 BLAST_SmithWatermanGetGappedScore | ( | EBlastProgramType | program_number, |
| BLAST_SequenceBlk * | query, | ||
| BlastQueryInfo * | query_info, | ||
| BLAST_SequenceBlk * | subject, | ||
| BlastGapAlignStruct * | gap_align, | ||
| const BlastScoringParameters * | score_params, | ||
| const BlastExtensionParameters * | ext_params, | ||
| const BlastHitSavingParameters * | hit_params, | ||
| const BlastInitialWordParameters * | word_params, | ||
| BlastInitHitList * | init_hitlist, | ||
| BlastHSPList ** | hsp_list_ptr, | ||
| BlastGappedStats * | gapped_stats, | ||
| Boolean * | fence_hit | ||
| ) |
Performs score-only Smith-Waterman gapped alignment of the subject sequence with all contexts in the query.
- Parameters
-
program_number Type of BLAST program [in] query The query sequence block [in] query_info Query information structure, containing offsets into the concatenated sequence [in] subject The subject sequence block [in] gap_align The auxiliary structure for gapped alignment [in] score_params Options and parameters related to scoring [in] ext_params Options and parameters related to extensions [in] hit_params Options related to saving hits [in] word_params Options related to ungapped alignments [in] init_hitlist List of initial HSPs (ignored) hsp_list_ptr Structure containing all saved HSPs. Note that there will be at most one HSP for each context that contains a gapped alignment that exceeds a cutoff score. [out] gapped_stats Return statistics (not filled if NULL) [out] fence_hit Partial range support (not used for S/W). [in]
Definition at line 629 of file blast_sw.c.
References BLAST_FrameToContext(), Blast_HSPInit(), Blast_HSPListNew(), Blast_HSPListSaveHSP(), Blast_ProgramIsRpsBlast(), BlastHspNumMax(), context, BlastQueryInfo::contexts, BlastGappedCutoffs::cutoff_score, BlastHitSavingParameters::cutoffs, SBlastScoreMatrix::data, eBlastTypeBlastn, eBlastTypeMapping, eBlastTypePhiBlastn, eBlastTypeRpsTblastn, BlastQueryInfo::first_context, BlastContextInfo::frame, BlastScoringParameters::gap_extend, BlastScoringParameters::gap_open, BlastContextInfo::is_valid, NULL, NUM_FRAMES, BlastHitSavingParameters::options, BlastScoreBlk::psi_matrix, SPsiBlastScoreMatrix::pssm, query, BlastContextInfo::query_length, BlastContextInfo::query_offset, s_NuclSmithWaterman(), s_SmithWatermanScoreOnly(), BlastGapAlignStruct::sbp, subject, and TRUE.
Referenced by s_BlastSetUpAuxStructures().
◆ BlastBuildArchive() [1/3]
| CRef< objects::CBlast4_archive > BlastBuildArchive | ( | blast::IQueryFactory & | queries, |
| blast::CBlastOptionsHandle & | options_handle, | ||
| const CSearchResultSet & | results, | ||
| blast::IQueryFactory & | subjects | ||
| ) |
Returns a blast archive object.
- Parameters
-
queries factory to provide queries options_handle BLAST options results set of BLAST results subjects factory to fetch subject sequences.
Definition at line 176 of file build_archive.cpp.
References results, and s_BuildArchiveAll().
◆ BlastBuildArchive() [2/3]
| CRef< objects::CBlast4_archive > BlastBuildArchive | ( | blast::IQueryFactory & | queries, |
| blast::CBlastOptionsHandle & | options_handle, | ||
| const CSearchResultSet & | results, | ||
| CRef< CSearchDatabase > | search_db, | ||
| unsigned int | num_iters = 0 |
||
| ) |
Returns a blast archive object.
- Parameters
-
queries factory to provide queries options_handle BLAST options results set of BLAST results CSearchDatabase search database num_iters psi iteration number
Definition at line 156 of file build_archive.cpp.
References kEmptyStr, CRef< C, Locker >::Reset(), results, and s_BuildArchiveAll().
Referenced by BOOST_AUTO_TEST_CASE().
◆ BlastBuildArchive() [3/3]
| CRef< objects::CBlast4_archive > BlastBuildArchive | ( | objects::CPssmWithParameters & | pssm, |
| blast::CBlastOptionsHandle & | options_handle, | ||
| const CSearchResultSet & | results, | ||
| CRef< CSearchDatabase > | search_db, | ||
| unsigned int | num_iters = 0 |
||
| ) |
Returns a blast archive object.
- Parameters
-
queries factory to provide queries options_handle BLAST options results set of BLAST results CSearchDatabase search database num_iters psi iteration number
Definition at line 190 of file build_archive.cpp.
References kEmptyStr, results, and s_BuildArchiveAll().
◆ BlastBuildSearchResultSet()
| CRef< CSearchResultSet > BlastBuildSearchResultSet | ( | const vector< CConstRef< CSeq_id > > & | query_ids, |
| const BlastScoreBlk * | sbp, | ||
| const BlastQueryInfo * | qinfo, | ||
| EBlastProgramType | program, | ||
| const TSeqAlignVector & | alignments, | ||
| TSearchMessages & | messages, | ||
| const vector< TSeqLocInfoVector > & | subj_masks, | ||
| const TSeqLocInfoVector * | query_masks = NULL, |
||
| const EResultType | result_type = ncbi::blast::eDatabaseSearch |
||
| ) |
Build a CSearchResultSet from internal BLAST data structures.
- Parameters
-
query_masks Masks for query sequences [in] subj_masks Masks for subject sequences [in]
Definition at line 305 of file blast_aux_priv.cpp.
References Blast_ProgramIsPhiBlast(), BuildBlastAncillaryData(), copy(), eSequenceComparison, i, NULL, BlastQueryInfo::pattern_info, and CSearchResultSet::size().
Referenced by CBlastTracebackSearch::Run().
◆ BlastDbFileExists()
Checks if a BLAST database exists at a given file path: looks for an alias file first, then for an index file.
Definition at line 1389 of file blast_setup_cxx.cpp.
References CFile::Exists().
Referenced by FindBlastDbPath().
◆ BlastErrorCode2String()
Returns a string containing a human-readable interpretation of the error_code passed as this function's argument.
Definition at line 112 of file blast_aux_priv.cpp.
References Blast_MessageFree(), Blast_PerrorWithLocation, kBlastMessageNoContext, kEmptyStr, Blast_Message::message, and NULL.
Referenced by CLocalBlast::Run(), CBlastPrelimSearch::Run(), and CBlastPrelimSearch::x_LaunchMultiThreadedSearch().
◆ BlastFindMatrixPath()
Returns the path to a specified matrix.
This is the implementation of the GET_MATRIX_PATH callback.
- Parameters
-
matrix_name matrix name (e.g., BLOSUM62) [in] is_prot matrix is for proteins if TRUE [in]
- Returns
- path to matrix, should be deallocated by user.
Definition at line 1301 of file blast_setup_cxx.cpp.
References g_FindDataFile(), CNcbiEnvironment::Get(), CNcbiApplicationAPI::GetEnvironment(), CDirEntry::GetPathSeparator(), CNcbiApplication::Instance(), mtx, NULL, s_GetCStringOfMatrixPath(), and NStr::ToUpper().
Referenced by AascanTestFixture::AascanTestFixture(), BOOST_AUTO_TEST_CASE(), CompressedAascanTestFixture::CompressedAascanTestFixture(), CPhiblastTestFixture::CPhiblastTestFixture(), CSetupFactory::CreateScoreBlock(), CompressedAalookupTestFixture::FillLookupTable(), AalookupTestFixture::FillLookupTable(), InitializeBlastScoreBlk(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), LinkHspTestFixture::setupScoreBlk(), CBlastExtendTestFixture::setupStructures(), CPssmEngine::x_InitializeScoreBlock(), CSeedTop::x_MakeScoreBlk(), and CTracebackTestFixture::x_SetupMain().
◆ BlastHitList2SeqAlign_OMF()
| CRef<CSeq_align_set> BlastHitList2SeqAlign_OMF | ( | const BlastHitList * | hit_list, |
| EBlastProgramType | prog, | ||
| const CSeq_loc & | query_loc, | ||
| TSeqPos | query_length, | ||
| const IBlastSeqInfoSrc * | seqinfo_src, | ||
| bool | is_gapped, | ||
| bool | is_ooframe, | ||
| TSeqLocInfoVector & | subj_masks | ||
| ) |
Definition at line 1545 of file blast_seqalign.cpp.
References _ASSERT, Blast_HSPListSortByEvalue(), BLASTHspListToSeqAlign(), BLASTUngappedHspListToSeqAlign(), IBlastSeqInfoSrc::CanReturnPartialSequence(), CreateEmptySeq_align_set(), CRef< C, Locker >::Empty(), BlastSeg::end, GetFilteredRedundantSeqids(), IBlastSeqInfoSrc::GetMasks(), IBlastSeqInfoSrc::GetSeqLoc(), GetSequenceLengthAndId(), BlastHSPList::hsp_array, BlastHSPList::hspcnt, BlastHitList::hsplist_array, BlastHitList::hsplist_count, i, Info(), CSeq_id_Base::IsGi(), LOG_POST, NON_CONST_ITERATE, BlastSeg::offset, BlastHSPList::oid, prog, RemapToQueryLoc(), s_RemapToSubjectLoc(), SerialAssign(), CSeq_align_set_Base::Set(), CRange_Base::SetFrom(), CRange_Base::SetTo(), BlastHSP::subject, and NStr::UIntToString().
Referenced by PhiBlastResults2SeqAlign_OMF(), and s_BlastResults2SeqAlignDatabaseSearch_OMF().
◆ BLASTHspListToSeqAlign()
| void BLASTHspListToSeqAlign | ( | EBlastProgramType | program, |
| BlastHSPList * | hsp_list, | ||
| CRef< CSeq_id > | query_id, | ||
| CRef< CSeq_id > | subject_id, | ||
| Int4 | query_length, | ||
| Int4 | subject_length, | ||
| bool | is_ooframe, | ||
| const vector< string > & | seqid_list, | ||
| vector< CRef< CSeq_align > > & | sa_vector | ||
| ) |
This is called for each query and each subject in a BLAST search.
- Parameters
-
program BLAST program [in] hsp_list HSP list structure [in] query_id Query sequence identifier [in] subject_id Subject sequence identifier [in] query_length Length of query sequence [in] subject_length Length of subject sequence [in] is_ooframe Was this a search with out-of-frame gapping? [in] gi_list List of GIs for the subject sequence [in] sa_vector Resulting Seq-align object [in|out]
Definition at line 1461 of file blast_seqalign.cpp.
References eBlastTypePsiBlast, CRef< C, Locker >::Empty(), BlastHSPList::hsp_array, BlastHSPList::hspcnt, BlastHSP::num_ident, s_AddScoresToSeqAlign(), s_AddUserObjectToSeqAlign(), s_BlastHSP2SeqAlign(), and s_OOFBlastHSP2SeqAlign().
Referenced by BlastHitList2SeqAlign_OMF(), and s_BLAST_OneSubjectResults2CSeqAlign().
◆ BLASTPrelminSearchHitListToStdSeg()
| void BLASTPrelminSearchHitListToStdSeg | ( | EBlastProgramType | program, |
| BlastHitList * | hit_list, | ||
| const CSeq_loc & | query_loc, | ||
| TSeqPos | query_length, | ||
| const IBlastSeqInfoSrc * | subject_seqinfo, | ||
| list< CRef< CStd_seg > > & | seg_list | ||
| ) |
Definition at line 2091 of file blast_seqalign.cpp.
References _ASSERT, GetFilteredRedundantSeqids(), GetSequenceLengthAndId(), BlastHSPList::hsp_array, BlastHSPList::hspcnt, BlastHitList::hsplist_array, BlastHitList::hsplist_count, i, CSeq_id_Base::IsGi(), NULL, BlastHSPList::oid, SerialAssign(), TRANSLATED_QUERY_MASK, TRANSLATED_SUBJECT_MASK, x_NonTranslatedHSPToStdSeg(), and x_UngappedHSPToStdSeg().
Referenced by CBlastPrelimSearch::x_BuildStdSegList().
◆ BlastSetup_GetStrand()
| objects::ENa_strand BlastSetup_GetStrand | ( | const objects::CSeq_loc & | query_seqloc, |
| EBlastProgramType | program, | ||
| objects::ENa_strand | strand_option | ||
| ) |
Choose between a Seq-loc specified query strand and the strand obtained from the CBlastOptions.
- Parameters
-
query_seqloc Seq-loc corresponding to a given query sequence [in] program program type from the CORE's point of view [in] strand_option strand as specified by the BLAST options [in]
Definition at line 117 of file blast_setup_cxx.cpp.
References s_BlastSetup_GetStrand().
Referenced by CQuerySplitter::x_ComputeQueryContextsForChunks(), and CQuerySplitter::x_ComputeQueryIndicesForChunks().
◆ BlastSetupPreliminarySearch()
| CRef< SBlastSetupData > BlastSetupPreliminarySearch | ( | CRef< IQueryFactory > | query_factory, |
| CRef< CBlastOptions > | options, | ||
| size_t | num_threads = 1 |
||
| ) |
Set up internal data structures used by the BLAST CORE engine.
- Parameters
-
query_factory source of query sequence data structures [in] options BLAST options [in] num_threads number of threads [in]
Definition at line 122 of file blast_aux_priv.cpp.
References BlastSetupPreliminarySearchEx(), and NULL.
◆ BlastSetupPreliminarySearchEx()
| CRef< SBlastSetupData > BlastSetupPreliminarySearchEx | ( | CRef< IQueryFactory > | qf, |
| CRef< CBlastOptions > | options, | ||
| CConstRef< CPssmWithParameters > | pssm, | ||
| BlastSeqSrc * | seqsrc, | ||
| size_t | num_threads | ||
| ) |
Extended interface to set up internal data structures used by the BLAST CORE engine.
- Parameters
-
query_factory source of query sequence data structures [in] options BLAST options [in] pssm PSSM [in] seqsrc source of database/subject sequence data [in] num_threads number of threads to use [in]
Definition at line 132 of file blast_aux_priv.cpp.
References Blast_CMT_LOCKInit(), Blast_DiagnosticsFree(), Blast_ProgramIsRpsBlast(), BlastHSPStreamFree(), BlastHSPStreamRegisterMTLock(), BlastHSPStreamRegisterPipe(), BlastScoreBlkFree(), BlastSeqSrcGetName(), ClearDbIndexCallbacks(), CSetupFactory::CreateDiagnosticsStructure(), CSetupFactory::CreateDiagnosticsStructureMT(), CSetupFactory::CreateHspPipe(), CSetupFactory::CreateHspStream(), CSetupFactory::CreateHspWriter(), CSetupFactory::CreateLookupTable(), CSetupFactory::CreateRpsStructures(), CSetupFactory::CreateScoreBlock(), CBlastOptions::CreateSnapshot(), eTracebackSearch, ILocalQueryData::FlushSequenceData(), ILocalQueryData::GetMessages(), CException::GetMsg(), ILocalQueryData::GetNumQueries(), CBlastOptions::GetProgramType(), ILocalQueryData::GetQueryInfo(), ILocalQueryData::GetSequenceBlk(), CBlastOptions::GetUseIndex(), CSetupFactory::InitializeMegablastDbIndex(), kBlastErrMsg_CantCalculateUngappedKAParams, LookupTableWrapFree(), IQueryFactory::MakeLocalQueryData(), NCBI_RETHROW, NCBI_THROW, CConstRef< C, Locker >::NotEmpty(), NULL, PsiBlastSetupScoreBlock(), CRef< C, Locker >::Reset(), SetUpDbIndexCallbacks(), and CBlastOptions::Validate().
Referenced by BlastSetupPreliminarySearch(), SplitQuery_CreateChunkData(), and CBlastPrelimSearch::x_Init().
◆ BLASTUngappedHspListToSeqAlign()
| void BLASTUngappedHspListToSeqAlign | ( | EBlastProgramType | program, |
| BlastHSPList * | hsp_list, | ||
| CRef< CSeq_id > | query_id, | ||
| CRef< CSeq_id > | subject_id, | ||
| Int4 | query_length, | ||
| Int4 | subject_length, | ||
| const vector< string > & | seqid_list, | ||
| vector< CRef< CSeq_align > > & | sa_vector | ||
| ) |
Creates a Seq-align from an HSP list for an ungapped search.
- Parameters
-
program BLAST program [in] hsp_list HSP list structure [in] query_id Query sequence identifier [in] subject_id Subject sequence identifier [in] query_length Length of the query [in] subject_length Length of the subject [in] gi_list List of GIs for the subject sequence.
Definition at line 1397 of file blast_seqalign.cpp.
References eBlastTypeBlastn, eBlastTypeBlastp, eBlastTypeRpsBlast, CSeq_align_Base::eType_diags, BlastHSPList::hsp_array, BlastHSPList::hspcnt, s_AddUserObjectToSeqAlign(), CSeq_align_Base::SetSegs(), CSeq_align_Base::SetType(), x_UngappedHSPToDenseDiag(), and x_UngappedHSPToStdSeg().
Referenced by BlastHitList2SeqAlign_OMF(), and s_BLAST_OneSubjectResults2CSeqAlign().
◆ BuildBlastAncillaryData()
| void BuildBlastAncillaryData | ( | EBlastProgramType | program, |
| const vector< CConstRef< CSeq_id > > & | query_ids, | ||
| const BlastScoreBlk * | sbp, | ||
| const BlastQueryInfo * | qinfo, | ||
| const TSeqAlignVector & | alignments, | ||
| const EResultType | result_type, | ||
| CSearchResultSet::TAncillaryVector & | retval | ||
| ) |
Builds an CSearchResultSet::TAncillaryVector.
- Parameters
-
program BLAST program [in] query_ids the sequence identifiers for the queries [in] sbp BlastScoreBlk structure used during the search [in] qinfo BlastQueryInfo structure used during the search [in] alignments alignments that were the result of the search [in] result_type are these results for bl2seq or a database search? [in] retval the output of this function is returned through this parameter [in|out]
Definition at line 264 of file blast_aux_priv.cpp.
References Blast_ProgramIsPhiBlast(), eSequenceComparison, and i.
Referenced by BlastBuildSearchResultSet().
◆ CalculateSeqBufferLength()
| TSeqPos CalculateSeqBufferLength | ( | TSeqPos | sequence_length, |
| EBlastEncoding | encoding, | ||
| objects::ENa_strand | strand = objects::eNa_strand_unknown, |
||
| ESentinelType | sentinel = eSentinels |
||
| ) |
Calculates the length of the buffer to allocate given the desired encoding, strand (if applicable) and use of sentinel bytes around sequence.
- Parameters
-
sequence_length Length of the sequence [in] encoding Desired encoding for calculation (supported encodings are listed in GetSequence()) [in] strand Which strand to use for calculation [in] sentinel Whether to include or not sentinels in calculation. Same criteria as GetSequence() applies [in]
- Returns
- Length of the buffer to allocate to contain original sequence of length sequence_length for given encoding and parameter constraints. If the sequence_length is 0, the return value will be 0 too
- Exceptions
-
CBlastException in case of unsupported encoding
Definition at line 1197 of file blast_setup_cxx.cpp.
References _ASSERT, COMPRESSION_RATIO, eBlastEncodingNcbi2na, eBlastEncodingNcbi4na, eBlastEncodingNucleotide, eBlastEncodingProtein, eNa_strand_both, eNa_strand_plus, eNa_strand_unknown, eNoSentinels, eSentinels, and NCBI_THROW.
Referenced by CompressNcbi2na(), GetSequenceNucleotideBothStrands(), GetSequenceProtein(), and GetSequenceSingleNucleotideStrand().
◆ CanReturnPartialSequence() [1/4]
|
inlinevirtual |
Return true if the implementation can return anything besides a seq-loc for the entire sequence.
If in doubt, the implementation must return true.
Implements IBlastSeqInfoSrc.
Definition at line 114 of file seqinfosrc_seqdb.hpp.
◆ CanReturnPartialSequence() [2/4]
|
inlinevirtual |
Return true if the implementation can return anything besides a seq-loc for the entire sequence.
If in doubt, the implementation must return true.
Implements IBlastSeqInfoSrc.
Definition at line 103 of file seqinfosrc_seqvec.hpp.
◆ CanReturnPartialSequence() [3/4]
|
inlinevirtual |
Return true if the implementation can return anything besides a seq-loc for the entire sequence.
If in doubt, the implementation must return true. GetSeqLoc use CreateWholeSeqLocFromIds, so false is returned for this implementation.
Implements IBlastSeqInfoSrc.
Definition at line 116 of file seqinfosrc_bioseq.hpp.
◆ CanReturnPartialSequence() [4/4]
|
pure virtual |
Return true if the implementation can return anything besides a seq-loc for the entire sequence.
If in doubt, the implementation must return true.
Implemented in CBioseqSeqInfoSrc, CSeqVecSeqInfoSrc, and CSeqDbSeqInfoSrc.
Referenced by BlastHitList2SeqAlign_OMF().
◆ CAutomaticGenCodeSingleton()
| CAutomaticGenCodeSingleton::CAutomaticGenCodeSingleton | ( | int | genetic_code = 0 | ) |
Default constructor.
- Parameters
-
genetic_code Integer representing the genetic code, if 0 is passed the default BLAST_GENETIC_CODE will be used [in]
- See also
- BLAST_GENETIC_CODE
Definition at line 629 of file blast_aux.cpp.
References BLAST_GENETIC_CODE, FindGeneticCode(), GenCodeSingletonAdd(), GenCodeSingletonFind(), GenCodeSingletonInit(), AutoPtr< X, Del >::get(), CAutomaticGenCodeSingleton::m_RefCounter, and NULL.
◆ CAutoNcbiConfigFile() [1/2]
|
privatedelete |
◆ CAutoNcbiConfigFile() [2/2]
|
inline |
Definition at line 63 of file blast_input_unit_test_aux.hpp.
References _ASSERT, CMetaRegistry::fAlwaysReload, CAutoNcbiConfigFile::kDataLoaders, CAutoNcbiConfigFile::kSection, CAutoNcbiConfigFile::m_App, CAutoNcbiConfigFile::m_Registry, NcbiTestGetRWConfig(), CNcbiApplicationAPI::ReloadConfig(), IRWRegistry::Set(), and rapidjson::value.
◆ CBioseqSeqInfoSrc() [1/2]
Parametrized constructor.
- Parameters
-
bs CBioseq object from which to obtain the data [in] is_prot true if sequence in bs argument is protein, else false [in]
Definition at line 54 of file seqinfosrc_bioseq.cpp.
◆ CBioseqSeqInfoSrc() [2/2]
Parametrized constructor.
- Parameters
-
bss CBioseq_set object from which to obtain the data [in] is_prot true if sequences in bss argument are all proteins, else false [in]
Definition at line 58 of file seqinfosrc_bioseq.cpp.
◆ CBl2Seq() [1/7]
◆ CBl2Seq() [2/7]
| CBl2Seq::CBl2Seq | ( | const SSeqLoc & | query, |
| const SSeqLoc & | subject, | ||
| CBlastOptionsHandle & | opts | ||
| ) |
Constructor to compare 2 sequences with specified options.
Definition at line 77 of file bl2seq.cpp.
References CBl2Seq::m_OptsHandle, query, CRef< C, Locker >::Reset(), subject, and CBl2Seq::x_Init().
◆ CBl2Seq() [3/7]
Constructor to compare 2 sequences with default options.
Definition at line 48 of file bl2seq.cpp.
References CBlastOptionsFactory::Create(), query, and subject.
◆ CBl2Seq() [4/7]
| CBl2Seq::CBl2Seq | ( | const SSeqLoc & | query, |
| const TSeqLocVector & | subjects, | ||
| CBlastOptionsHandle & | opts, | ||
| bool | dbscan_mode = false |
||
| ) |
Constructor to compare query against all subject sequences with specified options.
- Parameters
-
dbscan_mode Database search mode (as opposed to pairwise)
Definition at line 101 of file bl2seq.cpp.
References CBl2Seq::m_OptsHandle, query, CRef< C, Locker >::Reset(), and CBl2Seq::x_Init().
◆ CBl2Seq() [5/7]
| CBl2Seq::CBl2Seq | ( | const SSeqLoc & | query, |
| const TSeqLocVector & | subjects, | ||
| EProgram | p, | ||
| bool | dbscan_mode = false |
||
| ) |
Constructor to compare query against all subject sequences with default options.
- Parameters
-
dbscan_mode Database search mode (as opposed to pairwise)
Definition at line 90 of file bl2seq.cpp.
References CBlastOptionsFactory::Create(), CBl2Seq::m_OptsHandle, query, CRef< C, Locker >::Reset(), and CBl2Seq::x_Init().
◆ CBl2Seq() [6/7]
| CBl2Seq::CBl2Seq | ( | const TSeqLocVector & | queries, |
| const TSeqLocVector & | subjects, | ||
| CBlastOptionsHandle & | opts, | ||
| bool | dbscan_mode = false |
||
| ) |
Constructor to allow query concatenation with specified options.
- Parameters
-
dbscan_mode Database search mode (as opposed to pairwise)
Definition at line 120 of file bl2seq.cpp.
References CBl2Seq::m_OptsHandle, CRef< C, Locker >::Reset(), and CBl2Seq::x_Init().
◆ CBl2Seq() [7/7]
| CBl2Seq::CBl2Seq | ( | const TSeqLocVector & | queries, |
| const TSeqLocVector & | subjects, | ||
| EProgram | p, | ||
| bool | dbscan_mode = false |
||
| ) |
Constructor to allow query concatenation with default options.
- Parameters
-
dbscan_mode Database search mode (as opposed to pairwise)
Definition at line 112 of file bl2seq.cpp.
References CBlastOptionsFactory::Create(), CBl2Seq::m_OptsHandle, CRef< C, Locker >::Reset(), and CBl2Seq::x_Init().
◆ CBlast_ExtendWord() [1/2]
|
inline |
Definition at line 322 of file blast_aux.hpp.
◆ CBlast_ExtendWord() [2/2]
|
inline |
Definition at line 322 of file blast_aux.hpp.
◆ CBlast_Message() [1/2]
|
inline |
Definition at line 352 of file blast_aux.hpp.
◆ CBlast_Message() [2/2]
|
inline |
Definition at line 352 of file blast_aux.hpp.
◆ CBLAST_SequenceBlk() [1/2]
|
inline |
Definition at line 309 of file blast_aux.hpp.
◆ CBLAST_SequenceBlk() [2/2]
|
inline |
Definition at line 309 of file blast_aux.hpp.
◆ CBlastAdvancedProteinOptionsHandle() [1/3]
|
private |
Disallow copy constructor.
◆ CBlastAdvancedProteinOptionsHandle() [2/3]
|
inline |
Definition at line 64 of file blast_advprot_options.hpp.
◆ CBlastAdvancedProteinOptionsHandle() [3/3]
| CBlastAdvancedProteinOptionsHandle::CBlastAdvancedProteinOptionsHandle | ( | EAPILocality | locality = CBlastOptions::eLocal | ) |
Creates object with default options set.
Definition at line 46 of file blast_advprot_options.cpp.
References eBlastp.
◆ CBlastAncillaryData() [1/3]
| CBlastAncillaryData::CBlastAncillaryData | ( | const CBlastAncillaryData & | rhs | ) |
Copy-constructor.
Definition at line 150 of file blast_results.cpp.
References CBlastAncillaryData::do_copy().
◆ CBlastAncillaryData() [2/3]
| CBlastAncillaryData::CBlastAncillaryData | ( | EBlastProgramType | program_type, |
| int | query_number, | ||
| const BlastScoreBlk * | sbp, | ||
| const BlastQueryInfo * | query_info | ||
| ) |
constructor
- Parameters
-
program_type Type of blast search [in] query_number The index of the query for which information will be retrieved [in] sbp Score block, containing Karlin parameters [in] query_info Structure with per-context information [in]
Definition at line 72 of file blast_results.cpp.
References BLAST_GetNumberOfContexts(), BlastQueryInfo::contexts, ctx, BlastScoreBlk::gbp, i, BlastScoreBlk::kbp_gap, BlastScoreBlk::kbp_gap_psi, BlastScoreBlk::kbp_psi, BlastScoreBlk::kbp_std, CBlastAncillaryData::m_GappedKarlinBlk, CBlastAncillaryData::m_GumbelBlk, CBlastAncillaryData::m_LengthAdjustment, CBlastAncillaryData::m_PsiGappedKarlinBlk, CBlastAncillaryData::m_PsiUngappedKarlinBlk, CBlastAncillaryData::m_SearchSpace, CBlastAncillaryData::m_UngappedKarlinBlk, s_InitializeGumbelBlk(), and s_InitializeKarlinBlk().
◆ CBlastAncillaryData() [3/3]
| CBlastAncillaryData::CBlastAncillaryData | ( | pair< double, double > | lambda, |
| pair< double, double > | k, | ||
| pair< double, double > | h, | ||
| Int8 | effective_search_space, | ||
| bool | is_psiblast = false |
||
| ) |
Parametrized constructor taking pairs of values for ungapped and gapped Karlin-Altschul parameters as well as the effective search space.
- Parameters
-
lambda Pair of ungapped and gapped lambda (in that order) [in] k Pair of ungapped and gapped k (in that order) [in] h Pair of ungapped and gapped h (in that order) [in] effective_search_space effective search space [in] is_psiblast true if the statistical parameters are for PSI-BLAST [in]
Definition at line 117 of file blast_results.cpp.
References Blast_KarlinBlkNew(), Blast_KarlinBlk::H, Blast_KarlinBlk::K, Blast_KarlinBlk::Lambda, lambda(), CBlastAncillaryData::m_GappedKarlinBlk, CBlastAncillaryData::m_PsiGappedKarlinBlk, CBlastAncillaryData::m_PsiUngappedKarlinBlk, CBlastAncillaryData::m_SearchSpace, and CBlastAncillaryData::m_UngappedKarlinBlk.
◆ CBlastAppDiagHandler()
|
inline |
Constructor.
Definition at line 252 of file blast_aux.hpp.
◆ CBlastDatabaseOptions() [1/2]
|
inline |
Definition at line 331 of file blast_aux.hpp.
◆ CBlastDatabaseOptions() [2/2]
|
inline |
Definition at line 331 of file blast_aux.hpp.
◆ CBlastEffectiveLengthsOptions() [1/2]
|
inline |
Definition at line 338 of file blast_aux.hpp.
◆ CBlastEffectiveLengthsOptions() [2/2]
|
inline |
Definition at line 338 of file blast_aux.hpp.
◆ CBlastEffectiveLengthsParameters() [1/2]
|
inline |
Definition at line 340 of file blast_aux.hpp.
◆ CBlastEffectiveLengthsParameters() [2/2]
|
inline |
Definition at line 340 of file blast_aux.hpp.
◆ CBlastExtensionOptions() [1/2]
|
inline |
Definition at line 323 of file blast_aux.hpp.
◆ CBlastExtensionOptions() [2/2]
|
inline |
Definition at line 323 of file blast_aux.hpp.
◆ CBlastExtensionParameters() [1/2]
|
inline |
Definition at line 324 of file blast_aux.hpp.
◆ CBlastExtensionParameters() [2/2]
|
inline |
Definition at line 324 of file blast_aux.hpp.
◆ CBlastGapAlignStruct() [1/2]
|
inline |
Definition at line 342 of file blast_aux.hpp.
◆ CBlastGapAlignStruct() [2/2]
|
inline |
Definition at line 342 of file blast_aux.hpp.
◆ CBlastHitSavingOptions() [1/2]
|
inline |
Definition at line 326 of file blast_aux.hpp.
◆ CBlastHitSavingOptions() [2/2]
|
inline |
Definition at line 326 of file blast_aux.hpp.
◆ CBlastHitSavingParameters() [1/2]
|
inline |
Definition at line 328 of file blast_aux.hpp.
◆ CBlastHitSavingParameters() [2/2]
|
inline |
Definition at line 328 of file blast_aux.hpp.
◆ CBlastHSPListQueueData()
| CBlastHSPListQueueData::CBlastHSPListQueueData | ( | ) |
Constructor.
◆ CBlastHSPResults() [1/2]
|
inline |
Definition at line 343 of file blast_aux.hpp.
◆ CBlastHSPResults() [2/2]
|
inline |
Definition at line 343 of file blast_aux.hpp.
◆ CBlastInitialWordOptions() [1/2]
|
inline |
Definition at line 318 of file blast_aux.hpp.
◆ CBlastInitialWordOptions() [2/2]
|
inline |
Definition at line 318 of file blast_aux.hpp.
◆ CBlastInitialWordParameters() [1/2]
|
inline |
Definition at line 320 of file blast_aux.hpp.
◆ CBlastInitialWordParameters() [2/2]
|
inline |
Definition at line 320 of file blast_aux.hpp.
◆ CBlastMaskLoc() [1/2]
|
inline |
Definition at line 354 of file blast_aux.hpp.
◆ CBlastMaskLoc() [2/2]
|
inline |
Definition at line 354 of file blast_aux.hpp.
◆ CBlastNucleotideOptionsHandle() [1/3]
|
private |
Disallow copy constructor.
◆ CBlastNucleotideOptionsHandle() [2/3]
| CBlastNucleotideOptionsHandle::CBlastNucleotideOptionsHandle | ( | CRef< CBlastOptions > | opt | ) |
Create Options Handle from Existing CBlastOptions Object.
Definition at line 55 of file blast_nucl_options.cpp.
◆ CBlastNucleotideOptionsHandle() [3/3]
| CBlastNucleotideOptionsHandle::CBlastNucleotideOptionsHandle | ( | EAPILocality | locality = CBlastOptions::eLocal | ) |
Creates object with default options set.
Definition at line 48 of file blast_nucl_options.cpp.
◆ CBlastOptions()
| CBlastOptions::CBlastOptions | ( | EAPILocality | locality = eLocal | ) |
Constructor which allows specification of local or remote version of the options (might change in the future)
- Parameters
-
locality specification of whether this type will be used with a remote or local BLAST search database class
Definition at line 299 of file blast_options_cxx.cpp.
References CBlastOptions::eBoth, CBlastOptions::eLocal, CBlastOptions::eRemote, CBlastOptions::m_Local, and CBlastOptions::m_Remote.
Referenced by CBlastOptions::Clone().
◆ CBlastOptionsBuilder()
| CBlastOptionsBuilder::CBlastOptionsBuilder | ( | const string & | program, |
| const string & | service, | ||
| CBlastOptions::EAPILocality | locality = CBlastOptions::eLocal, |
||
| bool | ignore_unsupported_options = false |
||
| ) |
Constructor.
This takes the program and service strings, using them to determine the type of CBlastOptionsHandle to return. Some of the name/value pairs also influence the type of blast options handle required.
- Parameters
-
program Blast4 program string (e.g. blastn or blastp). service Blast4 service string (e.g. plain or rpsblast). locality Locality of the resulting object.
Definition at line 47 of file blast_options_builder.cpp.
◆ CBlastOptionsFactory()
|
private |
Private c-tor.
◆ CBlastOptionsHandle() [1/2]
|
protected |
Create Options Handle from Existing CBlastOptions Object.
Definition at line 67 of file blast_options_handle.cpp.
◆ CBlastOptionsHandle() [2/2]
| CBlastOptionsHandle::CBlastOptionsHandle | ( | EAPILocality | locality | ) |
Default c-tor.
Definition at line 61 of file blast_options_handle.cpp.
◆ CBlastOptionsLocal() [1/2]
| CBlastOptionsLocal::CBlastOptionsLocal | ( | ) |
Definition at line 49 of file blast_options_local_priv.cpp.
References BlastDatabaseOptionsNew(), BlastEffectiveLengthsOptionsNew(), BlastQuerySetUpOptionsNew(), calloc(), eBlastNotSet, CBlastOptionsLocal::m_DbOpts, CBlastOptionsLocal::m_DeltaBlastOpts, CBlastOptionsLocal::m_EffLenOpts, CBlastOptionsLocal::m_ExtnOpts, CBlastOptionsLocal::m_ForceMBIndex, CBlastOptionsLocal::m_HitSaveOpts, CBlastOptionsLocal::m_InitWordOpts, CBlastOptionsLocal::m_LutOpts, CBlastOptionsLocal::m_MBIndexLoaded, CBlastOptionsLocal::m_Program, CBlastOptionsLocal::m_PSIBlastOpts, CBlastOptionsLocal::m_QueryOpts, CBlastOptionsLocal::m_ScoringOpts, CBlastOptionsLocal::m_UseMBIndex, NULL, PSIBlastOptionsNew(), CBlastExtensionOptions::Reset(), CBlastHitSavingOptions::Reset(), CBlastInitialWordOptions::Reset(), CBlastScoringOptions::Reset(), CLookupTableOptions::Reset(), and CQuerySetUpOptions::Reset().
◆ CBlastOptionsLocal() [2/2]
| CBlastOptionsLocal::CBlastOptionsLocal | ( | const CBlastOptionsLocal & | optsLocal | ) |
Copy constructor.
Definition at line 74 of file blast_options_local_priv.cpp.
References CBlastOptionsLocal::x_DoDeepCopy().
◆ CBlastOptionsMemento()
|
inlineprivate |
Definition at line 64 of file blast_memento_priv.hpp.
References CQuerySetUpOptions::Get(), CLookupTableOptions::Get(), CBlastInitialWordOptions::Get(), CBlastExtensionOptions::Get(), CBlastHitSavingOptions::Get(), CPSIBlastOptions::Get(), CBlastDatabaseOptions::Get(), CBlastScoringOptions::Get(), CBlastEffectiveLengthsOptions::Get(), CBlastOptionsLocal::GetProgramType(), CBlastOptionsLocal::m_DbOpts, CBlastOptionsLocal::m_EffLenOpts, CBlastOptionsLocal::m_ExtnOpts, CBlastOptionsLocal::m_HitSaveOpts, CBlastOptionsLocal::m_InitWordOpts, CBlastOptionsLocal::m_LutOpts, CBlastOptionsLocal::m_PSIBlastOpts, CBlastOptionsLocal::m_QueryOpts, and CBlastOptionsLocal::m_ScoringOpts.
◆ CBlastOptionsRemote() [1/2]
|
inline |
Copy constructor.
Definition at line 74 of file blast_options_cxx.cpp.
References CBlastOptionsRemote::x_DoDeepCopy().
◆ CBlastOptionsRemote() [2/2]
|
inline |
Definition at line 63 of file blast_options_cxx.cpp.
References CBlastOptionsRemote::m_ReqOpts, and CRef< C, Locker >::Reset().
◆ CBlastpKmerOptionsHandle() [1/3]
|
private |
Disallow copy constructor.
◆ CBlastpKmerOptionsHandle() [2/3]
|
inline |
Definition at line 59 of file blastp_kmer_options.hpp.
◆ CBlastpKmerOptionsHandle() [3/3]
| CBlastpKmerOptionsHandle::CBlastpKmerOptionsHandle | ( | EAPILocality | locality = CBlastOptions::eLocal | ) |
Creates object with default options set.
Definition at line 46 of file blastp_kmer_options.cpp.
◆ CBlastPrelimSearch() [1/4]
|
private |
Prohibit copy constructor.
◆ CBlastPrelimSearch() [2/4]
| CBlastPrelimSearch::CBlastPrelimSearch | ( | CRef< IQueryFactory > | query_factory, |
| CRef< CBlastOptions > | options, | ||
| BlastSeqSrc * | seqsrc, | ||
| CConstRef< objects::CPssmWithParameters > | pssm = null |
||
| ) |
Constructor which takes a PSSM and an already initialized BlastSeqSrc object.
- Note
- we don't own the BlastSeqSrc
Definition at line 91 of file prelim_stage.cpp.
References CBlastPrelimSearch::m_InternalData, SInternalData::m_SeqSrc, and CBlastPrelimSearch::x_Init().
◆ CBlastPrelimSearch() [3/4]
| CBlastPrelimSearch::CBlastPrelimSearch | ( | CRef< IQueryFactory > | query_factory, |
| CRef< CBlastOptions > | options, | ||
| const CSearchDatabase & | dbinfo | ||
| ) |
Constructor which creates and manages a BLAST database handle for the caller.
- Note
- we create a BlastSeqSrc using CSeqDB as its implementation
Definition at line 62 of file prelim_stage.cpp.
References BlastSeqSrcFree(), and CSetupFactory::CreateBlastSeqSrc().
◆ CBlastPrelimSearch() [4/4]
| CBlastPrelimSearch::CBlastPrelimSearch | ( | CRef< IQueryFactory > | query_factory, |
| CRef< CBlastOptions > | options, | ||
| CRef< CLocalDbAdapter > | db, | ||
| size_t | num_threads = 1 |
||
| ) |
Constructor which creates BlastSeqSrc object from the already constructed BLAST database handle.
- Note
- we don't own the BlastSeqSrc
Definition at line 75 of file prelim_stage.cpp.
References CBlastPrelimSearch::m_InternalData, SInternalData::m_SeqSrc, CLocalDbAdapter::MakeSeqSrc(), CBlastPrelimSearch::SetNumberOfThreads(), and CBlastPrelimSearch::x_Init().
◆ CBlastProteinOptionsHandle() [1/3]
|
private |
Disallow copy constructor.
◆ CBlastProteinOptionsHandle() [2/3]
|
inline |
Create Options Handle from Existing CBlastOptions Object.
Definition at line 62 of file blast_prot_options.hpp.
◆ CBlastProteinOptionsHandle() [3/3]
| CBlastProteinOptionsHandle::CBlastProteinOptionsHandle | ( | EAPILocality | locality = CBlastOptions::eLocal | ) |
Creates object with default options set.
Definition at line 49 of file blast_prot_options.cpp.
References eBlastp.
◆ CBlastQueryFilteredFrames() [1/3]
|
private |
Prevent copy construction.
◆ CBlastQueryFilteredFrames() [2/3]
| CBlastQueryFilteredFrames::CBlastQueryFilteredFrames | ( | EBlastProgramType | program | ) |
Construct container for frame values and BlastSeqLocs for the specified search program.
- Parameters
-
program The type of search being done.
Definition at line 1523 of file blast_setup_cxx.cpp.
References CBlastQueryFilteredFrames::m_TranslateCoords, and CBlastQueryFilteredFrames::x_NeedsTrans().
◆ CBlastQueryFilteredFrames() [3/3]
| CBlastQueryFilteredFrames::CBlastQueryFilteredFrames | ( | EBlastProgramType | program, |
| const TMaskedQueryRegions & | mqr | ||
| ) |
Construct container for frame values and BlastSeqLocs from a TMaskedQueryRegions vector.
- Parameters
-
program Search program value used [in] mqr MaskedQueryRegions to convert [in]
Definition at line 1530 of file blast_setup_cxx.cpp.
References CBlastQueryFilteredFrames::AddSeqLoc(), Blast_QueryIsTranslated(), set< Key, Compare >::insert(), ITERATE, CBlastQueryFilteredFrames::m_TranslateCoords, and CBlastQueryFilteredFrames::x_NeedsTrans().
◆ CBlastQueryInfo() [1/2]
|
inline |
Definition at line 311 of file blast_aux.hpp.
◆ CBlastQueryInfo() [2/2]
|
inline |
Definition at line 311 of file blast_aux.hpp.
◆ CBlastQuerySourceBioseqSet() [1/2]
| CBlastQuerySourceBioseqSet::CBlastQuerySourceBioseqSet | ( | const objects::CBioseq & | bioseq, |
| bool | is_prot | ||
| ) |
Parametrized constructor for a Bioseq.
- Parameters
-
bioseq bioseq from which to extract the data [in] is_prot whether the bioseq argument contains a protein or nucleotide sequence [in]
Definition at line 242 of file bioseq_extract_data_priv.cpp.
References CBlastQuerySourceBioseqSet::m_Bioseqs, and CBlastQuerySourceBioseqSet::x_BioseqSanityCheck().
◆ CBlastQuerySourceBioseqSet() [2/2]
| CBlastQuerySourceBioseqSet::CBlastQuerySourceBioseqSet | ( | const objects::CBioseq_set & | bss, |
| bool | is_prot | ||
| ) |
Parametrized constructor for a Bioseq-set.
- Parameters
-
bss set of bioseqs from which to extract the data [in] is_prot whether the bss argument contains protein or nucleotide sequences [in]
Definition at line 230 of file bioseq_extract_data_priv.cpp.
References ConstBegin(), eDetectLoops, CBlastQuerySourceBioseqSet::m_Bioseqs, and CBlastQuerySourceBioseqSet::x_BioseqSanityCheck().
◆ CBlastQuerySourceOM() [1/4]
| CBlastQuerySourceOM::CBlastQuerySourceOM | ( | CBlastQueryVector & | v, |
| const CBlastOptions * | opts | ||
| ) |
Constructor which takes a CBlastQueryVector.
This version will compute masking information with dust.
- Parameters
-
v Object containing the queries, scopes and masking info [in] opts BLAST algorithm options [in]
Definition at line 99 of file blast_objmgr_tools.cpp.
References CBlastQuerySourceOM::x_AutoDetectGeneticCodes().
◆ CBlastQuerySourceOM() [2/4]
| CBlastQuerySourceOM::CBlastQuerySourceOM | ( | CBlastQueryVector & | v, |
| EBlastProgramType | prog | ||
| ) |
Constructor which takes a CBlastQueryVector.
This version assumes the masking information (if any) was provided with the CBlastQueryVector.
- Parameters
-
v Object containing the queries, scopes and masking info [in] prog type of program to run [in]
Definition at line 88 of file blast_objmgr_tools.cpp.
References CBlastQuerySourceOM::x_AutoDetectGeneticCodes().
◆ CBlastQuerySourceOM() [3/4]
| CBlastQuerySourceOM::CBlastQuerySourceOM | ( | TSeqLocVector & | v, |
| const CBlastOptions * | opts | ||
| ) |
Constructor which takes a TSeqLocVector.
This version will compute masking information with dust.
- Parameters
-
v vector of SSeqLoc structures containing the queries [in] opts BLAST algorithm options [in]
- Note
- that the v argument might be changed with the filtering locations
Definition at line 77 of file blast_objmgr_tools.cpp.
References CBlastQuerySourceOM::x_AutoDetectGeneticCodes().
◆ CBlastQuerySourceOM() [4/4]
| CBlastQuerySourceOM::CBlastQuerySourceOM | ( | TSeqLocVector & | v, |
| EBlastProgramType | prog | ||
| ) |
Constructor which takes a TSeqLocVector.
This version assumes the masking information (if any) was provided with the TSeqLocVector.
- Parameters
-
v vector of SSeqLoc structures containing the queries [in] prog program type of this search [in]
Definition at line 66 of file blast_objmgr_tools.cpp.
◆ CBlastRPSAuxInfo() [1/2]
|
private |
Prohibit copy-constructor.
◆ CBlastRPSAuxInfo() [2/2]
| CBlastRPSAuxInfo::CBlastRPSAuxInfo | ( | const string & | matrix, |
| int | gap_open, | ||
| int | gap_extend, | ||
| double | scale_factor, | ||
| const vector< double > & | karlin_k | ||
| ) |
Parametrized constructor.
- Parameters
-
matrix name of the scoring matrix used to build the RPS-BLAST database gap_open gap opening cost gap_extend gap extension cost scale_factor scaling factor karlin_k statistical K parameter calculated when building the RPS-BLAST database
Definition at line 95 of file rps_aux.cpp.
References _ASSERT, copy(), BlastRPSAuxInfo::gap_extend_penalty, BlastRPSAuxInfo::gap_open_penalty, BlastRPSAuxInfo::karlin_k, CBlastRPSAuxInfo::m_Data, NCBI_THROW, BlastRPSAuxInfo::orig_score_matrix, BlastRPSAuxInfo::scale_factor, strdup, and CBlastRPSAuxInfo::x_DoDestroy().
◆ CBlastRPSInfo() [1/3]
|
private |
Prohibit copy-constructor.
◆ CBlastRPSInfo() [2/3]
Parametrized constructor.
- Parameters
-
rps_dbname name of the RPS-BLAST database
Definition at line 508 of file rps_aux.cpp.
References CBlastRPSInfo::fRpsBlast, and CBlastRPSInfo::x_Init().
◆ CBlastRPSInfo() [3/3]
Parametrized constructor.
- Parameters
-
rps_dbname name of the RPS-BLAST database flags Flags for which database files to open
Definition at line 513 of file rps_aux.cpp.
References flags, and CBlastRPSInfo::x_Init().
◆ CBlastRPSOptionsHandle() [1/3]
|
private |
Disallow copy constructor.
◆ CBlastRPSOptionsHandle() [2/3]
| CBlastRPSOptionsHandle::CBlastRPSOptionsHandle | ( | CRef< CBlastOptions > | opt | ) |
Create Options Handle from Existing CBlastOptions Object.
Definition at line 55 of file blast_rps_options.cpp.
◆ CBlastRPSOptionsHandle() [3/3]
| CBlastRPSOptionsHandle::CBlastRPSOptionsHandle | ( | EAPILocality | locality = CBlastOptions::eLocal | ) |
Creates object with default options set.
Definition at line 48 of file blast_rps_options.cpp.
References eRPSBlast.
◆ CBlastScopeSourceWrapper() [1/2]
|
inline |
Definition at line 120 of file blast_input_unit_test_aux.hpp.
References CBlastScopeSourceWrapper::m_ScopeSrc, and CRef< C, Locker >::Reset().
◆ CBlastScopeSourceWrapper() [2/2]
|
inline |
Definition at line 123 of file blast_input_unit_test_aux.hpp.
References CBlastScopeSourceWrapper::m_ScopeSrc, and CRef< C, Locker >::Reset().
◆ CBlastScoreBlk() [1/2]
|
inline |
Definition at line 333 of file blast_aux.hpp.
◆ CBlastScoreBlk() [2/2]
|
inline |
Definition at line 333 of file blast_aux.hpp.
◆ CBlastScoringOptions() [1/2]
|
inline |
Definition at line 334 of file blast_aux.hpp.
◆ CBlastScoringOptions() [2/2]
|
inline |
Definition at line 334 of file blast_aux.hpp.
◆ CBlastScoringParameters() [1/2]
|
inline |
Definition at line 335 of file blast_aux.hpp.
◆ CBlastScoringParameters() [2/2]
|
inline |
Definition at line 335 of file blast_aux.hpp.
◆ CBlastSeqLoc() [1/2]
|
inline |
Definition at line 355 of file blast_aux.hpp.
◆ CBlastSeqLoc() [2/2]
|
inline |
Definition at line 355 of file blast_aux.hpp.
◆ CBlastSeqSrc() [1/2]
|
inline |
Definition at line 350 of file blast_aux.hpp.
◆ CBlastSeqSrc() [2/2]
|
inline |
Definition at line 350 of file blast_aux.hpp.
◆ CBlastSeqSrcIterator() [1/2]
|
inline |
Definition at line 351 of file blast_aux.hpp.
◆ CBlastSeqSrcIterator() [2/2]
|
inline |
Definition at line 351 of file blast_aux.hpp.
◆ CBlastSeqVectorFromCSeq_data()
| CBlastSeqVectorFromCSeq_data::CBlastSeqVectorFromCSeq_data | ( | const objects::CSeq_data & | seq_data, |
| TSeqPos | length | ||
| ) |
Parametrized constructor.
- Parameters
-
seq_data sequence data [in] length length of the sequence data (not of the buffer containing the data!) [in]
Definition at line 78 of file bioseq_extract_data_priv.cpp.
References CSeqConvert::Convert(), CSeq_data_Base::e_Iupacaa, CSeqUtil::e_Iupacaa, CSeq_data_Base::e_Iupacna, CSeqUtil::e_Iupacna, CSeq_data_Base::e_Ncbi2na, CSeqUtil::e_Ncbi2na, CSeqUtil::e_Ncbi2na_expand, CSeq_data_Base::e_Ncbi4na, CSeqUtil::e_Ncbi4na, CSeqUtil::e_Ncbi4na_expand, CSeq_data_Base::e_Ncbieaa, CSeqUtil::e_Ncbieaa, CSeq_data_Base::e_Ncbistdaa, CSeqUtil::e_Ncbistdaa, eNa_strand_plus, NStr::IntToString(), NCBI_CURRENT_FUNCTION, and NCBI_THROW.
◆ CBlastSeqVectorOM()
Definition at line 487 of file blast_objmgr_tools.cpp.
References CSeq_loc::GetStrand(), CBlastSeqVectorOM::m_SeqLoc, and IBlastSeqVector::m_Strand.
◆ CBlastServices() [1/2]
|
inline |
Default constructor.
Definition at line 110 of file blast_services.hpp.
◆ CBlastServices() [2/2]
|
private |
Prohibit copy construction.
◆ CBlastTracebackSearch() [1/3]
|
private |
Prohibit copy constructor.
◆ CBlastTracebackSearch() [2/3]
| CBlastTracebackSearch::CBlastTracebackSearch | ( | CRef< IQueryFactory > | qf, |
| CRef< CBlastOptions > | opts, | ||
| BlastSeqSrc * | seqsrc, | ||
| CRef< IBlastSeqInfoSrc > | seqinfosrc, | ||
| CRef< TBlastHSPStream > | hsps, | ||
| CConstRef< objects::CPssmWithParameters > | pssm = null |
||
| ) |
Create a BlastSeqSrc re-using an already created BlastSeqSrc.
- Note
- We don't own the BlastSeqSrc
Definition at line 60 of file traceback_stage.cpp.
References BlastSeqSrcGetName(), and NULL.
◆ CBlastTracebackSearch() [3/3]
| CBlastTracebackSearch::CBlastTracebackSearch | ( | CRef< IQueryFactory > | query_factory, |
| CRef< SInternalData > | internal_data, | ||
| CRef< CBlastOptions > | opts, | ||
| CRef< IBlastSeqInfoSrc > | seqinfosrc, | ||
| TSearchMessages & | search_msgs | ||
| ) |
Use the internal data and return value of the preliminary search to proceed with the traceback.
Definition at line 80 of file traceback_stage.cpp.
References Blast_ProgramIsPhiBlast(), CBlastOptions::GetProgramType(), int, BlastUngappedStats::lookup_hits, SInternalData::m_Diagnostics, CBlastTracebackSearch::m_InternalData, SDatabaseScanData::m_NumPatOccurInDB, CBlastTracebackSearch::SetDBScanInfo(), and BlastDiagnostics::ungapped_stat.
◆ CBlastVersion()
|
inline |
Definition at line 55 of file version.hpp.
◆ CBlastxOptionsHandle() [1/2]
|
private |
Disallow copy constructor.
◆ CBlastxOptionsHandle() [2/2]
| CBlastxOptionsHandle::CBlastxOptionsHandle | ( | EAPILocality | locality = CBlastOptions::eLocal | ) |
Creates object with default options set.
Definition at line 47 of file blastx_options.cpp.
References eBlastx.
◆ CCddInputData()
| CCddInputData::CCddInputData | ( | const Uint1 * | query, |
| unsigned int | query_length, | ||
| CConstRef< objects::CSeq_align_set > | seqaligns, | ||
| const PSIBlastOptions & | opts, | ||
| const string & | dbname, | ||
| const string & | matrix_name = "BLOSUM62", |
||
| int | gap_existence = 0, |
||
| int | gap_extension = 0, |
||
| PSIDiagnosticsRequest * | diags = NULL, |
||
| const string & | query_title = "" |
||
| ) |
Constructor.
- Parameters
-
query Query sequence in ncbistdaa encoding [in] query_length Query sequence length [in] seqaligns List of pair-wise alignments of query to CDs. PSSM will be computed based on those alignments [in] opts CD-related PSSM engine options [in] dbname Name of CDD database used for searching matches to query. The alignments in seqaligns come from searching this database [in] matrix_name Name of the scoring system [in] gap_existence Gap opening cost, if zero default from IPssmInput_Base will be used [in] gap_extension Gap extension cost, if zero default from IPssmInput_Base will be used [in] diags Options for pssm engine diagnostics [in]
Definition at line 71 of file cdd_pssm_input.cpp.
References CConstRef< C, Locker >::Empty(), CCddInputData::m_QueryData, NCBI_THROW, and query.
◆ CContextTranslator()
| CContextTranslator::CContextTranslator | ( | const CSplitQueryBlk & | sqb, |
| vector< CRef< IQueryFactory > > * | query_chunk_factories = NULL, |
||
| const CBlastOptions * | options = NULL |
||
| ) |
Constructor.
- Parameters
-
sqb Split query block structure [in] query_chunk_factories query factories corresponding to each of the chunks needed to report unit testing data (optional) [in] options BLAST options, also needed to report unit test data (optional) [in]
Definition at line 212 of file split_query_aux_priv.cpp.
References ctx, BlastQueryInfo::first_context, CContextTranslator::GetAbsoluteContext(), CSplitQueryBlk::GetNumChunks(), CSplitQueryBlk::GetQueryContexts(), ILocalQueryData::GetQueryInfo(), CContextTranslator::GetStartingChunk(), i, CContextTranslator::m_AbsoluteContexts, CContextTranslator::m_ContextsPerChunk, CContextTranslator::m_StartingChunks, IQueryFactory::MakeLocalQueryData(), and NULL.
◆ CDeltaBlast() [1/3]
|
protected |
Prohibit copy constructor.
◆ CDeltaBlast() [2/3]
| CDeltaBlast::CDeltaBlast | ( | CRef< IQueryFactory > | query_factory, |
| CRef< CLocalDbAdapter > | blastdb, | ||
| CRef< CLocalDbAdapter > | domaindb, | ||
| CConstRef< CDeltaBlastOptionsHandle > | options | ||
| ) |
Constructor to compare a single sequence against a database of protein sequences, and use RPS-BLAST to search CDD.
- Parameters
-
query_factory Protein query sequence to search [in] blastdb Adapter to the BLAST database to search [in] domaindb Adapter to the BLAST conserved domain database for making Pssm [in] options DELTA-BLAST options [in]
Definition at line 55 of file deltablast.cpp.
◆ CDeltaBlast() [3/3]
| CDeltaBlast::CDeltaBlast | ( | CRef< IQueryFactory > | query_factory, |
| CRef< CLocalDbAdapter > | blastdb, | ||
| CRef< CLocalDbAdapter > | domaindb, | ||
| CConstRef< CDeltaBlastOptionsHandle > | options, | ||
| CRef< CBlastRPSOptionsHandle > | rps_options | ||
| ) |
Constructor to compare a single sequence against a database of protein sequences, and use RPS-BLAST to search CDD.
- Parameters
-
query_factory Protein query sequence to search [in] blastdb Adapter to the BLAST database to search [in] domaindb Adapter to the BLAST conserved domain database for making Pssm [in] options DELTA-BLAST options [in] rps_options RPSBLAST options to be used in CDD search [in]
Definition at line 68 of file deltablast.cpp.
References CDeltaBlast::x_Validate().
◆ CDeltaBlastOptionsHandle() [1/2]
|
private |
Disallow copy constructor.
◆ CDeltaBlastOptionsHandle() [2/2]
| CDeltaBlastOptionsHandle::CDeltaBlastOptionsHandle | ( | EAPILocality | locality = CBlastOptions::eLocal | ) |
Creates object with default options set.
Definition at line 46 of file deltablast_options.cpp.
References eDeltaBlast, and CBlastOptions::eRemote.
◆ CDiscNucleotideOptionsHandle() [1/2]
|
private |
Disallow copy constructor.
◆ CDiscNucleotideOptionsHandle() [2/2]
| CDiscNucleotideOptionsHandle::CDiscNucleotideOptionsHandle | ( | EAPILocality | locality = CBlastOptions::eLocal | ) |
Creates object with default options set.
Definition at line 47 of file disc_nucl_options.cpp.
References eDiscMegablast.
◆ CEffectiveSearchSpaceCalculator()
| CEffectiveSearchSpaceCalculator::CEffectiveSearchSpaceCalculator | ( | CRef< IQueryFactory > | query_factory, |
| const CBlastOptions & | options, | ||
| Int4 | db_num_seqs, | ||
| Int8 | db_num_bases, | ||
| BlastScoreBlk * | sbp = NULL |
||
| ) |
Constructor.
- Parameters
-
query_factory source for query sequence(s) [in] options BLAST options [in] db_num_seqs number of sequences in the database/subjects to search [in] db_num_bases number of bases/residues in the database/subjects to search [in] sbp BlastScoreBlk to be used. If NULL another instance will be created [in]
Definition at line 83 of file effsearchspace_calc.cpp.
References _ASSERT, BLAST_CalcEffLengths(), BlastEffectiveLengthsParametersNew(), BlastScoreBlkFree(), CSetupFactory::CreateScoreBlock(), CBlastOptions::CreateSnapshot(), ILocalQueryData::GetQueryInfo(), TSearchMessages::HasMessages(), CEffectiveSearchSpaceCalculator::m_Program, CEffectiveSearchSpaceCalculator::m_QueryFactory, CEffectiveSearchSpaceCalculator::m_QueryInfo, IQueryFactory::MakeLocalQueryData(), NCBI_THROW, and NULL.
◆ CEffectiveSearchSpacesMemento()
|
inline |
Parametrized constructor.
- Parameters
-
options the BLAST options [in]
Definition at line 112 of file blast_memento_priv.hpp.
References _ASSERT, BlastEffectiveLengthsOptionsNew(), CBlastOptionsLocal::m_EffLenOpts, CEffectiveSearchSpacesMemento::m_EffLenOrig, CEffectiveSearchSpacesMemento::m_EffLenReplace, CBlastOptions::m_Local, malloc(), BlastEffectiveLengthsOptions::num_searchspaces, CBlastEffectiveLengthsOptions::Release(), CBlastEffectiveLengthsOptions::Reset(), and BlastEffectiveLengthsOptions::searchsp_eff.
◆ CExportStrategy() [1/5]
|
private |
◆ CExportStrategy() [2/5]
| CExportStrategy::CExportStrategy | ( | CRef< CBlastOptionsHandle > | opts_handle, |
| const string & | client_id = kEmptyStr |
||
| ) |
Construct search strategy with :-.
- Parameters
-
opts_handle Blast options handle (Note: only eRemote or eBoth mode are supported)
Definition at line 303 of file search_strategy.cpp.
References CExportStrategy::x_Process_BlastOptions().
◆ CExportStrategy() [3/5]
| CExportStrategy::CExportStrategy | ( | CRef< CPssmWithParameters > | pssm, |
| CRef< CBlastOptionsHandle > | opts_handle, | ||
| CRef< CSearchDatabase > | db, | ||
| const string & | client_id = kEmptyStr, |
||
| unsigned int | psi_num_iterations = 0 |
||
| ) |
Construct search strategy with :-.
- Parameters
-
pssm Search matrix for a PSSM search. opts_handle Blast options handle. (Note: only eRemote or eBoth mode are supported) db Database used for this search.
Definition at line 337 of file search_strategy.cpp.
References CExportStrategy::x_AddPsiNumOfIterationsToFormatOptions(), CExportStrategy::x_Process_BlastOptions(), CExportStrategy::x_Process_Pssm(), and CExportStrategy::x_Process_SearchDb().
◆ CExportStrategy() [4/5]
| CExportStrategy::CExportStrategy | ( | CRef< IQueryFactory > | query, |
| CRef< CBlastOptionsHandle > | opts_handle, | ||
| CRef< CSearchDatabase > | db, | ||
| const string & | client_id = kEmptyStr, |
||
| unsigned int | psi_num_iterations = 0 |
||
| ) |
Construct search strategy with :-.
- Parameters
-
queries Queries corresponding to Seq-loc-list or Bioseq-set. opts_handle Blast options handle. (Note: only eRemote or eBoth mode are supported) db Database used for this search.
Definition at line 310 of file search_strategy.cpp.
References query, CExportStrategy::x_AddPsiNumOfIterationsToFormatOptions(), CExportStrategy::x_Process_BlastOptions(), CExportStrategy::x_Process_Query(), and CExportStrategy::x_Process_SearchDb().
◆ CExportStrategy() [5/5]
| CExportStrategy::CExportStrategy | ( | CRef< IQueryFactory > | query, |
| CRef< CBlastOptionsHandle > | opts_handle, | ||
| CRef< IQueryFactory > | subject, | ||
| const string & | client_id = kEmptyStr |
||
| ) |
Construct search strategy with :-.
- Parameters
-
queries Queries corresponding to Seq-loc-list or Bioseq-set. opts_handle Blast options handle. (Note: only eRemote or eBoth mode are supported) subjects Subject corresponding to Seq-loc-list or Bioseq-set.
Definition at line 325 of file search_strategy.cpp.
References query, subject, CExportStrategy::x_Process_BlastOptions(), CExportStrategy::x_Process_Query(), and CExportStrategy::x_Process_Subject().
◆ CFilteringMemento()
|
inline |
Parametrized constructor.
- Parameters
-
opts_memento snapshopt of the BLAST options [in]
Definition at line 57 of file effsearchspace_calc.cpp.
References eEmpty, QuerySetUpOptions::filter_string, QuerySetUpOptions::filtering_options, CBlastOptionsMemento::m_QueryOpts, NULL, and SBlastFilterOptionsNew().
◆ CFrameFinder()
|
inline |
◆ CheckDone()
| bool CRemoteBlast::CheckDone | ( | void | ) |
Check whether the search has completed.
This checks the status of the search. Please delay at least 10 seconds between subsequent calls. If this function returns true, it will already have gotten the results as part of its processing. With the common technique of polling with CheckDone before calling GetAlignments (or other results access operations), the first CheckDone call after results are available will perform the CPU, network, and memory intensive processing, and the GetAlignments() (for example) call will simply return a pointer to part of this data.
- Returns
- true If search is not still running.
Definition at line 354 of file remote_blast.cpp.
References CRemoteBlast::eDone, CRemoteBlast::eFailed, CRemoteBlast::eStart, CRemoteBlast::eWait, CRemoteBlast::m_use_disk_cache, CRemoteBlast::Submit(), CRemoteBlast::x_CheckResults(), CRemoteBlast::x_CheckResultsDC(), CRemoteBlast::x_GetState(), and CRemoteBlast::x_IsUnknownRID().
Referenced by BOOST_AUTO_TEST_CASE(), and CRemoteBlast::CheckStatus().
◆ CheckInternalData()
| int CBlastPrelimSearch::CheckInternalData | ( | ) |
Checks that internal data is valid.
Used to know whether or not run should proceed or just print statistics for user. This would most often be called if the problems in constructor are not bad enough to throw but there is no need to scan subject sequences.
Definition at line 322 of file prelim_stage.cpp.
References BlastScoreBlkCheck(), CBlastPrelimSearch::m_InternalData, and SInternalData::m_ScoreBlk.
Referenced by CLocalBlast::Run(), and CMagicBlast::x_Run().
◆ CheckOid() [1/3]
Check whether any results were reported for a given subject sequence.
- Note
- Overrides CIndexedDb::CheckOid()
- Parameters
-
oid The subject sequence id.
- Returns
- 0 — if no seeds were found for oid; 1 — if seeds were found for oid;
Implements CIndexedDb.
Definition at line 261 of file blast_dbindex.cpp.
References eHasResults, eNoResults, i, CIndexedDb_Old::LocateIndex(), results, CIndexedDb_Old::results_, and CIndexedDb_Old::seqmap_.
◆ CheckOid() [2/3]
Check whether any results were reported for a given subject sequence.
- Note
- Overrides CIndexedDb::CheckOid().
- Parameters
-
oid The subject sequence id. last_vol_id The volume id checked just before oid
- Returns
- 0 — if oid was handled by indexed search but no seeds found; 1 — if oid was handled by indexed search and seeds were found; 2 — if oid was not handled by indexed search
Implements CIndexedDb.
Definition at line 860 of file blast_dbindex.cpp.
References eHasResults, eNoResults, eNotIndexed, CIndexedDb_New::FindVolume(), LAST_VOL_IDX_NULL, CIndexedDb_New::results_holder_, CIndexedDb_New::UpdateIndex(), and CIndexedDb_New::volumes_.
◆ CheckOid() [3/3]
Check whether any results were reported for a given subject sequence.
- Parameters
-
oid The subject sequence id last_vol_id The volume id checked just before oid
- Returns
- 0 — if oid was handled by indexed search but no seeds found; 1 — if oid was handled by indexed search and seeds were found; 2 — if oid was not handled by indexed search
Implemented in CIndexedDb_New, and CIndexedDb_Old.
Referenced by s_MB_IdbCheckOid().
◆ CheckStatus()
| CRemoteBlast::ESearchStatus CRemoteBlast::CheckStatus | ( | ) |
Returns the status of a previously submitted search/RID.
Definition at line 321 of file remote_blast.cpp.
References CRemoteBlast::CheckDone(), done, CRemoteBlast::eStatus_Done, CRemoteBlast::eStatus_Failed, CRemoteBlast::eStatus_Pending, CRemoteBlast::eStatus_Unknown, CRemoteBlast::GetErrors(), kEmptyStr, and NPOS.
Referenced by BOOST_AUTO_TEST_CASE(), CBlastFormatterApp::Run(), and CBlastFormatterVdbApp::Run().
◆ CHit() [1/2]
Copy constructor.
- Parameters
-
hit Hit [in]
Definition at line 382 of file cdd_pssm_input.cpp.
References ITERATE, and CCddInputData::CHit::m_SegmentList.
◆ CHit() [2/2]
| CCddInputData::CHit::CHit | ( | const objects::CDense_seg & | denseg, |
| double | evalue | ||
| ) |
Constructor.
- Parameters
-
denseg Alignment as Dense_seg [in] evalue E-value [in]
◆ CHitSegment() [1/2]
|
inline |
Copy constructor.
MSA data is not copied.
- Parameters
-
seg Hit segment [in]
Definition at line 216 of file cdd_pssm_input.hpp.
◆ CHitSegment() [2/2]
Constructor.
- Parameters
-
q Segment range on query [in] s Segment range on subject [i]
Definition at line 211 of file cdd_pssm_input.hpp.
◆ CIgAnnotation()
|
inline |
Constructor.
Definition at line 117 of file igblast.hpp.
References i, CIgAnnotation::m_CDomain, CIgAnnotation::m_DframeStart, CIgAnnotation::m_DomainInfo, CIgAnnotation::m_DomainInfo_S, CIgAnnotation::m_FrameInfo, CIgAnnotation::m_GeneInfo, CIgAnnotation::m_JDomain, and CIgAnnotation::m_TopGeneIds.
◆ CIgAnnotationInfo()
| CIgAnnotationInfo::CIgAnnotationInfo | ( | CConstRef< CIgBlastOptions > & | ig_options | ) |
Definition at line 83 of file igblast.cpp.
References ERR_POST, NStr::fSplit_Tokenize, i, ITERATE, l(), CIgBlastOptions::m_AuxFilename, CIgBlastOptions::m_CustomInternalData, CIgBlastOptions::m_DFrameFileName, CIgAnnotationInfo::m_DJChainType, CIgAnnotationInfo::m_DomainChainType, CIgAnnotationInfo::m_DomainData, CIgAnnotationInfo::m_DomainIndex, CIgBlastOptions::m_DomainSystem, CIgAnnotationInfo::m_FrameOffset, CIgAnnotationInfo::m_Fwr4EndOffset, CIgBlastOptions::m_IgDataPath, CIgBlastOptions::m_IsProtein, CIgAnnotationInfo::m_JDomainInfo, CIgBlastOptions::m_Origin, NCBI_THROW, NcbiEmptyString, s_ReadLinesFromFile(), SeqDB_ResolveDbPath(), NStr::Split(), NStr::StringToInt(), and Warning().
◆ CIgBlast() [1/3]
◆ CIgBlast() [2/3]
|
inline |
Local Igblast search API.
- Parameters
-
query_factory Concatenated query sequences [in] blastdb Adapter to the BLAST database to search [in] options Blast search options [in] ig_options Additional Ig-BLAST specific options [in]
Definition at line 244 of file igblast.hpp.
References CIgBlast::m_RID, and NcbiEmptyString.
◆ CIgBlast() [3/3]
|
inline |
Remote Igblast search API.
- Parameters
-
query_factory Concatenated query sequences [in] blastdb Remote BLAST database to search [in] subjects Subject sequences to search [in] options Blast search options [in] ig_options Additional Ig-BLAST specific options [in]
Definition at line 264 of file igblast.hpp.
References CIgBlast::m_RID, and NcbiEmptyString.
◆ CIgBlastResults()
|
inline |
Constructor.
- Parameters
-
query List of query identifiers [in] align alignments for a single query sequence [in] errs error messages for this query sequence [in] ancillary_data Miscellaneous output from the blast engine [in] query_masks Mask locations for this query [in] rid RID (if applicable, else empty string) [in]
Definition at line 225 of file igblast.hpp.
◆ CIgBlastVersion()
|
inline |
Definition at line 56 of file igblast.hpp.
◆ CImportStrategy() [1/2]
|
private |
Prohibit copy constructor.
◆ CImportStrategy() [2/2]
| CImportStrategy::CImportStrategy | ( | CRef< objects::CBlast4_request > | request, |
| bool | ignore_unsupported_options = false |
||
| ) |
Constructor, imports the CBlast4_request.
Definition at line 62 of file search_strategy.cpp.
References NCBI_THROW.
◆ CImportStrategyData()
|
inline |
Constructor.
Definition at line 86 of file search_strategy.hpp.
References eNoSubjMasking, COpenRange< TSeqPos >::GetEmpty(), kEmptyStr, and CRef< C, Locker >::Reset().
◆ CIndexedDb_New()
Object constructor.
If all database indices were resolved successfully, then 'false' is returned in partial; otherwise 'true' is returned.
- Parameters
-
indexname MegaBLAST database name (can be a space separated list of databases) partial [O] returns 'true' if not all database indices were resolved
Definition at line 753 of file blast_dbindex.cpp.
References CIndexedDb_New::AddIndexInfo(), CIndexedDb_New::EnumerateDbVolumes(), i, IDX_TRACE, ITERATE, NCBI_THROW, CIndexedDb_New::ParseDBNames(), CIndexedDb_New::results_holder_, CIndexedDb_New::TraceNames(), CIndexedDb_New::TraceVolumes(), and CIndexedDb_New::volumes_.
◆ CIndexedDb_Old()
Object constructor.
- Parameters
-
indexname A string that is a comma separated list of index file prefix, number of threads, first and last chunks of the index.
Definition at line 944 of file blast_dbindex.cpp.
References ERR_POST, Error(), i, CIndexedDb_Old::index_names_, msg(), NCBI_THROW, SeqDB_CompareVolume(), SeqDB_ResolveDbPath(), and ct::sort().
◆ clear() [1/2]
|
inline |
Clears the contents of this object.
Definition at line 446 of file blast_results.hpp.
References CSearchResultSet::m_NumQueries, and CSearchResultSet::m_Results.
Referenced by s_CombineSearchSets().
◆ clear() [2/2]
|
inline |
Clear all results.
Definition at line 283 of file magicblast.hpp.
References CMagicBlastResultSet::m_Results.
◆ ClearDbIndexCallbacks()
| void ClearDbIndexCallbacks | ( | void | ) |
Definition at line 1183 of file blast_dbindex.cpp.
References NullRunSearch(), NullSetNumThreads(), NullSetQueryInfo(), NullSetUsingThreads(), RunSearchFn, SetNumThreadsFn, SetQueryInfoFn, and SetUsingThreadsFn.
Referenced by BlastSetupPreliminarySearchEx().
◆ ClearDiskCacheError()
|
inline |
Definition at line 478 of file remote_blast.hpp.
References CRemoteBlast::m_disk_cache_error_flag.
◆ ClearFilterOptions() [1/2]
| void CBlastOptions::ClearFilterOptions | ( | ) |
Definition at line 1022 of file blast_options_cxx.cpp.
References NULL, CBlastOptions::SetDustFiltering(), CBlastOptions::SetMaskAtHash(), CBlastOptions::SetRepeatFiltering(), CBlastOptions::SetSegFiltering(), CBlastOptions::SetWindowMaskerDatabase(), and CBlastOptions::SetWindowMaskerTaxId().
Referenced by CBlastOptionsHandle::ClearFilterOptions(), CBlastOptions::SetFilterString(), CDeltaBlastOptionsHandle::SetQueryOptionDefaults(), and CPSIBlastOptionsHandle::SetQueryOptionDefaults().
◆ ClearFilterOptions() [2/2]
|
inline |
Clears the filtering options.
Definition at line 190 of file blast_options_handle.hpp.
References CBlastOptions::ClearFilterOptions(), and CBlastOptionsHandle::m_Opts.
Referenced by CBlastOptionsFactory::CreateTask().
◆ CLocalBlast() [1/3]
| CLocalBlast::CLocalBlast | ( | CRef< IQueryFactory > | query_factory, |
| CRef< CBlastOptionsHandle > | opts_handle, | ||
| BlastSeqSrc * | seqsrc, | ||
| CRef< IBlastSeqInfoSrc > | seqInfoSrc | ||
| ) |
Constructor with database description.
- Parameters
-
query_factory query sequence(s) [in] opts_handle BLAST options handle [in] seqsrc BlastSeqSrc object to search [in] seqInfoSrc user-specified IBlastSeqInfoSrc [in]
Definition at line 129 of file local_blast.cpp.
◆ CLocalBlast() [2/3]
| CLocalBlast::CLocalBlast | ( | CRef< IQueryFactory > | query_factory, |
| CRef< CBlastOptionsHandle > | opts_handle, | ||
| const CSearchDatabase & | dbinfo | ||
| ) |
Constructor with database description.
- Parameters
-
query_factory query sequence(s) [in] opts_handle BLAST options handle [in] dbinfo description of BLAST database to search [in]
Definition at line 108 of file local_blast.cpp.
◆ CLocalBlast() [3/3]
| CLocalBlast::CLocalBlast | ( | CRef< IQueryFactory > | query_factory, |
| CRef< CBlastOptionsHandle > | opts_handle, | ||
| CRef< CLocalDbAdapter > | db | ||
| ) |
Constructor with subject adapter (.
- See also
- CLocalDbAdapter)
- Parameters
-
query_factory query sequence(s) [in] opts_handle BLAST options handle [in] db subject adapter [in]
Definition at line 118 of file local_blast.cpp.
◆ CLocalDbAdapter() [1/4]
| CLocalDbAdapter::CLocalDbAdapter | ( | BlastSeqSrc * | seqSrc, |
| CRef< IBlastSeqInfoSrc > | seqInfoSrc | ||
| ) |
Constructor taking custom BlastSeqSrc and IBlastSeqInfoSrc objects.
- Parameters
-
seqSrc Custom BlastSeqSrc implementation provided by the user seqInfoSrc Custom IBlastSeqInfoSrc implementation provided by the user
Definition at line 86 of file local_db_adapter.cpp.
◆ CLocalDbAdapter() [2/4]
|
private |
Prohibit copy-constructor.
◆ CLocalDbAdapter() [3/4]
| CLocalDbAdapter::CLocalDbAdapter | ( | const CSearchDatabase & | dbinfo | ) |
Constructor.
- Parameters
-
dbinfo Description of BLAST database
Definition at line 54 of file local_db_adapter.cpp.
◆ CLocalDbAdapter() [4/4]
| CLocalDbAdapter::CLocalDbAdapter | ( | CRef< IQueryFactory > | subject_sequences, |
| CConstRef< CBlastOptionsHandle > | opts_handle, | ||
| bool | dbscan_mode = false |
||
| ) |
Constructor.
- Parameters
-
subject_sequences Set of sequences which should be used as subjects opts_handle Options to be used (needed to create the ILocalQueryData) dbscan_mode Database search mode (as opposed to pairwise)
Definition at line 60 of file local_db_adapter.cpp.
References _ASSERT, CRef< C, Locker >::Empty(), CConstRef< C, Locker >::Empty(), ePSIBlast, CPsiBlastValidate::eQFT_Subject, CBlastOptionsHandle::GetOptions(), CBlastOptions::GetProgram(), CObjMgr_QueryFactory::GetTSeqLocVector(), CLocalDbAdapter::m_SubjectFactory, CLocalDbAdapter::m_Subjects, NCBI_THROW, NULL, and CPsiBlastValidate::QueryFactory().
◆ clone()
|
inline |
Make a copy of this object, sharing the same SeqDB object.
Definition at line 71 of file seqsrc_seqdb.cpp.
References SSeqDB_SeqSrc_Data::mask_algo_id, SSeqDB_SeqSrc_Data::mask_type, SSeqDB_SeqSrc_Data::seqdb, and SSeqDB_SeqSrc_Data::SSeqDB_SeqSrc_Data().
◆ Clone()
| CRef< CBlastOptions > CBlastOptions::Clone | ( | ) | const |
Explicit deep copy of the Blast options object.
- Returns
- Copy of this Blast options object.
Definition at line 325 of file blast_options_cxx.cpp.
References CBlastOptions::CBlastOptions(), CBlastOptions::GetLocality(), CRef< C, Locker >::Reset(), and CBlastOptions::x_DoDeepCopy().
Referenced by BOOST_AUTO_TEST_CASE(), CBlastKmerThread::Main(), CMagicBlastApp::Run(), CBlastKmerApplication::Run(), and CLocalVDBBlast::RunThreadedSearch().
◆ CLookupTableOptions() [1/2]
|
inline |
Definition at line 314 of file blast_aux.hpp.
◆ CLookupTableOptions() [2/2]
|
inline |
Definition at line 314 of file blast_aux.hpp.
◆ CLookupTableWrap() [1/2]
|
inline |
Definition at line 315 of file blast_aux.hpp.
◆ CLookupTableWrap() [2/2]
|
inline |
Definition at line 315 of file blast_aux.hpp.
◆ Close()
| void CBlastHSPListQueueData::Close | ( | ) |
Close the queue for writing.
◆ CMagicBlast() [1/2]
|
protected |
Prohibit copy constructor.
◆ CMagicBlast() [2/2]
| CMagicBlast::CMagicBlast | ( | CRef< IQueryFactory > | query_factory, |
| CRef< CLocalDbAdapter > | blastdb, | ||
| CRef< CMagicBlastOptionsHandle > | options | ||
| ) |
Constructor to map short reads as queries to a genome as BLAST database.
- Parameters
-
query_factory Short reads sequence to map [in] blastdb Adapter to the BLAST database [in] options MAGIC-BLAST options [in]
Definition at line 54 of file magicblast.cpp.
References env, CMagicBlast::m_BtopSpliceSignals, and CMagicBlast::x_Validate().
◆ CMagicBlastOptionsHandle() [1/3]
|
private |
Disallow copy constructor.
◆ CMagicBlastOptionsHandle() [2/3]
| CMagicBlastOptionsHandle::CMagicBlastOptionsHandle | ( | CRef< CBlastOptions > | opt | ) |
Create Options Handle from Existing CBlastOptions Object.
Definition at line 55 of file magicblast_options.cpp.
◆ CMagicBlastOptionsHandle() [3/3]
| CMagicBlastOptionsHandle::CMagicBlastOptionsHandle | ( | EAPILocality | locality = CBlastOptions::eLocal | ) |
Creates object with default options set.
Definition at line 48 of file magicblast_options.cpp.
◆ CMagicBlastResults() [1/2]
| CMagicBlastResults::CMagicBlastResults | ( | CConstRef< CSeq_id > | query_id, |
| CConstRef< CSeq_id > | mate_id, | ||
| CRef< CSeq_align_set > | aligns, | ||
| const TMaskedQueryRegions * | query_mask = NULL, |
||
| const TMaskedQueryRegions * | mate_mask = NULL, |
||
| int | query_length = 0, |
||
| int | mate_length = 0 |
||
| ) |
Constructor for a pair.
Definition at line 555 of file magicblast.cpp.
References CMagicBlastResults::x_SetInfo().
◆ CMagicBlastResults() [2/2]
| CMagicBlastResults::CMagicBlastResults | ( | CConstRef< CSeq_id > | query_id, |
| CRef< CSeq_align_set > | aligns, | ||
| const TMaskedQueryRegions * | query_mask = NULL, |
||
| int | query_length = 0 |
||
| ) |
Constructor for a single read.
Definition at line 571 of file magicblast.cpp.
References CMagicBlastResults::x_SetInfo().
◆ CMagicBlastResultSet() [1/2]
|
private |
◆ CMagicBlastResultSet() [2/2]
|
inline |
Create an empty results set.
Definition at line 257 of file magicblast.hpp.
◆ CMultiSeqInfo()
| CMultiSeqInfo::CMultiSeqInfo | ( | TSeqLocVector & | seq_vector, |
| EBlastProgramType | program, | ||
| bool | dbscan_mode | ||
| ) |
Constructor from a vector of sequence location/scope pairs and a BLAST program type.
Constructor.
Definition at line 131 of file seqsrc_multiseq.cpp.
References CSeq_loc::Assign(), Blast_SubjectIsProtein(), Blast_SubjectIsTranslated(), eNa_strand_both, ITERATE, CMultiSeqInfo::m_DbScanMode, CMultiSeqInfo::m_iAvgLength, CMultiSeqInfo::m_ibIsProt, CMultiSeqInfo::m_iMaxLength, CMultiSeqInfo::m_iTotalLength, CMultiSeqInfo::m_ivSeqBlkVec, CSeq_loc::SetStrand(), SetupSubjects(), and true.
◆ CObjMgr_LocalQueryData() [1/2]
| CObjMgr_LocalQueryData::CObjMgr_LocalQueryData | ( | CBlastQueryVector & | queries, |
| const CBlastOptions * | options | ||
| ) |
Ctor that takes a CBlastQueryVector (preferred over TSeqLocVector).
- Parameters
-
queries queries as a CBlastQueryVector [in] options Blast options [in]
Definition at line 198 of file objmgr_query_data.cpp.
References CObjMgr_LocalQueryData::m_QuerySource, and CRef< C, Locker >::Reset().
◆ CObjMgr_LocalQueryData() [2/2]
| CObjMgr_LocalQueryData::CObjMgr_LocalQueryData | ( | TSeqLocVector * | queries, |
| const CBlastOptions * | options | ||
| ) |
Ctor that takes a vector of SSeqLocs.
- Parameters
-
queries queries as a vector of SSeqLoc [in] options Blast options [in]
Definition at line 191 of file objmgr_query_data.cpp.
References CObjMgr_LocalQueryData::m_QuerySource, and CRef< C, Locker >::Reset().
◆ CObjMgr_QueryFactory() [1/2]
| CObjMgr_QueryFactory::CObjMgr_QueryFactory | ( | CBlastQueryVector & | queries | ) |
ctor that takes a CBlastQueryVector (preferred)
- Parameters
-
queries for search [in]
Definition at line 375 of file objmgr_query_data.cpp.
References CBlastQueryVector::Empty(), and NCBI_THROW.
◆ CObjMgr_QueryFactory() [2/2]
| CObjMgr_QueryFactory::CObjMgr_QueryFactory | ( | TSeqLocVector & | queries | ) |
ctor that takes a vector of SSeqLoc
- Parameters
-
queries vector of SSeqLoc [in]
Definition at line 330 of file objmgr_query_data.cpp.
References ITERATE, CObjMgr_QueryFactory::m_SSeqLocVector, NCBI_THROW, NON_CONST_ITERATE, CSeq_loc::SetInt(), and CSeq_loc::SetPacked_int().
◆ CObjMgr_RemoteQueryData() [1/2]
| CObjMgr_RemoteQueryData::CObjMgr_RemoteQueryData | ( | CBlastQueryVector & | queries | ) |
Construct query data from a CBlastQueryVector.
- Parameters
-
queries Queries expressed as a CBlastQueryVector.
Definition at line 290 of file objmgr_query_data.cpp.
◆ CObjMgr_RemoteQueryData() [2/2]
| CObjMgr_RemoteQueryData::CObjMgr_RemoteQueryData | ( | const TSeqLocVector * | queries | ) |
Construct query data from a TSeqLocVector.
- Parameters
-
queries Queries expressed as a TSeqLocVector.
Definition at line 286 of file objmgr_query_data.cpp.
◆ CObjMgrFree_LocalQueryData()
| CObjMgrFree_LocalQueryData::CObjMgrFree_LocalQueryData | ( | CConstRef< CBioseq_set > | bioseq_set, |
| const CBlastOptions * | options | ||
| ) |
Definition at line 92 of file objmgrfree_query_data.cpp.
References Blast_QueryIsProtein(), CBlastOptions::GetProgramType(), CObjMgrFree_LocalQueryData::m_QuerySource, CRef< C, Locker >::Reset(), and true.
◆ CObjMgrFree_QueryFactory() [1/2]
| CObjMgrFree_QueryFactory::CObjMgrFree_QueryFactory | ( | CConstRef< objects::CBioseq > | bioseq | ) |
Parametrized constructor taking a single Bioseq.
- Parameters
-
bioseq Bioseq from which to obtain sequence data [in]
Definition at line 249 of file objmgrfree_query_data.cpp.
◆ CObjMgrFree_QueryFactory() [2/2]
| CObjMgrFree_QueryFactory::CObjMgrFree_QueryFactory | ( | CConstRef< objects::CBioseq_set > | bioseq_set | ) |
Parametrized constructor taking a Bioseq-set.
- Parameters
-
bioseq_set Bioseq-set from which to obtain sequence data [in]
Definition at line 254 of file objmgrfree_query_data.cpp.
◆ CObjMgrFree_RemoteQueryData()
| CObjMgrFree_RemoteQueryData::CObjMgrFree_RemoteQueryData | ( | CConstRef< CBioseq_set > | bioseq_set | ) |
Construct query data from a CBioseq_set.
- Parameters
-
queries Queries expressed as a CBioseq_set.
Definition at line 197 of file objmgrfree_query_data.cpp.
◆ Combine() [1/2]
| void TQueryMessages::Combine | ( | const TQueryMessages & | other | ) |
Combine other messages with these.
- Parameters
-
other The second list of messages.
Definition at line 978 of file blast_aux.cpp.
References _ASSERT, copy(), and TQueryMessages::m_IdString.
Referenced by CIgBlast::s_AppendResults(), and s_CombineSearchSets().
◆ Combine() [2/2]
| void TSearchMessages::Combine | ( | const TSearchMessages & | other_msgs | ) |
Combine another set of search messages with this one.
Another set of messages is combined with these; each element of the other set is combined with the element of this set having the same index. The size of both sets must match.
- Parameters
-
other_msgs Other messages to add to these.
Definition at line 1028 of file blast_aux.cpp.
References TSearchMessages::Combine(), ctll::empty(), i, and TSearchMessages::RemoveDuplicates().
Referenced by TSearchMessages::Combine(), CLocalBlast::Run(), and CMagicBlast::x_Run().
◆ CompressNcbi2na()
| SBlastSequence CompressNcbi2na | ( | const SBlastSequence & | source | ) |
Compresses the sequence data passed in to the function from 1 base per byte to 4 bases per byte.
- Parameters
-
source input sequence data in ncbi2na format, with ambiguities randomized [in]
- Returns
- compressed version of the input
- Exceptions
-
CBlastException in case of memory allocation failure
Definition at line 1154 of file blast_setup_cxx.cpp.
References _ASSERT, a, abort(), b, CalculateSeqBufferLength(), COMPRESSION_RATIO, SBlastSequence::data, eBlastEncodingNcbi2na, eNa_strand_plus, eNoSentinels, AutoPtr< X, Del >::get(), i, SBlastSequence::length, NCBI2NA_MASK, and rapidjson::source.
Referenced by GetSequenceCompressedNucleotide().
◆ ComputeBlastHSPResults()
| BlastHSPResults * CBlastPrelimSearch::ComputeBlastHSPResults | ( | BlastHSPStream * | stream, |
| Uint4 | max_num_hsps = 0, |
||
| bool * | rm_hsps = NULL, |
||
| vector< bool > * | rm_hsps_info = NULL |
||
| ) | const |
Return HSPs in a structure other than the HSPStream? Provide conversion? How to combine this with CBlastTracebackStage?
Definition at line 331 of file prelim_stage.cpp.
References _ASSERT, Blast_HSPResultsFromHSPStreamWithLimitEx(), Blast_HSPResultsSortByEvalue(), CBlastOptions::CreateSnapshot(), FALSE, false, CBlastPrelimSearch::m_InternalData, CBlastPrelimSearch::m_Options, SInternalData::m_QueryInfo, NULL, BlastQueryInfo::num_queries, and SBlastHitsParametersNew().
Referenced by BOOST_AUTO_TEST_CASE(), CBlastPrelimSearch::x_BuildStdSegList(), and x_ValidateResultsForShortProteinSearch().
◆ ComputeProgram()
|
static |
Compute the EProgram value to use for this search.
The blast4 protocol uses a notion of program and service to represent the type of search to do. This method computes the EProgram value corresponding to these strings. Sometimes this result should be modified based on the value of other options, specifically the existence of the PHI pattern indicates PHI blast and certain megablast template options that can indicate discontiguous megablast.
- See also
- AdjustProgram.
- Parameters
-
program The program string used by blast4. service The service string used by blast4.
- Returns
- The EProgram value corresponding to these strings.
Definition at line 64 of file blast_options_builder.cpp.
References msg(), NCBI_THROW, ProgramNameToEnum(), and NStr::ToLower().
Referenced by CBlastOptionsBuilder::GetSearchOptions().
◆ Convert2Matrix()
| void Convert2Matrix | ( | const list< T > & | source, |
| CNcbiMatrix< T > & | dest, | ||
| bool | by_row, | ||
| SIZE_TYPE | num_rows, | ||
| SIZE_TYPE | num_columns | ||
| ) |
Convert a list of values into a CNcbiMatrix.
- Parameters
-
source source of data [in] dest destination of data [out] by_row is the matrix data stored by row? [in] num_rows number of rows [in] num_cols number of columns [in]
Definition at line 219 of file psiblast_aux_priv.cpp.
References _ASSERT, r(), and rapidjson::source.
Referenced by CScorematPssmConverter::GetFreqRatios(), CScorematPssmConverter::GetResidueFrequencies(), CScorematPssmConverter::GetScores(), and CScorematPssmConverter::GetWeightedResidueFrequencies().
◆ ConvertToRemoteMasks()
|
static |
Convert a TSeqLocInfoVector to a list< CRef<CBlast4_mask> > objects.
- Parameters
-
masking_locations Masks to convert [in] program CORE BLAST program type [in] warnings optional argument where warnings will be returned [in|out]
Definition at line 1096 of file remote_blast.cpp.
References Blast_QueryIsTranslated(), CRef< C, Locker >::Empty(), FrameNumber2NetworkFrame(), ITERATE, CRef< C, Locker >::Reset(), and s_CreateBlastMask().
Referenced by BOOST_AUTO_TEST_CASE(), s_BuildArchiveAll(), CExportStrategy::x_Process_Query(), and CRemoteBlast::x_QueryMaskingLocationsToNetwork().
◆ CPHIBlastNuclOptionsHandle() [1/2]
|
private |
Disallow copy constructor.
◆ CPHIBlastNuclOptionsHandle() [2/2]
| CPHIBlastNuclOptionsHandle::CPHIBlastNuclOptionsHandle | ( | EAPILocality | locality = CBlastOptions::eLocal | ) |
Creates object with default options set.
Definition at line 46 of file phiblast_nucl_options.cpp.
References ePHIBlastn.
◆ CPHIBlastProtOptionsHandle() [1/2]
|
private |
Disallow copy constructor.
◆ CPHIBlastProtOptionsHandle() [2/2]
| CPHIBlastProtOptionsHandle::CPHIBlastProtOptionsHandle | ( | EAPILocality | locality = CBlastOptions::eLocal | ) |
Creates object with default options set.
Definition at line 46 of file phiblast_prot_options.cpp.
References ePHIBlastp.
◆ CPrelimSearchRunner() [1/2]
|
private |
Prohibit copy constructor.
◆ CPrelimSearchRunner() [2/2]
|
inline |
Definition at line 57 of file prelim_search_runner.hpp.
◆ CPrelimSearchThread()
|
inline |
Definition at line 111 of file prelim_search_runner.hpp.
References BlastQueryInfoDup(), BlastSeqSrcCopy(), BlastSeqSrcFree(), CSBlastProgress::Get(), CPrelimSearchThread::m_InternalData, SInternalData::m_ProgressMonitor, SInternalData::m_QueryInfo, SInternalData::m_SeqSrc, CRef< C, Locker >::Reset(), SBlastProgressNew(), and SBlastProgress::user_data.
◆ CPsiBl2Seq() [1/4]
|
private |
Prohibit copy constructor.
◆ CPsiBl2Seq() [2/4]
| CPsiBl2Seq::CPsiBl2Seq | ( | CRef< IQueryFactory > | query, |
| CRef< IQueryFactory > | subject, | ||
| CConstRef< CBlastProteinOptionsHandle > | options | ||
| ) |
Constructor to compare protein sequences in an object manager-free manner.
- Parameters
-
query Protein query sequence to search (only 1 is allowed!) [in] subject Protein sequence(s) to search [in] options Protein options [in]
Definition at line 65 of file psibl2seq.cpp.
References CConstRef< C, Locker >::GetPointer(), CPsiBl2Seq::m_Impl, CPsiBl2Seq::m_Subject, query, subject, and CPsiBl2Seq::x_InitSubject().
◆ CPsiBl2Seq() [3/4]
| CPsiBl2Seq::CPsiBl2Seq | ( | CRef< objects::CPssmWithParameters > | pssm, |
| CRef< CLocalDbAdapter > | subject, | ||
| CConstRef< CPSIBlastOptionsHandle > | options | ||
| ) |
Constructor to compare a PSSM against protein sequences.
- Parameters
-
pssm PSSM to use as query. This must contain the query sequence which represents the master sequence for the PSSM. PSSM data might be provided as scores or as frequency ratios, in which case the PSSM engine will be invoked to convert them to scores (and save them as a effect). If both the scores and frequency ratios are provided, the scores are given priority and are used in the search. [in|out] subject Subject sequence(s) to search [in] options PSI-BLAST options [in]
Definition at line 57 of file psibl2seq.cpp.
References CPsiBl2Seq::m_Impl, CPsiBl2Seq::m_Subject, and subject.
◆ CPsiBl2Seq() [4/4]
| CPsiBl2Seq::CPsiBl2Seq | ( | CRef< objects::CPssmWithParameters > | pssm, |
| CRef< IQueryFactory > | subject, | ||
| CConstRef< CPSIBlastOptionsHandle > | options | ||
| ) |
Constructor to compare a PSSM against protein sequences.
- Parameters
-
pssm PSSM to use as query. This must contain the query sequence which represents the master sequence for the PSSM. PSSM data might be provided as scores or as frequency ratios, in which case the PSSM engine will be invoked to convert them to scores (and save them as a effect). If both the scores and frequency ratios are provided, the scores are given priority and are used in the search. [in|out] subject Subject sequence(s) to search [in] options PSI-BLAST options [in]
Definition at line 49 of file psibl2seq.cpp.
References subject.
◆ CPsiBlast() [1/3]
◆ CPsiBlast() [2/3]
| CPsiBlast::CPsiBlast | ( | CRef< IQueryFactory > | query_factory, |
| CRef< CLocalDbAdapter > | blastdb, | ||
| CConstRef< CPSIBlastOptionsHandle > | options | ||
| ) |
Constructor to compare a single sequence against a database of protein sequences.
- Parameters
-
query_factory Protein query sequence to search (only 1 is allowed!) [in] blastdb Adapter to the BLAST database to search [in] options PSI-BLAST options [in]
Definition at line 58 of file psiblast.cpp.
◆ CPsiBlast() [3/3]
| CPsiBlast::CPsiBlast | ( | CRef< objects::CPssmWithParameters > | pssm, |
| CRef< CLocalDbAdapter > | blastdb, | ||
| CConstRef< CPSIBlastOptionsHandle > | options | ||
| ) |
Constructor to compare a PSSM against a database of protein sequences.
- Parameters
-
pssm PSSM to use as query. This must contain the query sequence which represents the master sequence for the PSSM. PSSM data might be provided as scores or as frequency ratios, in which case the PSSM engine will be invoked to convert them to scores (and save them as a effect). If both the scores and frequency ratios are provided, the scores are given priority and are used in the search. [in|out] blastdb Adapter to the BLAST database to search [in] options PSI-BLAST options [in]
Definition at line 67 of file psiblast.cpp.
References CPsiBlast::m_Impl, and CPsiBlast::m_Subject.
◆ CPsiBlastImpl() [1/3]
|
private |
Prohibit copy constructor.
◆ CPsiBlastImpl() [2/3]
| CPsiBlastImpl::CPsiBlastImpl | ( | CRef< IQueryFactory > | query, |
| CRef< CLocalDbAdapter > | subject, | ||
| CConstRef< CBlastProteinOptionsHandle > | options | ||
| ) |
Constructor to handle the first iteration of PSI-BLAST when the query is a protein sequence or when the performing an object manager free BLAST 2 Sequences search.
- Parameters
-
query Protein query sequence to search (only 1 is allowed!) [in] subject Protein sequence to search [in] options Protein options [in]
Definition at line 70 of file psiblast_impl.cpp.
References CPsiBlastImpl::x_Validate().
◆ CPsiBlastImpl() [3/3]
| CPsiBlastImpl::CPsiBlastImpl | ( | CRef< objects::CPssmWithParameters > | pssm, |
| CRef< CLocalDbAdapter > | subject, | ||
| CConstRef< CPSIBlastOptionsHandle > | options | ||
| ) |
Constructor for restarting PSI-BLAST iterations with a previously generated PSSM.
- Parameters
-
pssm same comment as in CPsiBl2Seq or CPsiBlast applies subject Subject sequence(s) to search [in] options PSI-BLAST options [in]
Definition at line 59 of file psiblast_impl.cpp.
◆ CPsiBlastInputClustalW() [1/2]
| CPsiBlastInputClustalW::CPsiBlastInputClustalW | ( | CNcbiIstream & | input_file, |
| const PSIBlastOptions & | opts, | ||
| const char * | matrix_name = NULL, |
||
| const PSIDiagnosticsRequest * | diags = NULL, |
||
| const unsigned char * | query = NULL, |
||
| unsigned int | query_length = 0, |
||
| int | gap_existence = 0, |
||
| int | gap_opening = 0, |
||
| unsigned int | msa_master_idx = 0 |
||
| ) |
Construct a concrete strategy, used to configure the CPssmEngine object.
- Parameters
-
input_file Input file containing the multiple sequence alignment. [in] opts options to be used in the PSSM engine matrix_name name of the substitution matrix to use to build PSSM If not provided, the default implementation of IPssmInputData::GetMatrixName() will be returned diags diagnostics data requests for the PSSM engine query query sequence for the alignment in ncbistdaa encoding. query_length length of the sequence above. gap_existence cost to open a gap, if zero default from IPssmInputData used. gap_extension cost to open a gap, if zero default from IPssmInputData used. msa_master_idx 0-based index of the multiple sequence alignment This is an alternative way to specify the query sequence to use (i.e.: don't use query and query_length if this is provided) [in]
Definition at line 68 of file msa_pssm_input.cpp.
References _ASSERT, input_file, NULL, PSIDiagnosticsRequestNew(), query, and string.
◆ CPsiBlastInputClustalW() [2/2]
|
private |
prohibit copy constructor
◆ CPsiBlastInputData() [1/2]
|
private |
prohibit copy constructor
◆ CPsiBlastInputData() [2/2]
| CPsiBlastInputData::CPsiBlastInputData | ( | const unsigned char * | query, |
| unsigned int | query_length, | ||
| CConstRef< objects::CSeq_align_set > | sset, | ||
| CRef< objects::CScope > | scope, | ||
| const PSIBlastOptions & | opts, | ||
| const char * | matrix_name = NULL, |
||
| int | gap_existence = 0, |
||
| int | gap_opening = 0, |
||
| const PSIDiagnosticsRequest * | diags = NULL, |
||
| const string & | query_title = "" |
||
| ) |
Construct a concrete strategy, used to configure the CPssmEngine object.
- Parameters
-
query query sequence for the alignment in ncbistdaa encoding. query_length length of the sequence above. sset pairwise alignment produced by BLAST where query was the query sequence. scope object manager scope from which to retrieve sequence data [in] opts options to be used in the PSSM engine matrix_name name of the substitution matrix to use to build PSSM If not provided, the default implementation of IPssmInputData::GetMatrixName() will be returned gap_existence cost to open a gap, if zero default from IPssmInputData used. gap_extension cost to open a gap, if zero default from IPssmInputData used. diags diagnostics data requests for the PSSM engine
Definition at line 77 of file psi_pssm_input.cpp.
References CPsiBlastInputData::m_DiagnosticsRequest, CPsiBlastInputData::m_MatrixName, CPsiBlastInputData::m_Msa, CPsiBlastInputData::m_MsaDimensions, CPsiBlastInputData::m_Opts, CPsiBlastInputData::m_Query, CPsiBlastInputData::m_QueryTitle, CPsiBlastInputData::m_Scope, CPsiBlastInputData::m_SeqAlignSet, NCBI_THROW, NULL, PSIMsaDimensions::num_seqs, query, PSIMsaDimensions::query_length, CRef< C, Locker >::Reset(), CConstRef< C, Locker >::Reset(), and string.
◆ CPsiBlastInputFreqRatios()
|
inline |
Constructor.
- Parameters
-
query pointer to query sequence data [in] query_length length of the query sequence data [in] freq_ratios matrix of frequency ratios [in] matrix_name name of underlying scoring matrix used [in] gap_existence cost to open a gap, if zero default from IPssmInputData used. gap_extension cost to open a gap, if zero default from IPssmInputData used.
Definition at line 78 of file psi_pssm_input.hpp.
◆ CPsiBlastIterationState() [1/2]
|
private |
Prohibit copy constructor.
◆ CPsiBlastIterationState() [2/2]
| CPsiBlastIterationState::CPsiBlastIterationState | ( | unsigned int | num_iterations = 1 | ) |
Constructor.
- Parameters
-
num_iterations Number of iterations to perform. Use 0 to indicate that iterations must take place until convergence or the number of iterations desired [in]
Definition at line 50 of file psiblast_iteration.cpp.
◆ CPSIBlastOptions() [1/2]
|
inline |
Definition at line 330 of file blast_aux.hpp.
◆ CPSIBlastOptions() [2/2]
|
inline |
Definition at line 330 of file blast_aux.hpp.
◆ CPSIBlastOptionsHandle() [1/3]
|
private |
Disallow copy constructor.
◆ CPSIBlastOptionsHandle() [2/3]
|
inline |
Definition at line 60 of file psiblast_options.hpp.
◆ CPSIBlastOptionsHandle() [3/3]
| CPSIBlastOptionsHandle::CPSIBlastOptionsHandle | ( | EAPILocality | locality = CBlastOptions::eLocal | ) |
Creates object with default options set.
Definition at line 46 of file psiblast_options.cpp.
References ePSIBlast, and CBlastOptions::eRemote.
◆ CPSIDiagnosticsRequest() [1/2]
|
inline |
Definition at line 347 of file blast_aux.hpp.
◆ CPSIDiagnosticsRequest() [2/2]
|
inline |
Definition at line 347 of file blast_aux.hpp.
◆ CPSIDiagnosticsResponse() [1/2]
|
inline |
Definition at line 348 of file blast_aux.hpp.
◆ CPSIDiagnosticsResponse() [2/2]
|
inline |
Definition at line 348 of file blast_aux.hpp.
◆ CPSIMatrix() [1/2]
|
inline |
Definition at line 346 of file blast_aux.hpp.
◆ CPSIMatrix() [2/2]
|
inline |
Definition at line 346 of file blast_aux.hpp.
◆ CPSIMsa() [1/2]
|
inline |
Definition at line 345 of file blast_aux.hpp.
◆ CPSIMsa() [2/2]
|
inline |
Definition at line 345 of file blast_aux.hpp.
◆ CPssmEngine() [1/5]
|
inlineprivate |
Default constructor available for derived test classes.
Definition at line 240 of file pssm_engine.hpp.
◆ CPssmEngine() [2/5]
|
private |
Prohibit copy constructor.
◆ CPssmEngine() [3/5]
| CPssmEngine::CPssmEngine | ( | IPssmInputCdd * | input | ) |
Constructor to configure the PSSM engine with a PSSM input data strategy object for CDD-based PSSM computation.
Definition at line 204 of file pssm_engine.cpp.
References input(), and CPssmEngine::x_InitializeScoreBlock().
◆ CPssmEngine() [4/5]
| CPssmEngine::CPssmEngine | ( | IPssmInputData * | input | ) |
Constructor to configure the PSSM engine with a PSSM input data strategy object Checks that no data returned by the IPssmInputData interface is NULL.
- Exceptions
-
CPssmEngineException if validation fails. Does not test the GetData() method as this is only populated after Process() is called.
Definition at line 188 of file pssm_engine.cpp.
References input(), s_CheckAgainstNullData(), CPssmEngine::x_GetGapExistence(), CPssmEngine::x_GetGapExtension(), CPssmEngine::x_GetMatrixName(), CPssmEngine::x_GetQuery(), CPssmEngine::x_GetQueryLength(), and CPssmEngine::x_InitializeScoreBlock().
◆ CPssmEngine() [5/5]
| CPssmEngine::CPssmEngine | ( | IPssmInputFreqRatios * | input | ) |
Constructor to perform the last 2 stages of the PSSM creation algorithm Checks that no data returned by the IPssmInputFreqRatios interface is NULL.
- Exceptions
-
CPssmEngineException if validation fails
Definition at line 196 of file pssm_engine.cpp.
References input(), s_CheckAgainstNullData(), CPssmEngine::x_GetGapExistence(), CPssmEngine::x_GetGapExtension(), CPssmEngine::x_GetMatrixName(), CPssmEngine::x_GetQuery(), CPssmEngine::x_GetQueryLength(), and CPssmEngine::x_InitializeScoreBlock().
◆ CQueryDataPerChunk()
| CQueryDataPerChunk::CQueryDataPerChunk | ( | const CSplitQueryBlk & | sqb, |
| EBlastProgramType | program, | ||
| CRef< ILocalQueryData > | local_query_data | ||
| ) |
Constructor.
- Parameters
-
sqb Split query block structure [in] program BLAST program type [in] local_query_data source of query data [in]
Definition at line 310 of file split_query_aux_priv.cpp.
References CSplitQueryBlk::GetNumChunks(), CSplitQueryBlk::GetQueryIndices(), ILocalQueryData::GetSeqLength(), i, set< Key, Compare >::insert(), ITERATE, CQueryDataPerChunk::kUninitialized, CQueryDataPerChunk::m_LastChunkForQueryCache, CQueryDataPerChunk::m_QueryIndicesPerChunk, CQueryDataPerChunk::m_QueryLengths, and set< Key, Compare >::size().
◆ CQueryFactoryInfo() [1/2]
| CQueryFactoryInfo::CQueryFactoryInfo | ( | const TSeqLocVector & | subject_seqs, |
| EBlastProgramType | program | ||
| ) |
Definition at line 106 of file seqsrc_query_factory.cpp.
References _ASSERT, CSeq_loc::Assign(), Blast_SubjectIsTranslated(), eNa_strand_both, ITERATE, CQueryFactoryInfo::m_MaxLength, CQueryFactoryInfo::m_SeqBlkVector, CSeq_loc::SetStrand(), and SetupSubjects().
◆ CQueryFactoryInfo() [2/2]
| CQueryFactoryInfo::CQueryFactoryInfo | ( | CRef< IQueryFactory > | qf, |
| EBlastProgramType | program | ||
| ) |
Constructor from a vector of sequence location/scope pairs and a BLAST program type.
Constructor.
Definition at line 86 of file seqsrc_query_factory.cpp.
References _ASSERT, IRemoteQueryData::GetBioseqSet(), CQueryFactoryInfo::m_IsProt, CQueryFactoryInfo::m_MaxLength, CQueryFactoryInfo::m_NumSeqs, CQueryFactoryInfo::m_QuerySource, CQueryFactoryInfo::m_SeqBlkVector, IQueryFactory::MakeRemoteQueryData(), NCBI_THROW, CRef< C, Locker >::NotEmpty(), CRef< C, Locker >::Reset(), SetupSubjects_OMF(), and IBlastQuerySource::Size().
◆ CQuerySetUpOptions() [1/2]
|
inline |
Definition at line 312 of file blast_aux.hpp.
◆ CQuerySetUpOptions() [2/2]
|
inline |
Definition at line 312 of file blast_aux.hpp.
◆ CQuerySplitter() [1/2]
|
private |
Prohibit copy constructor.
◆ CQuerySplitter() [2/2]
| CQuerySplitter::CQuerySplitter | ( | CRef< IQueryFactory > | query_factory, |
| const CBlastOptions * | options | ||
| ) |
Parametrized constructor.
- Parameters
-
query_factory Object containing query sequence(s) [in] options BLAST options for the search [in]
Definition at line 50 of file split_query_cxx.cpp.
References SplitQuery_CalculateNumChunks(), and SplitQuery_GetChunkSize().
◆ Create()
|
static |
Creates an options handle object configured with default options for the requested program, throws an exception if an unsupported program is requested.
- Parameters
-
program BLAST program [in] locality Local processing (default) or remote processing.
- Returns
- requested options handle with default values set
- Exceptions
-
CBlastException in case of an unhandled program type
Definition at line 110 of file blast_options_handle.cpp.
References abort(), eBlastn, eBlastNotSet, eBlastp, eBlastx, eDeltaBlast, eDiscMegablast, eKBlastp, eMapper, eMegablast, ePHIBlastn, ePHIBlastp, ePSIBlast, ePSITblastn, eRPSBlast, eRPSTblastn, eTblastn, eTblastx, eVecScreen, NCBI_THROW, NULL, CBlastNucleotideOptionsHandle::SetTraditionalBlastnDefaults(), CBlastNucleotideOptionsHandle::SetTraditionalMegablastDefaults(), and CBlastNucleotideOptionsHandle::SetVecScreenDefaults().
Referenced by BOOST_AUTO_TEST_CASE(), CBl2Seq::CBl2Seq(), CBlastOptionsFactory::CreateTask(), CIgBlastArgs::ExtractAlgorithmOptions(), CScoreBuilder::GetBlastScoreProtToNucl(), CLocalSearchFactory::GetOptions(), CRemoteSearchFactory::GetOptions(), CBlastOptionsBuilder::GetSearchOptions(), RpsTestFixture::NuclSearch(), CSplitQueryTestFixture::QuerySplitter_BlastnMultiQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastnSingleQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastxMultiQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastxSingleQueryMultiChunk(), CSeedTopApp::Run(), CVecScreenApp::Run(), CSeedTop::Run(), CBlastDemoApplication::Run(), setupQueryInfoForOffsetTranslation(), CBLASTParams::ToArgVecBlastOptions(), CBLASTParams::ToBlastOptions(), UniversalOptiosHandleFixture::UniversalOptiosHandleFixture(), CDeltaBlast::x_FindDomainHits(), CMultiAligner::x_FindRPSHits(), CSequenceDataTester::x_Init(), CSplitQueryTestFixture::x_PrepareBlastQueryStructures(), CSplignApp::x_SetupBlastOptions(), and CSplitQueryTestFixture::x_TestCContextTranslator().
◆ CreateBlastSeqSrc() [1/2]
|
static |
Create a BlastSeqSrc from a CSearchDatabase (uses CSeqDB)
- Parameters
-
db description of BLAST database to search [in]
Definition at line 406 of file setup_factory.cpp.
References CSearchDatabase::GetFilteringAlgorithm(), CSearchDatabase::GetMaskType(), and CSearchDatabase::GetSeqDb().
Referenced by CBlastPrelimSearch::CBlastPrelimSearch(), and CLocalDbAdapter::MakeSeqSrc().
◆ CreateBlastSeqSrc() [2/2]
|
static |
Create a BlastSeqSrc from an existing CSeqDB object.
- Parameters
-
db Existing CSeqDB object for the searched BLAST database [in]
Definition at line 414 of file setup_factory.cpp.
References BlastSeqSrcFree(), BlastSeqSrcGetInitError(), msg(), NCBI_THROW, SeqDbBlastSeqSrcInit(), and sfree.
◆ CreateDiagnosticsStructure()
|
static |
Create and initialize the BlastDiagnostics structure for single-threaded applications.
Definition at line 274 of file setup_factory.cpp.
References Blast_DiagnosticsInit().
Referenced by BlastSetupPreliminarySearchEx(), CBlastPrelimSearch::SetNumberOfThreads(), and CBlastTracebackSearch::x_Init().
◆ CreateDiagnosticsStructureMT()
|
static |
Create and initialize the BlastDiagnostics structure for multi-threaded applications.
Definition at line 280 of file setup_factory.cpp.
References Blast_CMT_LOCKInit(), and Blast_DiagnosticsInitMT().
Referenced by BlastSetupPreliminarySearchEx(), and CBlastPrelimSearch::SetNumberOfThreads().
◆ CreateEmptySeq_align_set()
| CRef< CSeq_align_set > CreateEmptySeq_align_set | ( | void | ) |
Constructs an empty Seq-align-set containing an empty discontinuous seq-align, and appends it to a previously constructed Seq-align-set.
- Parameters
-
sas Pointer to a Seq-align-set, to which new object should be appended (if not NULL).
- Returns
- Resulting Seq-align-set.
Definition at line 1507 of file blast_seqalign.cpp.
References _ASSERT, CSeq_align_set_Base::Get(), and CSeq_align_set_Base::Set().
Referenced by BlastHitList2SeqAlign_OMF(), CBl2Seq::CSearchResultSet2TSeqAlignVector(), s_BLAST_OneSubjectResults2CSeqAlign(), and CMagicBlast::x_CreateSeqAlignSet().
◆ CreateHspPipe()
|
static |
Create a pipe to be registered for use by stream.
- Parameters
-
opts_memento Memento options object [in] query_info Information about queries [in]
Definition at line 366 of file setup_factory.cpp.
References _ASSERT, BlastHSPFilteringOptions::best_hit, BlastHSPFilteringOptions::best_hit_stage, BlastHSPBestHitParamsNew(), BlastHSPBestHitPipeInfoNew(), BlastHSPCullingParamsNew(), BlastHSPCullingPipeInfoNew(), BlastHSPPipeInfo_Add(), BlastHSPPipeNew(), BlastExtensionOptions::compositionBasedStats, BlastHSPFilteringOptions::culling_opts, BlastHSPFilteringOptions::culling_stage, eTracebackSearch, BlastScoringOptions::gapped_calculation, BlastHitSavingOptions::hsp_filt_opt, CBlastOptionsMemento::m_ExtnOpts, CBlastOptionsMemento::m_HitSaveOpts, CBlastOptionsMemento::m_ScoringOpts, and NULL.
Referenced by BlastSetupPreliminarySearchEx().
◆ CreateHspStream()
|
static |
Create and initialize the BlastHSPStream structure.
- Parameters
-
opts_memento Memento options object [in] number_of_queries number of queries involved in the search [in] writer writer to be used within this stream [in]
Definition at line 286 of file setup_factory.cpp.
References _ASSERT, BlastHSPStreamNew(), CBlastOptionsMemento::m_ExtnOpts, CBlastOptionsMemento::m_ProgramType, and TRUE.
Referenced by BlastSetupPreliminarySearchEx().
◆ CreateHspWriter()
|
static |
Create a writer to be registered for use by stream.
- Parameters
-
opts_memento Memento options object [in] query Concatenanted query sequence [in] query_info Information about queries [in]
Definition at line 297 of file setup_factory.cpp.
References _ASSERT, BlastHSPFilteringOptions::best_hit, BlastHSPFilteringOptions::best_hit_stage, Blast_ProgramIsMapping(), BlastHSPBestHitInfoNew(), BlastHSPBestHitParamsNew(), BlastHSPCollectorInfoNew(), BlastHSPCollectorParamsNew(), BlastHSPCullingInfoNew(), BlastHSPCullingParamsNew(), BlastHSPMapperInfoNew(), BlastHSPMapperParamsNew(), BlastHSPWriterNew(), BlastExtensionOptions::compositionBasedStats, BlastHSPCullingParams::culling_max, BlastHSPFilteringOptions::culling_opts, BlastHSPFilteringOptions::culling_stage, ePrelimSearch, BlastScoringOptions::gapped_calculation, BlastHitSavingOptions::hsp_filt_opt, CBlastOptionsMemento::m_ExtnOpts, CBlastOptionsMemento::m_HitSaveOpts, CBlastOptionsMemento::m_ProgramType, CBlastOptionsMemento::m_ScoringOpts, NULL, BlastHSPBestHitParams::overhang, query, and BlastHSPBestHitOptions::score_edge.
Referenced by BlastSetupPreliminarySearchEx().
◆ CreateLookupTable()
|
static |
Initialize the lookup table.
Note that for the case of PSI-BLAST the PSSM must be initialized in the BlastScoreBlk for it to be recognized properly by the lookup table code. Caller owns the return value.
- Parameters
-
query_data source of query sequence data [in] opts_memento Memento options object [in] score_blk BlastScoreBlk structure, as obtained in CreateScoreBlock [in] lookup_segments query segments to be searched because they were not filtered, needed for the lookup table creation (otherwise pass NULL) [in|out] rps_info RPS-BLAST data structures as obtained from CreateRpsStructures [in] seqsrc BlastSeqSrc structure, only needed when performing megablast indexed-database searches [in] num_threads Number of threads to use. Multithreaded implementation is only avaliable for Magic-BLAST lookup tables. [in]
Definition at line 200 of file setup_factory.cpp.
References Blast_Message2TSearchMessages(), Blast_ProgramIsPhiBlast(), Blast_SetPHIPatternInfo(), CBlast_Message::Get(), GetDbIndexSetQueryInfoFn(), CBlastSeqLocWrap::getLocs(), ILocalQueryData::GetQueryInfo(), ILocalQueryData::GetSequenceBlk(), TSearchMessages::HasMessages(), NStr::IntToString(), LookupTableWrapInit_MT(), LookupTableWrap::lut, CBlastOptionsMemento::m_LutOpts, CBlastOptionsMemento::m_ProgramType, CBlastOptionsMemento::m_QueryOpts, msg(), NCBI_THROW, and TSearchMessages::ToString().
Referenced by BlastSetupPreliminarySearchEx(), and CBlastTracebackSearch::x_Init().
◆ CreateRpsStructures()
|
static |
Initializes RPS-BLAST data structures.
- Parameters
-
rps_dbname Name of the RPS-BLAST database [in] options BLAST options (matrix name and gap costs will be modified with data read from the RPS-BLAST auxiliary file) [in|out]
Definition at line 73 of file setup_factory.cpp.
References eNoCompositionBasedStats, CBlastRPSInfo::fRpsBlast, CBlastRPSInfo::fRpsBlastWithCBS, CBlastOptions::GetCompositionBasedStats(), CBlastRPSInfo::GetGapExtensionCost(), CBlastRPSInfo::GetGapOpeningCost(), CBlastRPSInfo::GetMatrixName(), CBlastOptions::SetGapExtensionCost(), CBlastOptions::SetGapOpeningCost(), and CBlastOptions::SetMatrixName().
Referenced by BlastSetupPreliminarySearchEx(), and CBlastTracebackSearch::x_Init().
◆ CreateScoreBlock()
|
static |
Initializes the BlastScoreBlk.
Caller owns the return value.
- Parameters
-
opts_memento Memento options object [in] query_data source of query sequence data [in] lookup_segments query segments to be searched because they were not filtered, needed for the lookup table creation (otherwise pass NULL). If this is passed to this function it should also be passed to CreateLookupTable [in|out] search_messages Error/warning messages [in|out] masked_query_regions Regions of the query which were masked including those masked outside the CORE. If non-NULL they will be populated and caller assumes ownership of the object [in|out] rps_info RPS-BLAST data structures as obtained from CreateRpsStructures [in]
Definition at line 122 of file setup_factory.cpp.
References _ASSERT, TSearchMessages::AddMessageAllQueries(), Blast_GetSeqLocInfoVector(), BLAST_MainSetUp(), Blast_Message2TSearchMessages(), Blast_ProgramIsRpsBlast(), BlastFindMatrixPath(), BlastScoreBlkFree(), BlastSeqLocFree(), BlastExtensionOptions::compositionBasedStats, eBlastSevError, eBlastSevWarning, CBlast_Message::Get(), ILocalQueryData::GetQueryInfo(), CBlastRPSInfo::GetScalingFactor(), ILocalQueryData::GetSequenceBlk(), TSearchMessages::HasMessages(), NStr::IntToString(), CBlastOptionsMemento::m_ExtnOpts, CBlastOptionsMemento::m_ProgramType, CBlastOptionsMemento::m_QueryOpts, CBlastOptionsMemento::m_ScoringOpts, BlastScoringOptions::matrix, msg(), NCBI_THROW, s_LocalQueryData2Packed_seqint(), Blast_Message::severity, strcasecmp, and TSearchMessages::ToString().
Referenced by BlastSetupPreliminarySearchEx(), BOOST_AUTO_TEST_CASE(), CEffectiveSearchSpaceCalculator::CEffectiveSearchSpaceCalculator(), CBlastPrelimSearch::Run(), and CBlastTracebackSearch::x_Init().
◆ CreateSnapshot()
| const CBlastOptionsMemento * CBlastOptions::CreateSnapshot | ( | ) | const |
Create a snapshot of the state of this object for internal use of its data structures (BLAST C++ APIs only)
Definition at line 797 of file blast_options_cxx.cpp.
References CBlastOptions::m_Local, and NCBI_THROW.
Referenced by BlastSetupPreliminarySearchEx(), BOOST_AUTO_TEST_CASE(), CEffectiveSearchSpaceCalculator::CEffectiveSearchSpaceCalculator(), CBlastPrelimSearch::ComputeBlastHSPResults(), CBlastPrelimSearch::Run(), CBlastPrelimSearch::SetNumberOfThreads(), CBlastTracebackSearch::x_Init(), and CBlastPrelimSearch::x_LaunchMultiThreadedSearch().
◆ CreateTask()
|
static |
Creates an options handle object configured with default options for the requested task, throws an exception if an unsupported task is requested.
- Parameters
-
task BLAST task [in] locality Local processing (default) or remote processing.
- Returns
- requested options handle with default values set
- Exceptions
-
CBlastException in case of an unhandled program type
- See also
- GetDocumentation
Definition at line 337 of file blast_options_handle.cpp.
References _ASSERT, abort(), BLAST_WORD_THRESHOLD_BLASTP_FAST, CBlastOptionsHandle::ClearFilterOptions(), NStr::CompareNocase(), CBlastOptionsFactory::Create(), eBlastn, eBlastp, eBlastx, eCompressedAaLookupTable, eDeltaBlast, eDiscMegablast, eKBlastp, eMapper, eMegablast, ePHIBlastp, ePSIBlast, ePSITblastn, eRPSBlast, eRPSTblastn, eTblastn, eTblastx, NULL, CBlastProteinOptionsHandle::SetChaining(), CBlastOptionsHandle::SetEvalueThreshold(), CBlastProteinOptionsHandle::SetGapExtensionCost(), CBlastProteinOptionsHandle::SetGapOpeningCost(), CMagicBlastOptionsHandle::SetGenomeToGenomeDefaults(), CBlastOptions::SetLookupTableType(), CBlastNucleotideOptionsHandle::SetMatchReward(), CBlastProteinOptionsHandle::SetMatrixName(), CBlastNucleotideOptionsHandle::SetMismatchPenalty(), CBlastOptionsHandle::SetOptions(), CMagicBlastOptionsHandle::SetRNAToGenomeDefaults(), CMagicBlastOptionsHandle::SetRNAToRNADefaults(), CBlastNucleotideOptionsHandle::SetVecScreenDefaults(), CBlastNucleotideOptionsHandle::SetWordSize(), CBlastProteinOptionsHandle::SetWordSize(), CBlastProteinOptionsHandle::SetWordThreshold(), ThrowIfInvalidTask(), and NStr::ToLower().
Referenced by BOOST_AUTO_TEST_CASE(), CVectorScreen::Run(), CBlastnVdbAppArgs::x_CreateOptionsHandle(), CBlastAppArgs::x_CreateOptionsHandleWithTask(), and CVecscreenRun::x_RunBlast().
◆ CreateWholeSeqLocFromIds()
| CConstRef<objects::CSeq_loc> CreateWholeSeqLocFromIds | ( | const list< CRef< objects::CSeq_id > > | seqids | ) |
Create a single CSeq_loc of type whole from the first id in the list.
- Parameters
-
seqids identifiers for the Seq-loc [in]
Definition at line 58 of file blast_aux_priv.cpp.
References _ASSERT, and CSeq_loc::SetWhole().
Referenced by CBioseqSeqInfoSrc::GetSeqLoc(), and CSeqDbSeqInfoSrc::GetSeqLoc().
◆ CReference() [1/2]
|
inlineprivate |
Prohibit constructing this class.
Definition at line 84 of file Reference.hpp.
◆ CReference() [2/2]
|
private |
Prohibit copy constructor.
◆ CRemoteBlast() [1/7]
| CRemoteBlast::CRemoteBlast | ( | CBlastOptionsHandle * | any_opts | ) |
Create a search using any kind of options handle.
Definition at line 1262 of file remote_blast.cpp.
References CRemoteBlast::x_Init(), and CRemoteBlast::x_InitDiskCache().
◆ CRemoteBlast() [2/7]
| CRemoteBlast::CRemoteBlast | ( | CNcbiIstream & | f | ) |
Uses the file to populate results.
The file may be text or binary ASN.1 or XML. type is automatically detected.
- Parameters
-
f istream to archive file
Definition at line 1250 of file remote_blast.cpp.
References f, CRemoteBlast::x_Init(), and CRemoteBlast::x_InitDiskCache().
◆ CRemoteBlast() [3/7]
|
private |
Prohibit copy construction.
◆ CRemoteBlast() [4/7]
Use the specified RID to get results for an existing search.
Definition at line 1256 of file remote_blast.cpp.
References CRemoteBlast::x_Init(), and CRemoteBlast::x_InitDiskCache().
◆ CRemoteBlast() [5/7]
| CRemoteBlast::CRemoteBlast | ( | CRef< IQueryFactory > | queries, |
| CRef< CBlastOptionsHandle > | opts_handle, | ||
| const CSearchDatabase & | db | ||
| ) |
Create a sequence search and set options, queries, and database.
- Parameters
-
queries Queries corresponding to Seq-loc-list or Bioseq-set. opts_handle Blast options handle. db Database used for this search.
Definition at line 1268 of file remote_blast.cpp.
References CRemoteBlast::x_Init(), CRemoteBlast::x_InitDiskCache(), and CRemoteBlast::x_InitQueries().
◆ CRemoteBlast() [6/7]
| CRemoteBlast::CRemoteBlast | ( | CRef< IQueryFactory > | queries, |
| CRef< CBlastOptionsHandle > | opts_handle, | ||
| CRef< IQueryFactory > | subjects | ||
| ) |
Create a search and set options, queries, and subject sequences.
- Parameters
-
queries Queries corresponding to Seq-loc-list or Bioseq-set. opts_handle Blast options handle. subjects Subject corresponding to Seq-loc-list or Bioseq-set.
Definition at line 1297 of file remote_blast.cpp.
References CRemoteBlast::SetSubjectSequences(), CRemoteBlast::x_Init(), CRemoteBlast::x_InitDiskCache(), and CRemoteBlast::x_InitQueries().
◆ CRemoteBlast() [7/7]
| CRemoteBlast::CRemoteBlast | ( | CRef< objects::CPssmWithParameters > | pssm, |
| CRef< CBlastOptionsHandle > | opts_handle, | ||
| const CSearchDatabase & | db | ||
| ) |
Create a PSSM search and set options, queries, and database.
- Parameters
-
pssm Search matrix for a PSSM search. opts_handle Blast options handle. db Database used for this search.
Definition at line 1379 of file remote_blast.cpp.
References CRef< C, Locker >::Empty(), NCBI_THROW, CRemoteBlast::SetQueries(), and CRemoteBlast::x_Init().
◆ CRpsAuxFile()
Parametrized constructor.
- Parameters
-
filename_no_extn name of the file without extension
Definition at line 180 of file rps_aux.cpp.
References CRpsAuxFile::kExtension, CRpsAuxFile::m_Data, NCBI_THROW, and CRpsAuxFile::x_ReadFromFile().
◆ CRpsFreqRatiosFile()
Parametrized constructor.
- Parameters
-
filename_no_extn name of the file without extension
Definition at line 486 of file rps_aux.cpp.
References CRpsFreqRatiosFile::kExtension, CRpsFreqRatiosFile::m_Data, CRpsMmappedFile::m_MmappedFile, BlastRPSFreqRatiosHeader::magic_number, NCBI_THROW, NULL, RPS_MAGIC_NUM, and RPS_MAGIC_NUM_28.
◆ CRpsFreqsFile()
Parametrized constructor.
- Parameters
-
filename_no_extn name of the file without extension
Definition at line 386 of file rps_aux.cpp.
References CRpsFreqsFile::kExtension, CRpsFreqsFile::m_Data, CRpsMmappedFile::m_MmappedFile, BlastRPSProfileHeader::magic_number, NCBI_THROW, NULL, RPS_MAGIC_NUM, and RPS_MAGIC_NUM_28.
◆ CRpsLookupTblFile()
Parametrized constructor.
- Parameters
-
filename_no_extn name of the file without extension
Definition at line 291 of file rps_aux.cpp.
References CRpsLookupTblFile::kExtension, CRpsLookupTblFile::m_Data, CRpsMmappedFile::m_MmappedFile, BlastRPSLookupFileHeader::magic_number, NCBI_THROW, NULL, RPS_MAGIC_NUM, and RPS_MAGIC_NUM_28.
◆ CRpsMmappedFile()
Parametrized constructor.
- Parameters
-
filename name of the file to mmap
Definition at line 255 of file rps_aux.cpp.
References CRpsMmappedFile::m_MmappedFile, and NCBI_RETHROW.
◆ CRpsObsrFile()
Parametrized constructor.
- Parameters
-
filename_no_extn name of the file without extension
Definition at line 436 of file rps_aux.cpp.
References CRpsObsrFile::kExtension, CRpsObsrFile::m_Data, CRpsMmappedFile::m_MmappedFile, BlastRPSProfileHeader::magic_number, NCBI_THROW, NULL, RPS_MAGIC_NUM, and RPS_MAGIC_NUM_28.
◆ CRpsPssmFile()
Parametrized constructor.
- Parameters
-
filename_no_extn name of the file without extension
Definition at line 338 of file rps_aux.cpp.
References CRpsPssmFile::kExtension, CRpsPssmFile::m_Data, CRpsMmappedFile::m_MmappedFile, BlastRPSProfileHeader::magic_number, NCBI_THROW, NULL, RPS_MAGIC_NUM, and RPS_MAGIC_NUM_28.
◆ CRPSTBlastnOptionsHandle() [1/2]
|
private |
Disallow copy constructor.
◆ CRPSTBlastnOptionsHandle() [2/2]
| CRPSTBlastnOptionsHandle::CRPSTBlastnOptionsHandle | ( | EAPILocality | locality = CBlastOptions::eLocal | ) |
Creates object with default options set.
Definition at line 46 of file rpstblastn_options.cpp.
References eRPSTblastn.
◆ CSBlastProgress() [1/2]
|
inline |
Definition at line 357 of file blast_aux.hpp.
◆ CSBlastProgress() [2/2]
|
inline |
Definition at line 357 of file blast_aux.hpp.
◆ CSearchDatabase() [1/2]
| CSearchDatabase::CSearchDatabase | ( | const string & | dbname, |
| EMoleculeType | mol_type | ||
| ) |
Simple constructor.
- Parameters
-
dbname database name [in] mol_type molecule type [in]
Definition at line 49 of file uniform_search.cpp.
◆ CSearchDatabase() [2/2]
| CSearchDatabase::CSearchDatabase | ( | const string & | dbname, |
| EMoleculeType | mol_type, | ||
| const string & | entrez_query | ||
| ) |
Constructor with allows an entrez query to be specified.
- Parameters
-
dbname database name [in] mol_type molecule type [in] entrez_query entrez query string [in]
Definition at line 55 of file uniform_search.cpp.
◆ CSearchResults() [1/2]
| CSearchResults::CSearchResults | ( | CConstRef< objects::CSeq_id > | query, |
| CRef< objects::CSeq_align_set > | align, | ||
| const TQueryMessages & | errs, | ||
| CRef< CBlastAncillaryData > | ancillary_data, | ||
| const TMaskedQueryRegions * | query_masks = NULL, |
||
| const string & | rid = kEmptyStr, |
||
| const SPHIQueryInfo * | phi_query_info = NULL |
||
| ) |
Constructor.
- Parameters
-
query List of query identifiers [in] align alignments for a single query sequence [in] errs error messages for this query sequence [in] ancillary_data Miscellaneous output from the blast engine [in] query_masks Mask locations for this query [in] rid RID (if applicable, else empty string) [in]
Definition at line 204 of file blast_results.cpp.
References CSearchResults::m_PhiQueryInfo, CSearchResults::SetMaskedQueryRegions(), and SPHIQueryInfoCopy().
◆ CSearchResults() [2/2]
|
private |
Prohibit copy constructor.
◆ CSearchResultSet() [1/3]
| CSearchResultSet::CSearchResultSet | ( | EResultType | res_type = eDatabaseSearch | ) |
Simplest constructor.
Definition at line 481 of file blast_results.cpp.
◆ CSearchResultSet() [2/3]
| CSearchResultSet::CSearchResultSet | ( | TQueryIdVector | ids, |
| TSeqAlignVector | aligns, | ||
| TSearchMessages | msg_vec, | ||
| TAncillaryVector | ancillary_data = TAncillaryVector(), |
||
| const TSeqLocInfoVector * | masks = NULL, |
||
| EResultType | res_type = eDatabaseSearch, |
||
| const SPHIQueryInfo * | phi_query_info = NULL |
||
| ) |
Parametrized constructor.
- Parameters
-
ids vector of all queries' ids [in] aligns vector of all queries' alignments [in] msg_vec vector of all queries' messages [in] ancillary_data vector of per-query search ancillary data [in] masks Mask locations for this query [in] res_type result type stored in this object [in]
- Note
- this constructor assumes that the ids, msg_vec, and ancillary_data vectors are of the SAME size as the aligns vector. The masks vector can be of the same size as aligns or have as many elements as there were queries in the search and they will be adjusted as necessary.
Definition at line 485 of file blast_results.cpp.
References CSearchResultSet::x_Init().
◆ CSearchResultSet() [3/3]
| CSearchResultSet::CSearchResultSet | ( | TSeqAlignVector | aligns, |
| TSearchMessages | msg_vec, | ||
| EResultType | res_type = eDatabaseSearch |
||
| ) |
Parametrized constructor.
- Parameters
-
aligns vector of all queries' alignments [in] msg_vec vector of all queries' messages [in] res_type result type stored in this object [in]
Definition at line 501 of file blast_results.cpp.
References i, NULL, s_ExtractSeqId(), and CSearchResultSet::x_Init().
◆ CSearchResultSet2TSeqAlignVector()
|
static |
Converts m_Results data member to a TSeqAlignVector.
Definition at line 153 of file bl2seq.cpp.
References CreateEmptySeq_align_set(), CRef< C, Locker >::Empty(), CSearchResultSet::GetNumResults(), ITERATE, r(), and CRef< C, Locker >::Reset().
Referenced by CBl2Seq::Run().
◆ CSeedTop()
Definition at line 54 of file seedtop.cpp.
◆ CSeqDbSeqInfoSrc() [1/2]
Constructor: includes initializing the CSeqDB object.
- Parameters
-
dbname Name of the BLAST database [in] is_protein Is this a protein or nucleotide database? [in]
Definition at line 49 of file seqinfosrc_seqdb.cpp.
References dbname(), CSeqDB::eNucleotide, and CSeqDB::eProtein.
◆ CSeqDbSeqInfoSrc() [2/2]
| CSeqDbSeqInfoSrc::CSeqDbSeqInfoSrc | ( | ncbi::CSeqDB * | seqdb | ) |
Constructor from an already existing CSeqDB object.
- Parameters
-
seqdb Pointer to the CSeqDB object to use.
Definition at line 57 of file seqinfosrc_seqdb.cpp.
References CSeqDbSeqInfoSrc::m_iSeqDb, CRef< C, Locker >::Reset(), and CSeqDbSeqInfoSrc::SetFilteringAlgorithmId().
◆ CSeqDbSrcNewArgs()
|
inline |
Constructor.
Definition at line 572 of file seqsrc_seqdb.cpp.
◆ CSeqLoc2BlastSeqLoc()
| BlastSeqLoc * CSeqLoc2BlastSeqLoc | ( | const objects::CSeq_loc * | slp | ) |
Converts a CSeq_loc into a BlastSeqLoc structure used in NewBlast.
- Parameters
-
slp CSeq_loc to convert [in]
- Returns
- Linked list of BlastSeqLoc structures
Definition at line 539 of file blast_aux.cpp.
References _ASSERT, BlastSeqLocNew(), CSeq_loc_Base::e_not_set, ITERATE, NCBI_THROW, NULL, and CBlastSeqLoc::Release().
Referenced by s_FillMaskLocFromBlastResults().
◆ CSeqVecSeqInfoSrc()
| CSeqVecSeqInfoSrc::CSeqVecSeqInfoSrc | ( | const TSeqLocVector & | seqv | ) |
Constructor from a vector of sequence locations.
Definition at line 48 of file seqinfosrc_seqvec.cpp.
References NCBI_THROW.
◆ CSplitQueryBlk() [1/2]
|
private |
Do not allow copy-construction.
◆ CSplitQueryBlk() [2/2]
Constructor for wrapper class for SSplitQueryBlk.
- Parameters
-
num_chunks number of chunks
Definition at line 47 of file split_query_blk.cpp.
References NCBI_THROW, and SplitQueryBlkNew().
◆ CStructWrapper() [1/2]
|
private |
Prohibit copy constructor.
◆ CStructWrapper() [2/2]
|
inline |
Constructor.
- Parameters
-
obj object to wrap [in] dfun deallocation function for object above [in]
Definition at line 105 of file setup_factory.hpp.
◆ CTBlastnOptionsHandle() [1/3]
|
private |
Disallow copy constructor.
◆ CTBlastnOptionsHandle() [2/3]
|
inline |
Definition at line 59 of file tblastn_options.hpp.
◆ CTBlastnOptionsHandle() [3/3]
| CTBlastnOptionsHandle::CTBlastnOptionsHandle | ( | EAPILocality | locality = CBlastOptions::eLocal | ) |
Creates object with default options set.
Definition at line 46 of file tblastn_options.cpp.
References eTblastn.
◆ CTBlastxOptionsHandle() [1/2]
|
private |
Disallow copy constructor.
◆ CTBlastxOptionsHandle() [2/2]
| CTBlastxOptionsHandle::CTBlastxOptionsHandle | ( | EAPILocality | locality | ) |
Creates object with default options set.
Definition at line 47 of file tblastx_options.cpp.
References eTblastx.
◆ CThreadable()
|
inline |
Default ctor.
Definition at line 169 of file setup_factory.hpp.
◆ DbIndexInit()
| std::string DbIndexInit | ( | const string & | indexname, |
| bool | old_style, | ||
| bool & | partial, | ||
| const int | word_size | ||
| ) |
Definition at line 1122 of file blast_dbindex.cpp.
References ERR_POST, CIndexedDb::Index_Set_Instance, Info(), kEmptyStr, CRef< C, Locker >::Reset(), result, s_CheckMinWordSize(), string, and CException::what().
Referenced by CSetupFactory::InitializeMegablastDbIndex().
◆ DebugDump() [1/33]
|
virtual |
Define method for dumping debug information.
Reimplemented from CObject.
Definition at line 113 of file blast_aux.cpp.
References BLAST_SequenceBlk::length, CDebugDumpContext::Log(), CBLAST_SequenceBlk::m_Ptr, BLAST_SequenceBlk::sequence, BLAST_SequenceBlk::sequence_allocated, BLAST_SequenceBlk::sequence_start, BLAST_SequenceBlk::sequence_start_allocated, and CDebugDumpContext::SetFrame().
◆ DebugDump() [2/33]
|
virtual |
Define method for dumping debug information.
Reimplemented from CObject.
Definition at line 128 of file blast_aux.cpp.
References BlastQueryInfo::contexts, BlastContextInfo::eff_searchsp, BlastQueryInfo::first_context, BlastContextInfo::frame, i, NStr::IntToString(), BlastContextInfo::is_valid, BlastQueryInfo::last_context, BlastContextInfo::length_adjustment, CDebugDumpContext::Log(), CBlastQueryInfo::m_Ptr, BlastQueryInfo::max_length, BlastQueryInfo::num_queries, BlastContextInfo::query_index, BlastContextInfo::query_length, BlastContextInfo::query_offset, CDebugDumpContext::SetFrame(), and string.
◆ DebugDump() [3/33]
|
virtual |
Define method for dumping debug information.
Reimplemented from CObject.
Definition at line 76 of file blast_aux.cpp.
References SRepeatFilterOptions::database, SBlastFilterOptions::dustOptions, QuerySetUpOptions::filter_string, QuerySetUpOptions::filtering_options, QuerySetUpOptions::genetic_code, SSegOptions::hicut, SDustOptions::level, SDustOptions::linker, SSegOptions::locut, CDebugDumpContext::Log(), CQuerySetUpOptions::m_Ptr, SBlastFilterOptions::mask_at_hash, SBlastFilterOptions::repeatFilterOptions, SBlastFilterOptions::segOptions, CDebugDumpContext::SetFrame(), QuerySetUpOptions::strand_option, SDustOptions::window, and SSegOptions::window.
Referenced by CBlastOptionsLocal::DebugDump().
◆ DebugDump() [4/33]
|
virtual |
Define method for dumping debug information.
Reimplemented from CObject.
Definition at line 154 of file blast_aux.cpp.
References CDebugDumpContext::Log(), LookupTableOptions::lut_type, CLookupTableOptions::m_Ptr, LookupTableOptions::mb_template_length, LookupTableOptions::mb_template_type, CDebugDumpContext::SetFrame(), LookupTableOptions::threshold, and LookupTableOptions::word_size.
Referenced by CBlastOptionsLocal::DebugDump().
◆ DebugDump() [5/33]
|
virtual |
Define method for dumping debug information.
Reimplemented from CObject.
Definition at line 168 of file blast_aux.cpp.
References CLookupTableWrap::m_Ptr, and CDebugDumpContext::SetFrame().
◆ DebugDump() [6/33]
|
virtual |
Define method for dumping debug information.
Reimplemented from CObject.
Definition at line 176 of file blast_aux.cpp.
References CDebugDumpContext::Log(), CBlastInitialWordOptions::m_Ptr, CDebugDumpContext::SetFrame(), BlastInitialWordOptions::window_size, and BlastInitialWordOptions::x_dropoff.
Referenced by CBlastOptionsLocal::DebugDump().
◆ DebugDump() [7/33]
|
virtual |
Define method for dumping debug information.
Reimplemented from CObject.
Definition at line 186 of file blast_aux.cpp.
References CBlastInitialWordParameters::m_Ptr, and CDebugDumpContext::SetFrame().
◆ DebugDump() [8/33]
|
virtual |
Define method for dumping debug information.
Reimplemented from CObject.
Definition at line 194 of file blast_aux.cpp.
References CBlast_ExtendWord::m_Ptr, and CDebugDumpContext::SetFrame().
◆ DebugDump() [9/33]
|
virtual |
Define method for dumping debug information.
Reimplemented from CObject.
Definition at line 203 of file blast_aux.cpp.
References BlastExtensionOptions::ePrelimGapExt, BlastExtensionOptions::eTbackExt, BlastExtensionOptions::gap_x_dropoff, BlastExtensionOptions::gap_x_dropoff_final, CDebugDumpContext::Log(), CBlastExtensionOptions::m_Ptr, and CDebugDumpContext::SetFrame().
Referenced by CBlastOptionsLocal::DebugDump().
◆ DebugDump() [10/33]
|
virtual |
Define method for dumping debug information.
Reimplemented from CObject.
Definition at line 216 of file blast_aux.cpp.
References BlastExtensionParameters::gap_x_dropoff, BlastExtensionParameters::gap_x_dropoff_final, CDebugDumpContext::Log(), CBlastExtensionParameters::m_Ptr, and CDebugDumpContext::SetFrame().
◆ DebugDump() [11/33]
|
virtual |
Define method for dumping debug information.
Reimplemented from CObject.
Definition at line 227 of file blast_aux.cpp.
References BlastHSPFilteringOptions::best_hit, BlastHSPFilteringOptions::best_hit_stage, BlastHitSavingOptions::culling_limit, BlastHSPFilteringOptions::culling_opts, BlastHSPFilteringOptions::culling_stage, BlastHitSavingOptions::cutoff_score, BlastHitSavingOptions::do_sum_stats, BlastHitSavingOptions::expect_value, BlastHitSavingOptions::hitlist_size, BlastHitSavingOptions::hsp_filt_opt, BlastHitSavingOptions::hsp_num_max, CDebugDumpContext::Log(), BlastHitSavingOptions::longest_intron, CBlastHitSavingOptions::m_Ptr, BlastHSPCullingOptions::max_hits, BlastHitSavingOptions::max_hsps_per_subject, BlastHitSavingOptions::min_diag_separation, BlastHitSavingOptions::min_hit_length, BlastHSPBestHitOptions::overhang, BlastHitSavingOptions::percent_identity, BlastHSPBestHitOptions::score_edge, CDebugDumpContext::SetFrame(), and BlastHitSavingOptions::total_hsp_limit.
Referenced by CBlastOptionsLocal::DebugDump().
◆ DebugDump() [12/33]
|
virtual |
Define method for dumping debug information.
Reimplemented from CObject.
Definition at line 263 of file blast_aux.cpp.
References CBlastHitSavingParameters::m_Ptr, and CDebugDumpContext::SetFrame().
◆ DebugDump() [13/33]
|
virtual |
Define method for dumping debug information.
Reimplemented from CObject.
Definition at line 271 of file blast_aux.cpp.
References PSIBlastOptions::impala_scaling_factor, PSIBlastOptions::inclusion_ethresh, CDebugDumpContext::Log(), CPSIBlastOptions::m_Ptr, PSIBlastOptions::nsg_compatibility_mode, PSIBlastOptions::pseudo_count, CDebugDumpContext::SetFrame(), and PSIBlastOptions::use_best_alignment.
Referenced by CBlastOptionsLocal::DebugDump().
◆ DebugDump() [14/33]
|
virtual |
Define method for dumping debug information.
Reimplemented from CObject.
Definition at line 376 of file blast_aux.cpp.
References CBlastDatabaseOptions::m_Ptr, and CDebugDumpContext::SetFrame().
Referenced by CBlastOptionsLocal::DebugDump().
◆ DebugDump() [15/33]
|
virtual |
Define method for dumping debug information.
Reimplemented from CObject.
Definition at line 321 of file blast_aux.cpp.
References BlastScoreBlk::alphabet_size, BlastScoreBlk::alphabet_start, BlastScoreBlk::ambig_occupy, BlastScoreBlk::ambig_size, BlastScoreBlk::hiscore, CDebugDumpContext::Log(), BlastScoreBlk::loscore, CBlastScoreBlk::m_Ptr, BlastScoreBlk::name, BlastScoreBlk::number_of_contexts, BlastScoreBlk::penalty, BlastScoreBlk::protein_alphabet, BlastScoreBlk::read_in_matrix, BlastScoreBlk::reward, BlastScoreBlk::scale_factor, and CDebugDumpContext::SetFrame().
◆ DebugDump() [16/33]
|
virtual |
Define method for dumping debug information.
Reimplemented from CObject.
Definition at line 343 of file blast_aux.cpp.
References BlastScoringOptions::gap_extend, BlastScoringOptions::gap_open, BlastScoringOptions::gapped_calculation, BlastScoringOptions::is_ooframe, CDebugDumpContext::Log(), CBlastScoringOptions::m_Ptr, BlastScoringOptions::matrix, BlastScoringOptions::penalty, BlastScoringOptions::reward, CDebugDumpContext::SetFrame(), and BlastScoringOptions::shift_pen.
Referenced by CBlastOptionsLocal::DebugDump().
◆ DebugDump() [17/33]
|
virtual |
Define method for dumping debug information.
Reimplemented from CObject.
Definition at line 360 of file blast_aux.cpp.
References BlastScoringParameters::gap_extend, BlastScoringParameters::gap_open, CDebugDumpContext::Log(), CBlastScoringParameters::m_Ptr, BlastScoringParameters::penalty, BlastScoringParameters::reward, BlastScoringParameters::scale_factor, CDebugDumpContext::SetFrame(), and BlastScoringParameters::shift_pen.
◆ DebugDump() [18/33]
|
virtual |
Define method for dumping debug information.
Reimplemented from CObject.
Definition at line 294 of file blast_aux.cpp.
References BlastEffectiveLengthsOptions::db_length, BlastEffectiveLengthsOptions::dbseq_num, i, NStr::IntToString(), CDebugDumpContext::Log(), CBlastEffectiveLengthsOptions::m_Ptr, BlastEffectiveLengthsOptions::num_searchspaces, BlastEffectiveLengthsOptions::searchsp_eff, CDebugDumpContext::SetFrame(), and string.
Referenced by CBlastOptionsLocal::DebugDump().
◆ DebugDump() [19/33]
|
virtual |
Define method for dumping debug information.
Reimplemented from CObject.
Definition at line 310 of file blast_aux.cpp.
References CDebugDumpContext::Log(), CBlastEffectiveLengthsParameters::m_Ptr, BlastEffectiveLengthsParameters::real_db_length, BlastEffectiveLengthsParameters::real_num_seqs, and CDebugDumpContext::SetFrame().
◆ DebugDump() [20/33]
|
virtual |
Define method for dumping debug information.
Reimplemented from CObject.
Definition at line 285 of file blast_aux.cpp.
References CBlastGapAlignStruct::m_Ptr, and CDebugDumpContext::SetFrame().
◆ DebugDump() [21/33]
|
virtual |
Define method for dumping debug information.
Reimplemented from CObject.
Definition at line 483 of file blast_aux.cpp.
References CDebugDumpContext::Log(), CBlastHSPResults::m_Ptr, BlastHSPResults::num_queries, and CDebugDumpContext::SetFrame().
◆ DebugDump() [22/33]
|
virtual |
Define method for dumping debug information.
Reimplemented from CObject.
Definition at line 385 of file blast_aux.cpp.
References PSIMsa::dimensions, CDebugDumpContext::Log(), CPSIMsa::m_Ptr, PSIMsaDimensions::num_seqs, PSIMsaDimensions::query_length, and CDebugDumpContext::SetFrame().
◆ DebugDump() [23/33]
|
virtual |
Define method for dumping debug information.
Reimplemented from CObject.
Definition at line 398 of file blast_aux.cpp.
References PSIMatrix::h, PSIMatrix::kappa, PSIMatrix::lambda, CDebugDumpContext::Log(), CPSIMatrix::m_Ptr, PSIMatrix::ncols, PSIMatrix::nrows, and CDebugDumpContext::SetFrame().
◆ DebugDump() [24/33]
|
virtual |
Define method for dumping debug information.
Reimplemented from CObject.
Definition at line 413 of file blast_aux.cpp.
References PSIDiagnosticsRequest::frequency_ratios, PSIDiagnosticsRequest::gapless_column_weights, PSIDiagnosticsRequest::information_content, CDebugDumpContext::Log(), CPSIDiagnosticsRequest::m_Ptr, PSIDiagnosticsRequest::residue_frequencies, CDebugDumpContext::SetFrame(), and PSIDiagnosticsRequest::weighted_residue_frequencies.
◆ DebugDump() [25/33]
|
virtual |
Define method for dumping debug information.
Reimplemented from CObject.
Definition at line 429 of file blast_aux.cpp.
References PSIDiagnosticsResponse::alphabet_size, CDebugDumpContext::Log(), CPSIDiagnosticsResponse::m_Ptr, and CDebugDumpContext::SetFrame().
◆ DebugDump() [26/33]
|
virtual |
Define method for dumping debug information.
Reimplemented from CObject.
Definition at line 440 of file blast_aux.cpp.
References CBlastSeqSrc::m_Ptr, and CDebugDumpContext::SetFrame().
◆ DebugDump() [27/33]
|
virtual |
Define method for dumping debug information.
Reimplemented from CObject.
Definition at line 451 of file blast_aux.cpp.
References abort(), BlastSeqSrcIterator::chunk_sz, BlastSeqSrcIterator::current_pos, eOidList, eOidRange, BlastSeqSrcIterator::itr_type, CDebugDumpContext::Log(), CBlastSeqSrcIterator::m_Ptr, and CDebugDumpContext::SetFrame().
◆ DebugDump() [28/33]
|
virtual |
Define method for dumping debug information.
Reimplemented from CObject.
Definition at line 471 of file blast_aux.cpp.
References CDebugDumpContext::Log(), CBlast_Message::m_Ptr, Blast_Message::message, CDebugDumpContext::SetFrame(), and Blast_Message::severity.
◆ DebugDump() [29/33]
|
virtual |
Define method for dumping debug information.
Reimplemented from CObject.
Definition at line 495 of file blast_aux.cpp.
References CDebugDumpContext::Log(), CBlastMaskLoc::m_Ptr, BlastSeqLoc::next, BlastMaskLoc::seqloc_array, CDebugDumpContext::SetFrame(), and BlastMaskLoc::total_size.
◆ DebugDump() [30/33]
|
virtual |
Define method for dumping debug information.
Reimplemented from CObject.
Definition at line 513 of file blast_aux.cpp.
References CDebugDumpContext::Log(), CBlastSeqLoc::m_Ptr, CDebugDumpContext::SetFrame(), and tmp.
◆ DebugDump() [31/33]
|
virtual |
Define method for dumping debug information.
Reimplemented from CObject.
Definition at line 526 of file blast_aux.cpp.
References CDebugDumpContext::Log(), CSBlastProgress::m_Ptr, CDebugDumpContext::SetFrame(), SBlastProgress::stage, and SBlastProgress::user_data.
◆ DebugDump() [32/33]
|
virtual |
Allows to dump a snapshot of the object.
Reimplemented from CObject.
Definition at line 2534 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::DebugDump(), depth, and CBlastOptions::m_Local.
◆ DebugDump() [33/33]
|
virtual |
Allows to dump a snapshot of the object.
Reimplemented from CObject.
Definition at line 399 of file blast_options_local_priv.cpp.
References CQuerySetUpOptions::DebugDump(), CLookupTableOptions::DebugDump(), CBlastInitialWordOptions::DebugDump(), CBlastExtensionOptions::DebugDump(), CBlastHitSavingOptions::DebugDump(), CPSIBlastOptions::DebugDump(), CBlastDatabaseOptions::DebugDump(), CBlastScoringOptions::DebugDump(), CBlastEffectiveLengthsOptions::DebugDump(), DebugDumpValue(), depth, CBlastOptionsLocal::m_DbOpts, CBlastOptionsLocal::m_DeltaBlastOpts, CBlastOptionsLocal::m_EffLenOpts, CBlastOptionsLocal::m_ExtnOpts, CBlastOptionsLocal::m_HitSaveOpts, CBlastOptionsLocal::m_InitWordOpts, CBlastOptionsLocal::m_LutOpts, CBlastOptionsLocal::m_Program, CBlastOptionsLocal::m_PSIBlastOpts, CBlastOptionsLocal::m_QueryOpts, CBlastOptionsLocal::m_ScoringOpts, and CDebugDumpContext::SetFrame().
Referenced by CBlastOptions::DebugDump().
◆ DECLARE_CLASS_STATIC_FAST_MUTEX()
|
private |
Reference counter for this object so that the genetic code singleton is.
◆ DEFINE_CLASS_STATIC_FAST_MUTEX()
| DEFINE_CLASS_STATIC_FAST_MUTEX | ( | CAutomaticGenCodeSingleton::sm_Mutex | ) |
◆ DEFINE_STATIC_MUTEX()
| DEFINE_STATIC_MUTEX | ( | InitMutex | ) |
◆ Delete()
|
inlinestatic |
Definition at line 73 of file blast_aux.hpp.
References BlastHSPStreamFree().
◆ DisableDiskCacheUse()
|
inline |
Definition at line 473 of file remote_blast.hpp.
References CRemoteBlast::m_use_disk_cache.
◆ do_copy()
|
private |
Workhorse for copy constructor and assignment operator.
- Parameters
-
other object to copy [in]
Definition at line 173 of file blast_results.cpp.
References Blast_KarlinBlkCopy(), Blast_KarlinBlkNew(), CBlastAncillaryData::m_GappedKarlinBlk, CBlastAncillaryData::m_GumbelBlk, CBlastAncillaryData::m_PsiGappedKarlinBlk, CBlastAncillaryData::m_PsiUngappedKarlinBlk, CBlastAncillaryData::m_SearchSpace, CBlastAncillaryData::m_UngappedKarlinBlk, NULL, and s_InitializeGumbelBlk().
Referenced by CBlastAncillaryData::CBlastAncillaryData(), and CBlastAncillaryData::operator=().
◆ DoneDefaults() [1/2]
|
inline |
Returns true if this object needs default values set.
Definition at line 176 of file blast_options_handle.hpp.
References CBlastOptions::DoneDefaults(), and CBlastOptionsHandle::m_Opts.
◆ DoneDefaults() [2/2]
| void CBlastOptions::DoneDefaults | ( | ) | const |
Definition at line 2542 of file blast_options_cxx.cpp.
References CBlastOptions::m_Remote, and CBlastOptionsRemote::SetDefaultsMode().
Referenced by CBlastOptionsHandle::DoneDefaults().
◆ DoNotSaveMessages()
| void CBlastAppDiagHandler::DoNotSaveMessages | ( | void | ) |
Call to turn off saving diag message, discard all saved message.
Definition at line 1189 of file blast_aux.cpp.
References CBlastAppDiagHandler::m_save, and CBlastAppDiagHandler::ResetMessages().
Referenced by CBlastnNode::Main(), CBlastpNode::Main(), CBlastxNode::Main(), CRPSBlastNode::Main(), CRPSTBlastnNode::Main(), CTblastnNode::Main(), CPsiBlastApp::Run(), CTblastxApp::Run(), CBlastnApp::x_RunMTBySplitDB(), CBlastpApp::x_RunMTBySplitDB(), CBlastxApp::x_RunMTBySplitDB(), CRPSBlastApp::x_RunMTBySplitDB(), CRPSTBlastnApp::x_RunMTBySplitDB(), and CTblastnApp::x_RunMTBySplitDB().
◆ DoPreSearch() [1/3]
|
inlinevirtual |
Wrapper around PreSearch().
Runs PreSearch() and then frees locs_wrap_.
- Note
- Overrides CIndexedDb::DoPreSearch().
Implements CIndexedDb.
Definition at line 299 of file blast_dbindex.cpp.
References CBlastSeqLocWrap::getLocs(), CIndexedDb::locs_wrap_, CIndexedDb_Old::PreSearch(), and CRef< C, Locker >::Release().
◆ DoPreSearch() [2/3]
|
virtual |
Run preliminary indexed search functionality.
- Note
- Overrides CIndexedDb::DoPreSearch().
- Parameters
-
queries Queries descriptor. locs Unmasked intervals of queries. lut_options Lookup table parameters, like target word size. word_options Contains window size of two-hits based search.
Implements CIndexedDb.
Definition at line 891 of file blast_dbindex.cpp.
References IDX_TRACE, CIndexedDb_New::queries_, CIndexedDb_New::sopt_, CDbIndex::SSearchOptions::two_hits, BlastInitialWordOptions::window_size, LookupTableOptions::word_size, and CDbIndex::SSearchOptions::word_size.
◆ DoPreSearch() [3/3]
|
pure virtual |
Run preliminary indexed search functionality.
- Parameters
-
queries Queries descriptor. locs Unmasked intervals of queries. lut_options Lookup table parameters, like target word size. word_options Contains window size of two-hits based search.
Implemented in CIndexedDb_New, and CIndexedDb_Old.
Referenced by IndexedDbRunSearch().
◆ Empty() [1/2]
| bool CBlastQueryFilteredFrames::Empty | ( | void | ) |
Returns true if this object contains any masking information.
Definition at line 1649 of file blast_setup_cxx.cpp.
References set< Key, Compare >::empty(), and CBlastQueryFilteredFrames::ListFrames().
Referenced by BOOST_AUTO_TEST_CASE().
◆ empty() [1/2]
|
inline |
Returns whether this container is empty or not.
Definition at line 427 of file blast_results.hpp.
References CSearchResultSet::size().
Referenced by CBl2Seq::GetFilteredSubjectRegions().
◆ empty() [2/2]
|
inline |
Is the container empty.
Definition at line 267 of file magicblast.hpp.
References CMagicBlastResultSet::size().
◆ Empty() [2/2]
|
inline |
Returns true if the container is empty, else false.
Definition at line 114 of file blast_setup.hpp.
References IBlastQuerySource::Size().
Referenced by SafeSetupQueries(), SafeSetupQueryInfo(), SetupQueries_OMF(), and SetupSubjects_OMF().
◆ EnableDiskCacheUse()
|
inline |
Controls disk cache usage for results retrieval.
Definition at line 472 of file remote_blast.hpp.
References CRemoteBlast::m_use_disk_cache.
◆ end() [1/4]
|
inline |
Returns iterator to end of container, provided to facilitate STL-style iteration.
Definition at line 443 of file blast_results.hpp.
References CSearchResultSet::m_Results.
◆ end() [2/4]
|
inline |
Returns iterator to the end of the container.
Definition at line 280 of file magicblast.hpp.
References CMagicBlastResultSet::m_Results.
◆ end() [3/4]
|
inline |
Returns const_iterator to end of container, provided to facilitate STL-style iteration.
Definition at line 435 of file blast_results.hpp.
References CSearchResultSet::m_Results.
Referenced by s_AddNewResultSet().
◆ end() [4/4]
|
inline |
Returns const iterator to the end of the container.
Definition at line 274 of file magicblast.hpp.
References CMagicBlastResultSet::m_Results.
◆ EndSearchIndication() [1/3]
|
virtual |
Function used by threads to indicate that they are done with iterating over the database sequences.
- Parameters
-
last_vol_id the last accessed volime index
Implements CIndexedDb.
Definition at line 877 of file blast_dbindex.cpp.
References i, IDX_TRACE, LAST_VOL_IDX_INIT, CIndexedDb_New::mtx_, CIndexedDb_New::results_holder_, and CIndexedDb_New::volumes_.
◆ EndSearchIndication() [2/3]
|
pure virtual |
Function used by threads to indicate that they are done with iterating over the database sequences.
- Parameters
-
last_vol_id the last accessed volime index
Implemented in CIndexedDb_Old, and CIndexedDb_New.
Referenced by s_MB_IdxEndSearchIndication().
◆ EndSearchIndication() [3/3]
|
inlinevirtual |
◆ EnumerateDbVolumes()
|
staticprivate |
Generate a list of leaf database volumes from a list of database names.
- Parameters
-
db_names BLAST database names db_vols [out] resulting list of leaf database volume names
Definition at line 646 of file blast_dbindex.cpp.
References CSeqDB::eNucleotide, and CSeqDB::FindVolumePaths().
Referenced by CIndexedDb_New::CIndexedDb_New().
◆ EProgramToEBlastProgramType()
| EBlastProgramType EProgramToEBlastProgramType | ( | EProgram | p | ) |
Convert EProgram to EBlastProgramType.
- Parameters
-
p Program expressed as an api layer EProgram.
- Returns
- Same program using the core enumeration.
Definition at line 709 of file blast_aux.cpp.
References eBlastn, eBlastp, eBlastTypeBlastn, eBlastTypeBlastp, eBlastTypeBlastx, eBlastTypeMapping, eBlastTypePhiBlastn, eBlastTypePhiBlastp, eBlastTypePsiBlast, eBlastTypePsiTblastn, eBlastTypeRpsBlast, eBlastTypeRpsTblastn, eBlastTypeTblastn, eBlastTypeTblastx, eBlastTypeUndefined, eBlastx, eDeltaBlast, eDiscMegablast, eMapper, eMegablast, ePHIBlastn, ePHIBlastp, ePSIBlast, ePSITblastn, eRPSBlast, eRPSTblastn, eTblastn, eTblastx, and eVecScreen.
Referenced by CheckMTByQueries_QuerySize(), CBlastFormatUtil::CreateSeqAnnotFromSeqAlignSet(), CBlastOptionsLocal::GetProgramType(), CBlastOptionsLocal::SetProgram(), CBlastOptionsLocal::SetSubjectBestHit(), SplitQuery_GetChunkSize(), CScoreBuilder::x_Initialize(), and CSplitQueryTestFixture::x_TestCContextTranslator().
◆ EProgramToTaskName()
Convert a EProgram enumeration value to a task name (as those used in the BLAST command line binaries)
- Parameters
-
p EProgram enumeration value to convert [in]
Definition at line 676 of file blast_aux.cpp.
References abort(), eBlastn, eBlastp, eBlastx, eDeltaBlast, eDiscMegablast, eMapper, eMegablast, ePHIBlastn, ePHIBlastp, ePSIBlast, ePSITblastn, eRPSBlast, eRPSTblastn, eTblastn, eTblastx, eVecScreen, int, and ThrowIfInvalidTask().
Referenced by CBlastFormatUtil::CreateSeqAnnotFromSeqAlignSet(), GetQueryBatchSize(), CBlastOptionsBuilder::GetSearchOptions(), CPsiBlastApp::Run(), s_CallAligner(), SplitQuery_GetChunkSize(), CBLASTParams::ToArgs(), CBLASTParams::ToArgVecBlastOptions(), CBLASTParams::ToBlastOptions(), CBLASTSeqToolJob::x_CreateProjectItems(), and CFindOverlapJob::x_PrepareAligner().
◆ ExportSearchStrategy_ASN1()
| void CExportStrategy::ExportSearchStrategy_ASN1 | ( | CNcbiOstream * | out | ) |
Definition at line 366 of file search_strategy.cpp.
References CExportStrategy::GetSearchStrategy(), MSerial_AsnText, and out().
◆ ExtractBlast4Request()
| CRef<objects::CBlast4_request> ExtractBlast4Request | ( | CNcbiIstream & | in | ) |
Extract a Blast4-request (a.k.a.
: a search strategy) from an input stream. This function supports reading binary and text ASN.1 as well as XML. A Blast4-get-search-strategy-reply will be attempted to read first (output of BLAST SOAP server), then a Blast4-request (output of BLAST C++ command line binaries).
- Parameters
-
in stream to read the data from [in]
- Exceptions
-
CException if input cannot be recognized
Definition at line 2258 of file remote_blast.cpp.
References _ASSERT, CFormatGuess::eBinaryASN, eSerial_Xml, CFormatGuess::eTextASN, CFormatGuess::eXml, in(), MSerial_AsnBinary, MSerial_AsnText, NCBI_THROW, CObjectIStream::Open(), and CRef< C, Locker >::Reset().
Referenced by BOOST_AUTO_TEST_CASE(), and s_ImportSearchStrategy().
◆ ExtractScopes()
Retrieve the CScope objects associated with the query sequences associated with this object.
In the case when CSeq_loc or TSeqLocs are provided, a newly constructed CScope object will be returned per query
- Note
- This method is intended to be used for query splitting only
Definition at line 384 of file objmgr_query_data.cpp.
References abort(), CBlastQueryVector::GetScope(), i, CObjMgr_QueryFactory::m_QueryVector, CObjMgr_QueryFactory::m_SSeqLocVector, NON_CONST_ITERATE, CRef< C, Locker >::NotEmpty(), and CBlastQueryVector::Size().
Referenced by CBlastKmerSearch::Run(), and CQuerySplitter::x_ExtractCScopesAndMasks().
◆ ExtractUserSpecifiedMasks()
| TSeqLocInfoVector CObjMgr_QueryFactory::ExtractUserSpecifiedMasks | ( | ) |
Retrieve any user specified masking locations.
- Note
- This method is intended to be used for query splitting only
Definition at line 445 of file objmgr_query_data.cpp.
References abort(), CBlastQueryVector::GetMaskedRegions(), i, CObjMgr_QueryFactory::m_QueryVector, CObjMgr_QueryFactory::m_SSeqLocVector, NON_CONST_ITERATE, CRef< C, Locker >::NotEmpty(), PackedSeqLocToMaskedQueryRegions(), s_GuessProgram(), and CBlastQueryVector::Size().
Referenced by CQuerySplitter::x_ExtractCScopesAndMasks(), CRemoteBlast::x_ExtractUserSpecifiedMasks(), and CExportStrategy::x_Process_Query().
◆ FetchData()
|
private |
Fills in CImportStrategyData and m_OptionsBuilder.
Definition at line 79 of file search_strategy.cpp.
References CBlast4_queue_search_request_Base::CanGetAlgorithm_options(), CBlast4_queue_search_request_Base::CanGetFormat_options(), CBlast4_queue_search_request_Base::CanGetProgram_options(), eBlastOpt_Web_StepNumber, CBlastOptions::eBoth, NStr::fConvErr_NoThrow, CBlast4_queue_search_request_Base::GetAlgorithm_options(), CBlast4_queue_search_request_Base::GetFormat_options(), CBlast4Field::GetName(), CBlast4_parameters::GetParamByName(), CBlast4_queue_search_request_Base::GetProgram(), CBlast4_queue_search_request_Base::GetProgram_options(), CBlast4_queue_search_request_Base::GetService(), CImportStrategy::m_Data, CImportStrategy::m_IgnoreUnsupportedOptions, CImportStrategy::m_OptionsBuilder, CImportStrategy::m_Request, CRef< C, Locker >::NotEmpty(), and NStr::StringToInt().
Referenced by CImportStrategy::GetDBFilteringID(), CImportStrategy::GetDBFilteringKey(), CImportStrategy::GetOptionsBuilder(), CImportStrategy::GetOptionsHandle(), CImportStrategy::GetPsiNumOfIterations(), CImportStrategy::GetQueryRange(), CImportStrategy::GetSubjectMaskingType(), and CImportStrategy::GetTask().
◆ FillData() [1/2]
| void CCddInputData::CHit::FillData | ( | const CSeqDB & | seqdb, |
| const CBlastRPSInfo & | profile_data | ||
| ) |
Allocate and populate arrays of data for PSSM computation.
- Parameters
-
seqdb Object accessing CDD [in] profile_data Object accssing data in CDD [in]
Definition at line 417 of file cdd_pssm_input.cpp.
References NON_CONST_ITERATE, and CSeqDB::SeqidToOid().
◆ FillData() [2/2]
| void CCddInputData::CHitSegment::FillData | ( | int | db_oid, |
| const CBlastRPSInfo & | profile_data | ||
| ) |
Allocate and populate arrays for MSA data (weighted residue counts and effective observations used for PSSM computation)
- Parameters
-
db_oid Subject index in CDD database [in] profile_data Object accessing data int CDD [in]
Definition at line 753 of file cdd_pssm_input.cpp.
References PSICdMsaCellData::iobsr, CCddInputData::m_MsaData, NULL, and PSICdMsaCellData::wfreqs.
◆ FindBlastDbPath()
Returns the path (including a trailing path separator) to the location where the BLAST database can be found.
- Parameters
-
dbname Database to search for is_prot true if this is a protein matrix
Definition at line 1403 of file blast_setup_cxx.cpp.
References BlastDbFileExists(), database, dbname(), eFollowLinks, CNcbiEnvironment::Get(), IRegistry::Get(), CNcbiApplicationAPI::GetConfig(), CNcbiApplicationAPI::GetEnvironment(), CDirEntry::GetPathSeparator(), IRegistry::HasEntry(), CNcbiApplication::Instance(), CDirEntry::MakePath(), CDirEntry::NormalizePath(), and registry.
◆ FindGeneticCode()
| TAutoUint1ArrayPtr FindGeneticCode | ( | int | genetic_code | ) |
Retrieves the requested genetic code in Ncbistdaa format.
- Parameters
-
genetic_code numeric identifier for genetic code requested [in]
- Returns
- NULL if genetic_code is invalid or in case of memory allocation failure, otherwise genetic code string.
- Note
- the returned string has length GENCODE_STRLEN
Definition at line 588 of file blast_aux.cpp.
References _ASSERT, CSeqportUtil::Convert(), CSeq_data_Base::e_Ncbieaa, CSeq_data_Base::e_Ncbistdaa, CAliasBase< TPrim >::Get(), CGen_code_table::GetNcbieaa(), CSeq_data_Base::GetNcbistdaa(), i, CSeq_data_Base::IsNcbistdaa(), kEmptyStr, max(), and NULL.
Referenced by CAutomaticGenCodeSingleton::AddGeneticCode(), BOOST_AUTO_TEST_CASE(), CAutomaticGenCodeSingleton::CAutomaticGenCodeSingleton(), SetupQueries_OMF(), and SetupSubjects_OMF().
◆ FindVolume()
|
inlineprivate |
Find a volume containing the given subject ordinal id.
Definition at line 460 of file blast_dbindex.cpp.
References ASSERT, r(), and CIndexedDb_New::volumes_.
Referenced by CIndexedDb_New::CheckOid(), CIndexedDb_New::GetResults(), and CIndexedDb_New::UpdateIndex().
◆ FirstAligned()
|
inline |
Is the query aligned.
Definition at line 201 of file magicblast.hpp.
References CMagicBlastResults::fUnaligned, and CMagicBlastResults::m_FirstInfo.
◆ FlattenBioseqSet()
| void FlattenBioseqSet | ( | const CBioseq_set & | bss, |
| list< CRef< CBioseq > > & | seqs | ||
| ) |
Definition at line 1278 of file remote_blast.cpp.
References _ASSERT, CBioseq_set_Base::CanGetSeq_set(), CSeq_entry_Base::GetSeq(), CBioseq_set_Base::GetSeq_set(), CSeq_entry_Base::GetSet(), CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), and ITERATE.
Referenced by CRemoteBlast::SetSubjectSequences(), and CExportStrategy::x_Process_Subject().
◆ FlushSequenceData()
| void ILocalQueryData::FlushSequenceData | ( | ) |
Frees the cached sequence data structure (as this is usually the larger data structure).
This is to be used in the context of query splitting, when the sequence data is only needed to set up global data structures, but not in the actual search.
Definition at line 148 of file query_data.cpp.
References ILocalQueryData::m_SeqBlk, and CBLAST_SequenceBlk::Reset().
Referenced by BlastSetupPreliminarySearchEx(), and CBlastPrelimSearch::Run().
◆ FrameNumber2NetworkFrame()
| EBlast4_frame_type FrameNumber2NetworkFrame | ( | int | frame, |
| EBlastProgramType | program | ||
| ) |
Converts the return value of CSeqLocInfo::GetFrame into the Blast4-frame-type field.
Note that for non-translated queries, this value should be set to notset (value = 0).
- Parameters
-
frame frame as specified by CSeqLocInfo::ETranslationFrame program CORE BLAST program type
Definition at line 1966 of file remote_blast.cpp.
References _ASSERT, _TROUBLE, abort(), Blast_QueryIsNucleotide(), Blast_QueryIsTranslated(), eBlast4_frame_type_minus1, eBlast4_frame_type_minus2, eBlast4_frame_type_minus3, eBlast4_frame_type_notset, eBlast4_frame_type_plus1, eBlast4_frame_type_plus2, and eBlast4_frame_type_plus3.
Referenced by CRemoteBlast::ConvertToRemoteMasks().
◆ Get() [1/32]
|
inline |
Get the value.
Definition at line 225 of file blast_options_builder.hpp.
Referenced by CBlastOptionsBuilder::GetDbFilteringAlgorithmId(), CBlastOptionsBuilder::GetDbFilteringAlgorithmKey(), CBlastOptionsBuilder::GetEntrezQuery(), CBlastOptionsBuilder::GetFinalDbSeq(), CBlastOptionsBuilder::GetFirstDbSeq(), CBlastOptionsBuilder::GetNegativeTaxidList(), CBlastOptionsBuilder::GetQueryMasks(), CBlastOptionsBuilder::GetSubjectMaskingType(), and CBlastOptionsBuilder::GetTaxidList().
◆ Get() [2/32]
|
inline |
Definition at line 309 of file blast_aux.hpp.
Referenced by BOOST_AUTO_TEST_CASE(), CObjMgr_LocalQueryData::GetSequenceBlk(), CObjMgrFree_LocalQueryData::GetSequenceBlk(), and InitializeBlastScoreBlk().
◆ Get() [3/32]
|
inline |
Definition at line 311 of file blast_aux.hpp.
Referenced by BOOST_AUTO_TEST_CASE(), CObjMgr_LocalQueryData::GetQueryInfo(), CObjMgrFree_LocalQueryData::GetQueryInfo(), SafeSetupQueryInfo(), SetupQueryInfo_OMF(), and CBlastExtendTestFixture::setupStructures().
◆ Get() [4/32]
|
inline |
Definition at line 312 of file blast_aux.hpp.
Referenced by CBlastOptionsMemento::CBlastOptionsMemento(), and CBlastOptionsLocal::x_Copy_CQuerySetUpOptions().
◆ Get() [5/32]
|
inline |
Definition at line 314 of file blast_aux.hpp.
Referenced by CBlastOptionsMemento::CBlastOptionsMemento(), and CBlastOptionsLocal::x_Copy_CLookupTableOptions().
◆ Get() [6/32]
|
inline |
Definition at line 315 of file blast_aux.hpp.
◆ Get() [7/32]
|
inline |
Definition at line 318 of file blast_aux.hpp.
Referenced by CBlastOptionsMemento::CBlastOptionsMemento(), and CBlastOptionsLocal::x_Copy_CBlastInitialWordOptions().
◆ Get() [8/32]
|
inline |
Definition at line 320 of file blast_aux.hpp.
◆ Get() [9/32]
|
inline |
Definition at line 322 of file blast_aux.hpp.
◆ Get() [10/32]
|
inline |
Definition at line 323 of file blast_aux.hpp.
Referenced by CBlastOptionsMemento::CBlastOptionsMemento(), and CBlastOptionsLocal::x_Copy_CBlastExtensionOptions().
◆ Get() [11/32]
|
inline |
Definition at line 324 of file blast_aux.hpp.
◆ Get() [12/32]
|
inline |
Definition at line 326 of file blast_aux.hpp.
Referenced by CBlastOptionsMemento::CBlastOptionsMemento(), and CBlastOptionsLocal::x_Copy_CBlastHitSavingOptions().
◆ Get() [13/32]
|
inline |
Definition at line 328 of file blast_aux.hpp.
◆ Get() [14/32]
|
inline |
Definition at line 330 of file blast_aux.hpp.
Referenced by CBlastOptionsMemento::CBlastOptionsMemento(), PsiBlastComputePssmFromAlignment(), CDeltaBlast::Run(), and CBlastOptionsLocal::x_Copy_CPSIBlastOptions().
◆ Get() [15/32]
|
inline |
Definition at line 331 of file blast_aux.hpp.
Referenced by CBlastOptionsMemento::CBlastOptionsMemento(), and CBlastOptionsLocal::x_Copy_CBlastDatabaseOptions().
◆ Get() [16/32]
|
inline |
Definition at line 333 of file blast_aux.hpp.
Referenced by BOOST_AUTO_TEST_CASE(), s_TestCreatePssmFromFreqs(), and CPssmEngine::SetUngappedStatisticalParams().
◆ Get() [17/32]
|
inline |
Definition at line 334 of file blast_aux.hpp.
Referenced by CBlastOptionsMemento::CBlastOptionsMemento(), and CBlastOptionsLocal::x_Copy_CBlastScoringOptions().
◆ Get() [18/32]
|
inline |
Definition at line 335 of file blast_aux.hpp.
◆ Get() [19/32]
|
inline |
Definition at line 338 of file blast_aux.hpp.
Referenced by CBlastOptionsMemento::CBlastOptionsMemento(), and CBlastOptionsLocal::x_Copy_CBlastEffectiveLengthsOptions().
◆ Get() [20/32]
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inline |
Definition at line 340 of file blast_aux.hpp.
◆ Get() [21/32]
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inline |
Definition at line 342 of file blast_aux.hpp.
◆ Get() [22/32]
|
inline |
Definition at line 343 of file blast_aux.hpp.
◆ Get() [23/32]
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inline |
Definition at line 345 of file blast_aux.hpp.
◆ Get() [24/32]
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inline |
Definition at line 346 of file blast_aux.hpp.
◆ Get() [25/32]
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inline |
Definition at line 347 of file blast_aux.hpp.
◆ Get() [26/32]
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inline |
Definition at line 348 of file blast_aux.hpp.
◆ Get() [27/32]
|
inline |
Definition at line 350 of file blast_aux.hpp.
Referenced by BOOST_AUTO_TEST_CASE(), and CTracebackSearchTestFixture::x_Traceback().
◆ Get() [28/32]
|
inline |
Definition at line 351 of file blast_aux.hpp.
◆ Get() [29/32]
|
inline |
Definition at line 352 of file blast_aux.hpp.
Referenced by BOOST_AUTO_TEST_CASE(), CSetupFactory::CreateLookupTable(), and CSetupFactory::CreateScoreBlock().
◆ Get() [30/32]
|
inline |
Definition at line 354 of file blast_aux.hpp.
◆ Get() [31/32]
|
inline |
Definition at line 355 of file blast_aux.hpp.
◆ Get() [32/32]
|
inline |
Definition at line 357 of file blast_aux.hpp.
Referenced by CPrelimSearchThread::CPrelimSearchThread(), CBlastTracebackSearch::Run(), CBlastTracebackSearch::RunSimple(), and SplitQuery_CreateChunkData().
◆ GetAbsoluteContext()
Get the context number in the absolute (i.e.
: unsplit) query
- Parameters
-
chunk_num Chunk number where the context is found in the split query [in] context_in_chunk Context in the split query [in]
- Returns
- the appropriate context, or if the context is invalid kInvalidContext
Definition at line 242 of file split_query_aux_priv.cpp.
References _ASSERT, CContextTranslator::m_ContextsPerChunk, and ncbi::grid::netcache::search::fields::size.
Referenced by CContextTranslator::CContextTranslator(), CContextTranslator::GetStartingChunk(), CQuerySplitter::x_ComputeContextOffsets_NonTranslatedQueries(), CQuerySplitter::x_ComputeContextOffsets_TranslatedQueries(), and CSplitQueryTestFixture::x_TestCContextTranslator().
◆ GetAlgoOptions()
| objects::CBlast4_parameters * CImportStrategy::GetAlgoOptions | ( | ) |
Options specific to blast searches (e.g, threshold, expect value).
- Returns
- the algorithm options or NULL if unavailable
Definition at line 231 of file search_strategy.cpp.
References CBlast4_queue_search_request_Base::CanGetAlgorithm_options(), CImportStrategy::m_Request, NULL, and CBlast4_queue_search_request_Base::SetAlgorithm_options().
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetAlignments()
| CRef< objects::CSeq_align_set > CRemoteBlast::GetAlignments | ( | void | ) |
Get the seqalign set from the results.
This method returns the alignment data as a seq align set. If this search contains multiple queries, this method will return all data as a single set. Most users will probably prefer to call GetSeqAlignSets() in this case.
- Returns
- Reference to a seqalign set.
Definition at line 392 of file remote_blast.cpp.
References CRemoteBlast::x_GetGSRR().
Referenced by BOOST_AUTO_TEST_CASE(), and CRemoteBlast::GetSeqAlignSets().
◆ GetAncillaryData()
|
inline |
Accessor for the query's search ancillary.
Definition at line 212 of file blast_results.hpp.
References CSearchResults::m_AncillaryData.
Referenced by CBlastFormat::PrintPhiResult(), CIgBlast::x_ConvertResultType(), and CPsiBlastApp::x_RunLocalPsiBlastIterations().
◆ GetAncillaryResults()
|
inline |
Get the ancillary results for a BLAST search (to be used with the Run() method)
- Parameters
-
retval the return value of this method [in|out]
Definition at line 311 of file bl2seq.hpp.
References CBl2Seq::m_AncillaryData.
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetAvgLength() [1/2]
|
inline |
Returns average length.
Definition at line 91 of file seqsrc_multiseq.cpp.
References CMultiSeqInfo::m_iAvgLength.
◆ GetAvgLength() [2/2]
|
inline |
Returns average length.
Definition at line 174 of file seqsrc_query_factory.cpp.
References CQueryFactoryInfo::m_AvgLength.
◆ GetBestHitOverhang() [1/2]
| double CBlastOptions::GetBestHitOverhang | ( | ) | const |
Definition at line 1868 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetBestHitOverhang(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetBestHitOverhang() [2/2]
|
inline |
Definition at line 1374 of file blast_options_local_priv.hpp.
References BlastHSPFilteringOptions::best_hit, BlastHitSavingOptions::hsp_filt_opt, kBestHit_OverhangMin, CBlastOptionsLocal::m_HitSaveOpts, and BlastHSPBestHitOptions::overhang.
Referenced by CBlastOptions::GetBestHitOverhang().
◆ GetBestHitScoreEdge() [1/2]
| double CBlastOptions::GetBestHitScoreEdge | ( | ) | const |
Definition at line 1887 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetBestHitScoreEdge(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetBestHitScoreEdge() [2/2]
|
inline |
Definition at line 1344 of file blast_options_local_priv.hpp.
References BlastHSPFilteringOptions::best_hit, BlastHitSavingOptions::hsp_filt_opt, kBestHit_ScoreEdgeMin, CBlastOptionsLocal::m_HitSaveOpts, and BlastHSPBestHitOptions::score_edge.
Referenced by CBlastOptions::GetBestHitScoreEdge().
◆ GetBioseqSet() [1/3]
|
virtual |
Accessor for the CBioseq_set.
Implements IRemoteQueryData.
Definition at line 295 of file objmgr_query_data.cpp.
References abort(), CRef< C, Locker >::Empty(), IRemoteQueryData::m_Bioseqs, CObjMgr_RemoteQueryData::m_Queries, CObjMgr_RemoteQueryData::m_QueryVector, CRef< C, Locker >::NotEmpty(), CRef< C, Locker >::Reset(), s_QueryVectorToBioseqSet(), and s_TSeqLocVectorToBioseqSet().
◆ GetBioseqSet() [2/3]
|
virtual |
Accessor for the CBioseq_set.
Implements IRemoteQueryData.
Definition at line 203 of file objmgrfree_query_data.cpp.
References CRef< C, Locker >::Empty(), IRemoteQueryData::m_Bioseqs, CObjMgrFree_RemoteQueryData::m_ClientBioseqSet, NCBI_CURRENT_FUNCTION, NCBI_THROW, CConstRef< C, Locker >::NotEmpty(), and CRef< C, Locker >::Reset().
◆ GetBioseqSet() [3/3]
|
pure virtual |
Accessor for the CBioseq_set.
Implemented in CObjMgrFree_RemoteQueryData, and CObjMgr_RemoteQueryData.
Referenced by CQueryFactoryInfo::CQueryFactoryInfo(), CLocalDbAdapter::MakeSeqInfoSrc(), CRemoteBlast::SetSubjectSequences(), CRemoteBlast::x_InitQueries(), CExportStrategy::x_Process_Query(), CExportStrategy::x_Process_Subject(), CRemoteSeqSearch::x_RemoteBlast(), and CSequenceDataTester::x_TestSingleSequence_Remote().
◆ GetBlast4AlgoOpts() [1/2]
| CBlastOptions::TBlast4Opts * CBlastOptions::GetBlast4AlgoOpts | ( | ) |
Definition at line 2563 of file blast_options_cxx.cpp.
References CBlastOptionsRemote::GetBlast4AlgoOpts(), CBlastOptions::m_Remote, and result.
Referenced by BOOST_AUTO_TEST_CASE(), CRemoteBlast::x_Init(), and CExportStrategy::x_Process_BlastOptions().
◆ GetBlast4AlgoOpts() [2/2]
|
inline |
Definition at line 89 of file blast_options_cxx.cpp.
References CBlastOptionsRemote::m_ReqOpts.
Referenced by CBlastOptions::GetBlast4AlgoOpts().
◆ GetBlastDbLoaderName()
|
inline |
Definition at line 127 of file blast_input_unit_test_aux.hpp.
References CBlastScopeSourceWrapper::m_ScopeSrc.
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetBlastSequence() [1/3]
|
virtual |
Return the sequence data for a sequence.
- Parameters
-
i index of the sequence in the sequence container [in] encoding desired encoding [in] strand strand to fetch [in] sentinel specifies to use or not to use sentinel bytes around sequence data. Note that this is ignored for proteins, as in the CORE of BLAST, proteins always have sentinel bytes [in] warnings if not NULL, warnings will be returned in this string [in|out]
- Returns
- SBlastSequence structure containing sequence data requested
Definition at line 308 of file blast_objmgr_tools.cpp.
References CBlastQueryVector::GetQuerySeqLoc(), CBlastQueryVector::GetScope(), GetSequence(), i, CBlastQuerySourceOM::m_QueryVector, CBlastQuerySourceOM::m_TSeqLocVector, and CRef< C, Locker >::NotEmpty().
◆ GetBlastSequence() [2/3]
|
pure virtual |
Return the sequence data for a sequence.
- Parameters
-
index index of the sequence in the sequence container [in] encoding desired encoding [in] strand strand to fetch [in] sentinel specifies to use or not to use sentinel bytes around sequence data. Note that this is ignored for proteins, as in the CORE of BLAST, proteins always have sentinel bytes [in] warnings if not NULL, warnings will be returned in this string [in|out]
- Returns
- SBlastSequence structure containing sequence data requested
Referenced by SetupQueries_OMF(), and SetupSubjects_OMF().
◆ GetBlastSequence() [3/3]
|
virtual |
Return the sequence data for a sequence.
- Parameters
-
index index of the sequence in the sequence container [in] encoding desired encoding [in] strand strand to fetch [in] sentinel specifies to use or not to use sentinel bytes around sequence data [in] warnings if not NULL, warnings will be returned in this string [in|out]
- Returns
- SBlastSequence structure containing sequence data requested
Definition at line 311 of file bioseq_extract_data_priv.cpp.
References GetSequence_OMF(), CBlastQuerySourceBioseqSet::m_Bioseqs, and NCBI_THROW.
Referenced by PsiBlastComputePssmFromAlignment().
◆ GetCandidateSeqs()
|
inline |
Gets the max number of candidate matches to process with BLAST.
Definition at line 82 of file blastp_kmer_options.hpp.
Referenced by BOOST_AUTO_TEST_CASE(), CBlastKmerThread::Main(), and CBlastKmerSearch::Run().
◆ GetChaining() [1/2]
| bool CBlastOptions::GetChaining | ( | void | ) | const |
Definition at line 1750 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetChaining(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
◆ GetChaining() [2/2]
|
inline |
Definition at line 1256 of file blast_options_local_priv.hpp.
References BlastExtensionOptions::chaining, and CBlastOptionsLocal::m_ExtnOpts.
Referenced by CBlastOptions::GetChaining().
◆ GetChaning()
|
inline |
Returns true if chaining is enabled, false otherwise.
Definition at line 131 of file blast_prot_options.hpp.
◆ GetChunkBounds()
| TChunkRange CSplitQueryBlk::GetChunkBounds | ( | size_t | chunk_num | ) | const |
Get the boundaries of a chunk in the concatenated query.
- Parameters
-
chunk_num desired chunk [in]
Definition at line 135 of file split_query_blk.cpp.
References CSplitQueryBlk::m_SplitQueryBlk, COpenRange< Position >::SetOpen(), and SplitQueryBlk_GetChunkBounds().
Referenced by CQuerySplitter::x_ComputeQueryIndicesForChunks(), and CSplitQueryTestFixture::x_ValidateChunkBounds().
◆ GetChunkOverlapSize()
| size_t CSplitQueryBlk::GetChunkOverlapSize | ( | ) | const |
Gets the size (# of bases/residues) of overlap between query chunks.
Definition at line 210 of file split_query_blk.cpp.
References ERR_POST, CSplitQueryBlk::m_SplitQueryBlk, SplitQueryBlk_GetChunkOverlapSize(), and Warning().
◆ GetChunkSize()
|
inline |
Returns the number of bases/residues that make up a query chunk.
Definition at line 82 of file split_query.hpp.
References CQuerySplitter::m_ChunkSize.
Referenced by BOOST_AUTO_TEST_CASE(), CSplitQueryTestFixture::QuerySplitter_BlastnMultiQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastnSingleQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastxMultiQueryMultiChunk(), and CSplitQueryTestFixture::QuerySplitter_BlastxSingleQueryMultiChunk().
◆ GetClientId()
|
inline |
Retrieves the client ID used by this object to send requests.
Definition at line 461 of file remote_blast.hpp.
References CRemoteBlast::m_ClientId.
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetComplexityAdjMode() [1/3]
| bool CBlastOptions::GetComplexityAdjMode | ( | ) | const |
Returns true if cross_match-like complexity adjusted.
Definition at line 2117 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetComplexityAdjMode(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CBlastOptionsHandle::GetComplexityAdjMode().
◆ GetComplexityAdjMode() [2/3]
|
inline |
Returns Complexity Adjustment Mode -RMH-.
Definition at line 294 of file blast_options_handle.hpp.
References CBlastOptions::GetComplexityAdjMode(), and CBlastOptionsHandle::m_Opts.
◆ GetComplexityAdjMode() [3/3]
|
inline |
Returns true if cross_match-like complexity adjusted.
Definition at line 1608 of file blast_options_local_priv.hpp.
References BlastScoringOptions::complexity_adjusted_scoring, CBlastOptionsLocal::m_ScoringOpts, and true.
Referenced by CBlastOptions::GetComplexityAdjMode().
◆ GetCompositionBasedStats() [1/5]
|
inline |
Returns this mode, which mostly specifies whether composition of db sequence is taken into account when calculating expect values.
Definition at line 70 of file blast_advprot_options.hpp.
Referenced by BOOST_FIXTURE_TEST_CASE(), CDeltaBlastTestFixture::CDeltaBlastTestFixture(), and CPsiBlastTestFixture::CPsiBlastTestFixture().
◆ GetCompositionBasedStats() [2/5]
| ECompoAdjustModes CBlastOptions::GetCompositionBasedStats | ( | void | ) | const |
Definition at line 1645 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetCompositionBasedStats(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by BOOST_AUTO_TEST_CASE(), CheckForFreqRatioFile(), CSetupFactory::CreateRpsStructures(), LogBlastOptions(), and CPsiBlastApp::Run().
◆ GetCompositionBasedStats() [3/5]
|
inline |
Returns this mode, which mostly specifies whether composition of db sequence is taken into account when calculating expect values.
Definition at line 104 of file blastx_options.hpp.
◆ GetCompositionBasedStats() [4/5]
|
inline |
Definition at line 1190 of file blast_options_local_priv.hpp.
References BlastExtensionOptions::compositionBasedStats, and CBlastOptionsLocal::m_ExtnOpts.
Referenced by CBlastOptions::GetCompositionBasedStats().
◆ GetCompositionBasedStats() [5/5]
|
inline |
Get composition based statistics mode.
- Returns
- True if composition based statistics mode is enabled, false otherwise
Definition at line 105 of file blast_rps_options.hpp.
References eNoCompositionBasedStats.
◆ GetCompressedPlusStrand() [1/3]
|
virtual |
@inheritDoc
Implements IBlastSeqVector.
Definition at line 173 of file bioseq_extract_data_priv.cpp.
References SBlastSequence::data, CSeq_data_Base::e_Ncbi2na, AutoPtr< X, Del >::get(), i, ITERATE, CBlastSeqVectorFromCSeq_data::m_SequenceData, CBlastSeqVectorFromCSeq_data::SetCoding(), and IBlastSeqVector::size().
◆ GetCompressedPlusStrand() [2/3]
|
inlinevirtual |
@inheritDoc
Implements IBlastSeqVector.
Definition at line 515 of file blast_objmgr_tools.cpp.
References CSeqVector::begin(), SBlastSequence::data, CSeqVector::end(), AutoPtr< X, Del >::get(), CSeqVector::GetSeqData(), kEmptyStr, CBlastSeqVectorOM::m_SeqVector, s_Ncbi4naToNcbi2na(), and IBlastSeqVector::size().
◆ GetCompressedPlusStrand() [3/3]
|
pure virtual |
Returns the compressed nucleotide data for the plus strand, still occupying one base per byte.
Implemented in CBlastSeqVectorOM, and CBlastSeqVectorFromCSeq_data.
Referenced by GetSequenceCompressedNucleotide().
◆ GetContextInChunk()
Get the context number in the split query chunk.
This function is basically doing the reverse lookup that GetAbsoluteContext does
- Parameters
-
chunk_num Chunk number to search for this context [in] absolute_context context number in the absolute (i.e.: unsplit) query [in]
- Returns
- the appropriate context if found, else kInvalidContext
- See also
- GetAbsoluteContext
Definition at line 251 of file split_query_aux_priv.cpp.
References _ASSERT, kInvalidContext, and CContextTranslator::m_ContextsPerChunk.
Referenced by CContextTranslator::GetStartingChunk(), and s_GetAbsoluteContextLength().
◆ GetContextOffsets()
| vector< size_t > CSplitQueryBlk::GetContextOffsets | ( | size_t | chunk_num | ) | const |
Get the context offsets (corrections) of the queries contained in a given chunk.
- Parameters
-
chunk_num desired chunk [in]
Definition at line 117 of file split_query_blk.cpp.
References i, CSplitQueryBlk::m_SplitQueryBlk, NULL, sfree, SplitQueryBlk_GetContextOffsetsForChunk(), and UINT4_MAX.
Referenced by operator<<(), CQuerySplitter::x_ComputeContextOffsets_TranslatedQueries(), CSplitQueryTestFixture::x_TestCContextTranslator(), and CSplitQueryTestFixture::x_ValidateContextOffsetsPerChunkAssignment().
◆ GetCreatedBy() [1/2]
| string CRemoteBlast::GetCreatedBy | ( | ) |
Get the created-by string associated with this search.
The created by string for this search will be returned.
- Returns
- The value of the created-by string.
Definition at line 1909 of file remote_blast.cpp.
References CRemoteBlast::m_CreatedBy, and CRemoteBlast::x_GetRequestInfo().
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetCreatedBy() [2/2]
| string CImportStrategy::GetCreatedBy | ( | ) | const |
Returns ident field from a Blast4-request.
Definition at line 165 of file search_strategy.cpp.
References CImportStrategy::m_Request.
◆ GetCStruct()
| SSplitQueryBlk * CSplitQueryBlk::GetCStruct | ( | ) | const |
Returns the C structure managed by objects of this class.
- Note
- the caller of this method does NOT own the returned structure
Definition at line 194 of file split_query_blk.cpp.
References CSplitQueryBlk::m_SplitQueryBlk.
Referenced by BOOST_AUTO_TEST_CASE(), and CBlastPrelimSearch::Run().
◆ GetCullingLimit() [1/3]
| int CBlastOptions::GetCullingLimit | ( | ) | const |
Definition at line 1829 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetCullingLimit(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CBlastOptionsHandle::GetCullingLimit().
◆ GetCullingLimit() [2/3]
|
inline |
Returns Culling limit.
Definition at line 282 of file blast_options_handle.hpp.
References CBlastOptions::GetCullingLimit(), and CBlastOptionsHandle::m_Opts.
Referenced by BOOST_FIXTURE_TEST_CASE().
◆ GetCullingLimit() [3/3]
|
inline |
Definition at line 1306 of file blast_options_local_priv.hpp.
References _ASSERT, BlastHitSavingOptions::culling_limit, BlastHSPFilteringOptions::culling_opts, BlastHitSavingOptions::hsp_filt_opt, CBlastOptionsLocal::m_HitSaveOpts, BlastHSPCullingOptions::max_hits, and NULL.
Referenced by CBlastOptions::GetCullingLimit().
◆ GetCutoffScore() [1/4]
| int CBlastOptions::GetCutoffScore | ( | ) | const |
Definition at line 1925 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetCutoffScore(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CBlastOptionsHandle::GetCutoffScore().
◆ GetCutoffScore() [2/4]
|
inline |
Returns CutoffScore.
Definition at line 252 of file blast_options_handle.hpp.
References CBlastOptions::GetCutoffScore(), and CBlastOptionsHandle::m_Opts.
Referenced by BOOST_FIXTURE_TEST_CASE().
◆ GetCutoffScore() [3/4]
|
inline |
Return a single alignment cutoff score.
Definition at line 174 of file magicblast_options.hpp.
◆ GetCutoffScore() [4/4]
|
inline |
Definition at line 1444 of file blast_options_local_priv.hpp.
References BlastHitSavingOptions::cutoff_score, and CBlastOptionsLocal::m_HitSaveOpts.
Referenced by CBlastOptions::GetCutoffScore().
◆ GetCutoffScoreCoeffs() [1/3]
|
inline |
Get coefficients for alignment cutoff score as a linear function of query length: x[0] + x[1] * length.
Definition at line 182 of file magicblast_options.hpp.
◆ GetCutoffScoreCoeffs() [2/3]
| vector< double > CBlastOptions::GetCutoffScoreCoeffs | ( | ) | const |
Definition at line 1944 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetCutoffScoreCoeffs(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
◆ GetCutoffScoreCoeffs() [3/3]
|
inline |
Definition at line 1456 of file blast_options_local_priv.hpp.
References BlastHitSavingOptions::cutoff_score_fun, and CBlastOptionsLocal::m_HitSaveOpts.
Referenced by CBlastOptions::GetCutoffScoreCoeffs().
◆ GetData() [1/7]
|
inlinevirtual |
Obtain the multiple sequence alignment structure.
Implements IPssmInputData.
Definition at line 96 of file msa_pssm_input.hpp.
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetData() [2/7]
|
inlinevirtual |
Obtain a matrix of frequency ratios with this->GetQueryLength() columns and BLASTAA_SIZE rows.
Implements IPssmInputFreqRatios.
Definition at line 132 of file psi_pssm_input.hpp.
◆ GetData() [3/7]
|
inlinevirtual |
Obtain the multiple sequence alignment structure.
Implements IPssmInputData.
Definition at line 195 of file psi_pssm_input.cpp.
References CPsiBlastInputData::m_Msa.
◆ GetData() [4/7]
|
pure virtual |
Obtain the multiple sequence alignment structure.
Implemented in SU_PSSMInput, CNullPssmInput, CPssmInputFlankingGaps, CdPssmInput, CPsiBlastInputData, and CPsiBlastInputClustalW.
Referenced by s_Validate(), and CPssmEngine::x_CreatePssmFromMsa().
◆ GetData() [5/7]
|
pure virtual |
Obtain a matrix of frequency ratios with this->GetQueryLength() columns and BLASTAA_SIZE rows.
Implemented in CPsiBlastInputFreqRatios.
Referenced by s_CheckAgainstNullData(), s_Validate(), and CPssmEngine::x_CreatePssmFromFreqRatios().
◆ GetData() [6/7]
|
inlinevirtual |
Get data for PSSM computation.
- Returns
- Data for PSSM computation
Implements IPssmInputCdd.
Definition at line 160 of file cdd_pssm_input.hpp.
References CCddInputData::m_CddData.
◆ GetData() [7/7]
|
pure virtual |
Get CD data for PSSM computation.
Implemented in CPssmInputWithNoCDs, and CCddInputData.
Referenced by s_Validate(), and CPssmEngine::x_CreatePssmFromCDD().
◆ GetDatabaseInfo() [1/2]
| vector< CRef< objects::CBlast4_database_info > > CBlastServices::GetDatabaseInfo | ( | const string & | dbname, |
| bool | is_protein, | ||
| bool * | found_all, | ||
| vector< string > * | missing_names = NULL |
||
| ) |
Retrieve detailed information for databases listed in the string.
If more than one database is supplied, it they should be separated by spaces (e.g., "nt wgs est").
- Parameters
-
dbname string listing the database(s) is_protein is a protein for true, otherwise dna found_all true if all databases were found. missing_names pointer to an array with missing database(s)
- Returns
- Detailed information for the requested BLAST databases or an empty vector if no databases were found.
Definition at line 474 of file blast_services.cpp.
References CBlast4Client_Base::Ask(), dbname(), Get(), CBlastServices::GetDatabaseInfoLegacy(), NCBI_THROW, CRef< C, Locker >::Reset(), CBlast4_request_Base::SetBody(), CBlast4_request_body_Base::SetGet_databases_ex(), NStr::Split(), and NStr::TruncateSpaces().
◆ GetDatabaseInfo() [2/2]
| CRef< objects::CBlast4_database_info > CBlastServices::GetDatabaseInfo | ( | CRef< objects::CBlast4_database > | blastdb | ) |
Retrieve detailed information for one BLAST database If information about multiple databases is needed, use the other GetDatabaseInfo method.
- Parameters
-
blastdb object describing the database for which to get detailed information
- Returns
- Detailed information for the requested BLAST database or an empty object is the requested database wasn't found
Definition at line 422 of file blast_services.cpp.
References CRef< C, Locker >::Empty(), CBlastServices::m_AvailableDatabases, NCBI_THROW, CBlastServices::x_FindDbInfoFromAvailableDatabases(), and CBlastServices::x_GetAvailableDatabases().
Referenced by BOOST_AUTO_TEST_CASE(), CAlignFormatUtil::GetBlastDbInfo(), CBlastServices::GetDatabaseInfoLegacy(), and CBlastServices::IsValidBlastDb().
◆ GetDatabaseInfoLegacy()
| vector< CRef< objects::CBlast4_database_info > > CBlastServices::GetDatabaseInfoLegacy | ( | const string & | dbname, |
| bool | is_protein, | ||
| bool * | found_all, | ||
| vector< string > * | missing_names = NULL |
||
| ) |
Same as GetDatabaseInfo but retrieving whole list of database.
Definition at line 438 of file blast_services.cpp.
References dbname(), eBlast4_residue_type_nucleotide, eBlast4_residue_type_protein, CBlastServices::GetDatabaseInfo(), CBlast4_database_Base::GetName(), i, ITERATE, result, CBlast4_database_Base::SetName(), CBlast4_database_Base::SetType(), NStr::Split(), and NStr::TruncateSpaces().
Referenced by CBlastServices::GetDatabaseInfo().
◆ GetDatabaseName() [1/2]
|
inline |
Returns the database name if appropriate, else kEmptyStr for subject sequences.
Definition at line 121 of file local_db_adapter.hpp.
References CLocalDbAdapter::m_DbName.
Referenced by CIgBlastnApp::CIgFormatter::Main(), CDeltaBlast::Run(), CDeltaBlastApp::Run(), CIgBlastnApp::Run(), CIgBlastpApp::Run(), CBlastKmerSearch::Run(), and CIgBlast::x_AnnotateDomain().
◆ GetDatabaseName() [2/2]
| string CSearchDatabase::GetDatabaseName | ( | ) | const |
Accessor for the database name.
Definition at line 70 of file uniform_search.cpp.
References CSearchDatabase::m_DbName.
Referenced by CBlastDatabaseArgs::GetDatabaseName(), InitializeSubject(), s_InitializeSubject(), CRemoteBlast::x_Init(), CMagicBlastApp::x_LogBlastSearchInfo(), CExportStrategy::x_Process_SearchDb(), CRemoteSeqSearch::x_RemoteBlast(), CRemotePssmSearch::x_RemoteBlast(), and CSearchDatabase::x_ValidateMaskingAlgorithm().
◆ GetDatabases()
| CRef< CBlast4_database > CRemoteBlast::GetDatabases | ( | ) |
Get the database used by the search.
An object is returned, describing the name and type of database used as the subject of this search.
- Returns
- An object describing the searched database(s).
Definition at line 1837 of file remote_blast.cpp.
References CRef< C, Locker >::Empty(), CRemoteBlast::m_Dbs, and CRemoteBlast::x_GetRequestInfo().
Referenced by BOOST_AUTO_TEST_CASE(), CBlastFormatterApp::PrintFormattedOutput(), and CBlastFormatterVdbApp::PrintFormattedOutput().
◆ GetDbFilteringAlgorithmId() [1/2]
| int CBlastOptionsBuilder::GetDbFilteringAlgorithmId | ( | ) |
Get the database filtering algorithm ID.
Definition at line 742 of file blast_options_builder.cpp.
References CBlastOptionsBuilder::SOptional< T >::Get(), and CBlastOptionsBuilder::m_DbFilteringAlgorithmId.
Referenced by CRemoteBlast::GetSearchOptions(), and s_ImportDatabase().
◆ GetDbFilteringAlgorithmId() [2/2]
|
inline |
Returns the filtering algorithm ID used in the database.
Definition at line 446 of file remote_blast.hpp.
References CRemoteBlast::m_DbFilteringAlgorithmId.
Referenced by BOOST_AUTO_TEST_CASE(), and CBlastFormatterApp::PrintFormattedOutput().
◆ GetDbFilteringAlgorithmKey() [1/2]
| string CBlastOptionsBuilder::GetDbFilteringAlgorithmKey | ( | ) |
Get the database filtering algorithm key.
Definition at line 752 of file blast_options_builder.cpp.
References CBlastOptionsBuilder::SOptional< T >::Get(), and CBlastOptionsBuilder::m_DbFilteringAlgorithmKey.
Referenced by CRemoteBlast::GetSearchOptions(), and s_ImportDatabase().
◆ GetDbFilteringAlgorithmKey() [2/2]
|
inline |
Returns the filtering algorithm key used in the database.
Definition at line 451 of file remote_blast.hpp.
References CRemoteBlast::m_DbFilteringAlgorithmKey.
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetDBFilteringID()
| int CImportStrategy::GetDBFilteringID | ( | ) |
The DB filter ID.
Definition at line 180 of file search_strategy.cpp.
References CImportStrategy::FetchData(), and CImportStrategy::m_Data.
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetDBFilteringKey()
| string CImportStrategy::GetDBFilteringKey | ( | ) |
The DB filter key.
Definition at line 189 of file search_strategy.cpp.
References CImportStrategy::FetchData(), and CImportStrategy::m_Data.
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetDbGeneticCode() [1/5]
| int CBlastOptions::GetDbGeneticCode | ( | ) | const |
Definition at line 2402 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetDbGeneticCode(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CBlastnNode::Main(), CBlastpNode::Main(), CBlastxNode::Main(), CRPSBlastNode::Main(), CRPSTBlastnNode::Main(), CTblastnNode::Main(), CIgBlastnApp::CIgFormatter::Main(), CBlastFormatterApp::PrintFormattedOutput(), CDeltaBlastApp::Run(), CPsiBlastApp::Run(), CTblastxApp::Run(), CIgBlastnApp::Run(), CIgBlastpApp::Run(), CRMBlastnApp::Run(), CBlastnApp::x_RunMTBySplitDB(), CBlastpApp::x_RunMTBySplitDB(), CBlastxApp::x_RunMTBySplitDB(), CRPSBlastApp::x_RunMTBySplitDB(), CRPSTBlastnApp::x_RunMTBySplitDB(), and CTblastnApp::x_RunMTBySplitDB().
◆ GetDbGeneticCode() [2/5]
|
inline |
Returns DbGeneticCode.
Definition at line 63 of file rpstblastn_options.hpp.
◆ GetDbGeneticCode() [3/5]
|
inline |
Returns DbGeneticCode.
Definition at line 84 of file tblastn_options.hpp.
◆ GetDbGeneticCode() [4/5]
|
inline |
Returns DbGeneticCode.
Definition at line 77 of file tblastx_options.hpp.
◆ GetDbGeneticCode() [5/5]
|
inline |
Definition at line 1754 of file blast_options_local_priv.hpp.
References BlastDatabaseOptions::genetic_code, and CBlastOptionsLocal::m_DbOpts.
Referenced by CBlastOptions::GetDbGeneticCode().
◆ GetDbIndexRunSearchFn()
| DbIndexRunSearchFnType GetDbIndexRunSearchFn | ( | ) |
Return the appropriate callback to run indexed seed search.
- Returns
- No-op function if indexing is not being used; otherwise - the appropriate callback.
Definition at line 1199 of file blast_dbindex.cpp.
References RunSearchFn.
Referenced by CBlastPrelimSearch::Run().
◆ GetDbIndexSetNumThreadsFn()
| DbIndexSetNumThreadsFnType GetDbIndexSetNumThreadsFn | ( | ) |
Return the appropriate callback to set the number of threads in the index structure.
- Returns
- No-op function if indexing is not used; otherwise - the appropriate callback.
Definition at line 1195 of file blast_dbindex.cpp.
References SetNumThreadsFn.
Referenced by CBlastPrelimSearch::x_LaunchMultiThreadedSearch().
◆ GetDbIndexSetQueryInfoFn()
| DbIndexSetQueryInfoFnType GetDbIndexSetQueryInfoFn | ( | ) |
Return the appropriate callback to set query information in the index.
- Returns
- No-op function if indexing is not being used; otherwise - the appropriate callback.
Definition at line 1198 of file blast_dbindex.cpp.
References SetQueryInfoFn.
Referenced by CSetupFactory::CreateLookupTable().
◆ GetDbIndexSetUsingThreadsFn()
| DbIndexSetUsingThreadsFnType GetDbIndexSetUsingThreadsFn | ( | ) |
Return the appropriate callback to set the concurrency state in the index structure.
- Returns
- No-op function if indexing is not used; otherwise - the appropriate callback.
Definition at line 1192 of file blast_dbindex.cpp.
References SetUsingThreadsFn.
Referenced by CBlastPrelimSearch::Run().
◆ GetDbLength() [1/3]
| Int8 CBlastOptions::GetDbLength | ( | ) | const |
Definition at line 2332 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetDbLength(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by BOOST_AUTO_TEST_CASE(), CBlastOptionsHandle::GetDbLength(), and CLocalVDBBlast::x_AdjustDbSize().
◆ GetDbLength() [2/3]
|
inline |
Returns DbLength.
Definition at line 306 of file blast_options_handle.hpp.
References CBlastOptions::GetDbLength(), and CBlastOptionsHandle::m_Opts.
Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), and CBlastKmerSearch::Run().
◆ GetDbLength() [3/3]
|
inline |
Definition at line 1695 of file blast_options_local_priv.hpp.
References BlastEffectiveLengthsOptions::db_length, and CBlastOptionsLocal::m_EffLenOpts.
Referenced by CBlastOptions::GetDbLength().
◆ GetDbName()
Getter functions for the private fields.
Definition at line 582 of file seqsrc_seqdb.cpp.
Referenced by s_SeqDbSrcNew().
◆ GetDbOpts() [1/2]
|
private |
Returns BlastDatabaseOptions for eLocal objects, NULL for eRemote.
Definition at line 2682 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetDbOpts(), and CBlastOptions::m_Local.
Referenced by CTracebackTestFixture::x_ComputeTracebak().
◆ GetDbOpts() [2/2]
|
inlineprivate |
Definition at line 450 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_DbOpts.
Referenced by CBlastOptions::GetDbOpts(), and CBlastOptionsLocal::SetProgram().
◆ GetDbSeqNum() [1/3]
| unsigned int CBlastOptions::GetDbSeqNum | ( | ) | const |
Definition at line 2351 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetDbSeqNum(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CBlastOptionsHandle::GetDbSeqNum().
◆ GetDbSeqNum() [2/3]
|
inline |
Returns DbSeqNum.
Definition at line 312 of file blast_options_handle.hpp.
References CBlastOptions::GetDbSeqNum(), and CBlastOptionsHandle::m_Opts.
Referenced by BOOST_FIXTURE_TEST_CASE().
◆ GetDbSeqNum() [3/3]
|
inline |
Definition at line 1707 of file blast_options_local_priv.hpp.
References BlastEffectiveLengthsOptions::dbseq_num, and CBlastOptionsLocal::m_EffLenOpts.
Referenced by CBlastOptions::GetDbSeqNum().
◆ GetDbType()
|
inline |
Returns database type: protein or nucleotide.
Definition at line 584 of file seqsrc_seqdb.cpp.
Referenced by s_SeqDbSrcNew().
◆ GetDefaultsMode() [1/2]
|
inline |
Definition at line 143 of file blast_options_cxx.cpp.
References CBlastOptionsRemote::m_DefaultsMode.
Referenced by CBlastOptions::GetDefaultsMode().
◆ GetDefaultsMode() [2/2]
| bool CBlastOptions::GetDefaultsMode | ( | ) | const |
Definition at line 2712 of file blast_options_cxx.cpp.
References CBlastOptionsRemote::GetDefaultsMode(), and CBlastOptions::m_Remote.
Referenced by CDiscNucleotideOptionsHandle::SetMBInitialWordOptionsDefaults(), and CDiscNucleotideOptionsHandle::SetMBLookupTableDefaults().
◆ GetDiagnostics() [1/2]
| BlastDiagnostics * CLocalBlast::GetDiagnostics | ( | ) |
Get the diagnostics structure (deep copy, needs to be deleted by caller)
Definition at line 308 of file local_blast.cpp.
References Blast_DiagnosticsCopy(), SInternalData::m_Diagnostics, CLocalBlast::m_InternalData, and NULL.
◆ GetDiagnostics() [2/2]
|
inline |
Retrieves the diagnostics information returned from the engine.
Definition at line 290 of file bl2seq.hpp.
References CBl2Seq::mi_pDiagnostics.
Referenced by testBlastHitCounts(), and testRawCutoffs().
◆ GetDiagnosticsRequest() [1/5]
|
inlinevirtual |
Obtain the diagnostics data that is requested from the PSSM engine.
Reimplemented from IPssmInputData.
Definition at line 125 of file msa_pssm_input.hpp.
◆ GetDiagnosticsRequest() [2/5]
|
inlinevirtual |
Obtain the diagnostics data that is requested from the PSSM engine.
Reimplemented from IPssmInputData.
Definition at line 229 of file psi_pssm_input.cpp.
References CPsiBlastInputData::m_DiagnosticsRequest.
◆ GetDiagnosticsRequest() [3/5]
|
inlinevirtual |
Obtain the diagnostics data that is requested from the PSSM engine Its results will be populated in the PssmWithParameters ASN.1 object.
Reimplemented in SU_PSSMInput, CNullPssmInput, CPssmInputFlankingGaps, CdPssmInput, CPsiBlastInputData, and CPsiBlastInputClustalW.
Definition at line 123 of file pssm_input.hpp.
References NULL.
Referenced by CPssmEngine::x_CreatePssmFromMsa().
◆ GetDiagnosticsRequest() [4/5]
|
inlinevirtual |
Get diagnostics options.
Reimplemented in CCddInputData.
Definition at line 85 of file cdd_pssm_input.hpp.
References NULL.
Referenced by CPssmEngine::x_CreatePssmFromCDD().
◆ GetDiagnosticsRequest() [5/5]
|
inlinevirtual |
Get options for PSSM engine diagnostics.
- Returns
- PSSM engine diagnostics request
Reimplemented from IPssmInputCdd.
Definition at line 154 of file cdd_pssm_input.hpp.
References CCddInputData::m_DiagnosticsRequest.
◆ GetDiskCacheErrorMessahe()
|
inline |
Definition at line 479 of file remote_blast.hpp.
References CRemoteBlast::m_disk_cache_error_msg.
◆ GetDJChainType()
Definition at line 179 of file igblast.hpp.
References map_checker< Container >::end(), map_checker< Container >::find(), and CIgAnnotationInfo::m_DJChainType.
Referenced by CIgBlast::x_FindDJAln(), and CIgBlast::x_ProcessDGeneResult().
◆ GetDocumentation()
Return the documentation for the provided task.
- Parameters
-
task_name Task name for which to provide documentation [in]
Definition at line 259 of file blast_options_handle.cpp.
References NStr::StartsWith(), and NStr::ToLower().
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetDomainChainType()
Definition at line 148 of file igblast.hpp.
References map_checker< Container >::end(), map_checker< Container >::find(), and CIgAnnotationInfo::m_DomainChainType.
Referenced by CIgBlast::x_AnnotateDomain().
◆ GetDomainInclusionThreshold() [1/3]
|
inline |
Definition at line 1817 of file blast_options_local_priv.hpp.
References PSIBlastOptions::inclusion_ethresh, and CBlastOptionsLocal::m_DeltaBlastOpts.
Referenced by CBlastOptions::GetDomainInclusionThreshold().
◆ GetDomainInclusionThreshold() [2/3]
| double CBlastOptions::GetDomainInclusionThreshold | ( | void | ) | const |
Definition at line 2513 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetDomainInclusionThreshold(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
◆ GetDomainInclusionThreshold() [3/3]
|
inline |
Get e-value threshold for including domains in Pssm calculation.
- Returns
- E-value cutoff for domains
Definition at line 65 of file deltablast_options.hpp.
Referenced by CDeltaBlast::Run(), and CDeltaBlast::x_FindDomainHits().
◆ GetDomainInfo()
Definition at line 137 of file igblast.hpp.
References map_checker< Container >::end(), map_checker< Container >::find(), i, CIgAnnotationInfo::m_DomainData, and CIgAnnotationInfo::m_DomainIndex.
Referenced by CIgBlast::x_AnnotateDomain().
◆ GetDomainResults()
|
inline |
Get results of conserved domain search (intermediate results)
- Returns
- Conserved domain search results
Definition at line 112 of file deltablast.hpp.
References CDeltaBlast::m_DomainResults.
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetDustFiltering() [1/3]
|
inline |
Is dust filtering enabled?
Definition at line 103 of file blast_nucl_options.hpp.
Referenced by Blast_FindDustFilterLoc(), BOOST_AUTO_TEST_CASE(), and BOOST_FIXTURE_TEST_CASE().
◆ GetDustFiltering() [2/3]
| bool CBlastOptions::GetDustFiltering | ( | ) | const |
Definition at line 1153 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetDustFiltering(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CBlastQuerySourceOM::x_CalculateMasks().
◆ GetDustFiltering() [3/3]
|
inline |
Definition at line 751 of file blast_options_local_priv.hpp.
References SBlastFilterOptions::dustOptions, QuerySetUpOptions::filtering_options, and CBlastOptionsLocal::m_QueryOpts.
Referenced by CBlastOptions::GetDustFiltering(), and CBlastOptions::SetFilterString().
◆ GetDustFilteringLevel() [1/3]
|
inline |
Get level parameter for dust.
Definition at line 109 of file blast_nucl_options.hpp.
Referenced by Blast_FindDustFilterLoc(), BOOST_AUTO_TEST_CASE(), and BOOST_FIXTURE_TEST_CASE().
◆ GetDustFilteringLevel() [2/3]
| int CBlastOptions::GetDustFilteringLevel | ( | ) | const |
Definition at line 1172 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetDustFilteringLevel(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CBlastQuerySourceOM::x_CalculateMasks().
◆ GetDustFilteringLevel() [3/3]
|
inline |
Definition at line 775 of file blast_options_local_priv.hpp.
References SBlastFilterOptions::dustOptions, QuerySetUpOptions::filtering_options, kInvalidFilterValue, SDustOptions::level, CBlastOptionsLocal::m_QueryOpts, and NULL.
Referenced by CBlastOptions::GetDustFilteringLevel(), and CBlastOptions::SetFilterString().
◆ GetDustFilteringLinker() [1/3]
|
inline |
Get linker parameter for dust.
Definition at line 121 of file blast_nucl_options.hpp.
Referenced by Blast_FindDustFilterLoc(), BOOST_AUTO_TEST_CASE(), and BOOST_FIXTURE_TEST_CASE().
◆ GetDustFilteringLinker() [2/3]
| int CBlastOptions::GetDustFilteringLinker | ( | ) | const |
Definition at line 1210 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetDustFilteringLinker(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CBlastQuerySourceOM::x_CalculateMasks().
◆ GetDustFilteringLinker() [3/3]
|
inline |
Definition at line 812 of file blast_options_local_priv.hpp.
References SBlastFilterOptions::dustOptions, QuerySetUpOptions::filtering_options, kInvalidFilterValue, SDustOptions::linker, CBlastOptionsLocal::m_QueryOpts, and NULL.
Referenced by CBlastOptions::GetDustFilteringLinker(), and CBlastOptions::SetFilterString().
◆ GetDustFilteringWindow() [1/3]
|
inline |
Get window parameter for dust.
Definition at line 115 of file blast_nucl_options.hpp.
Referenced by Blast_FindDustFilterLoc(), BOOST_AUTO_TEST_CASE(), and BOOST_FIXTURE_TEST_CASE().
◆ GetDustFilteringWindow() [2/3]
| int CBlastOptions::GetDustFilteringWindow | ( | ) | const |
Definition at line 1191 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetDustFilteringWindow(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CBlastQuerySourceOM::x_CalculateMasks().
◆ GetDustFilteringWindow() [3/3]
|
inline |
Definition at line 793 of file blast_options_local_priv.hpp.
References SBlastFilterOptions::dustOptions, QuerySetUpOptions::filtering_options, kInvalidFilterValue, CBlastOptionsLocal::m_QueryOpts, NULL, and SDustOptions::window.
Referenced by CBlastOptions::GetDustFilteringWindow(), and CBlastOptions::SetFilterString().
◆ GetEffectiveSearchSpace() [1/3]
| Int8 CBlastOptions::GetEffectiveSearchSpace | ( | ) | const |
Definition at line 2370 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetEffectiveSearchSpace(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CBlastDatabaseArgs::ExtractAlgorithmOptions(), CBlastOptionsHandle::GetEffectiveSearchSpace(), SplitQuery_SetEffectiveSearchSpace(), and CLocalVDBBlast::x_AdjustDbSize().
◆ GetEffectiveSearchSpace() [2/3]
|
inline |
Returns EffectiveSearchSpace.
Definition at line 318 of file blast_options_handle.hpp.
References CBlastOptions::GetEffectiveSearchSpace(), and CBlastOptionsHandle::m_Opts.
Referenced by BOOST_AUTO_TEST_CASE(), and BOOST_FIXTURE_TEST_CASE().
◆ GetEffectiveSearchSpace() [3/3]
|
inline |
Definition at line 1719 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_EffLenOpts, BlastEffectiveLengthsOptions::num_searchspaces, and BlastEffectiveLengthsOptions::searchsp_eff.
Referenced by CBlastOptions::GetEffectiveSearchSpace().
◆ GetEffLenOpts() [1/2]
|
private |
Returns BlastEffectiveLengthsOptions for eLocal objects, NULL for eRemote.
Definition at line 2694 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetEffLenOpts(), and CBlastOptions::m_Local.
Referenced by CBlastSetupTestFixture::s_GetEffLenOpts(), and CTracebackTestFixture::x_SetupGapAlign().
◆ GetEffLenOpts() [2/2]
|
inlineprivate |
Definition at line 462 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_EffLenOpts.
Referenced by CBlastOptions::GetEffLenOpts().
◆ GetEffSearchSpace()
| Int8 CEffectiveSearchSpaceCalculator::GetEffSearchSpace | ( | size_t | query_index = 0 | ) | const |
Retrieve the effective search space calculated for a given query.
- Parameters
-
query_index index of the query sequence of interest
Definition at line 133 of file effsearchspace_calc.cpp.
References _ASSERT, BlastQueryInfoGetEffSearchSpace(), CEffectiveSearchSpaceCalculator::m_Program, and CEffectiveSearchSpaceCalculator::m_QueryInfo.
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetEffSearchSpaceForContext()
| Int8 CEffectiveSearchSpaceCalculator::GetEffSearchSpaceForContext | ( | size_t | ctx_index | ) | const |
Retrieve the effective search space calculated for a given query context.
This is needed because translated searches might have slightly different search spaces for each of its contexts.
- Parameters
-
ctx_index index of the query sequence of interest
Definition at line 140 of file effsearchspace_calc.cpp.
References _ASSERT, BlastQueryInfo::contexts, BlastContextInfo::eff_searchsp, and CEffectiveSearchSpaceCalculator::m_QueryInfo.
Referenced by SplitQuery_SetEffectiveSearchSpace().
◆ GetEntrezQuery()
| string CBlastOptionsBuilder::GetEntrezQuery | ( | ) |
Get the Entrez query.
Definition at line 702 of file blast_options_builder.cpp.
References CBlastOptionsBuilder::SOptional< T >::Get(), and CBlastOptionsBuilder::m_EntrezQuery.
Referenced by CRemoteBlast::GetSearchOptions(), and s_ImportDatabase().
◆ GetEntrezQueryLimitation()
| string CSearchDatabase::GetEntrezQueryLimitation | ( | ) | const |
Accessor for the entrez query.
Definition at line 94 of file uniform_search.cpp.
References CSearchDatabase::m_EntrezQueryLimitation.
Referenced by CRemoteBlast::x_Init(), CExportStrategy::x_Process_SearchDb(), CRemoteSeqSearch::x_RemoteBlast(), and CRemotePssmSearch::x_RemoteBlast().
◆ GetErrCodeString() [1/6]
|
inlineoverridevirtual |
Get a message describing the situation leading to the throw.
Reimplemented from CException.
Definition at line 93 of file uniform_search.hpp.
References CException::GetErrCodeString().
◆ GetErrCodeString() [2/6]
|
inlineoverridevirtual |
Get a message describing the situation leading to the throw.
Reimplemented from CException.
Definition at line 85 of file blast_services.hpp.
References CException::GetErrCodeString().
◆ GetErrCodeString() [3/6]
|
inlineoverridevirtual |
Translate from the error code value to its string representation.
Reimplemented from CException.
Definition at line 57 of file blast_exception.hpp.
References CException::GetErrCodeString().
◆ GetErrCodeString() [4/6]
|
inlineoverridevirtual |
Translate from the error code value to its string representation.
Reimplemented from CException.
Reimplemented in CRemoteBlastException, and CPssmEngineException.
Definition at line 91 of file blast_exception.hpp.
References CBlastException::eCoreBlastError, CBlastException::eInvalidArgument, CBlastException::eInvalidCharacter, CBlastException::eInvalidOptions, CBlastException::eNotSupported, CBlastException::eRpsInit, CBlastException::eSeqSrcInit, CBlastException::eSystem, CException::GetErrCode(), and CException::GetErrCodeString().
◆ GetErrCodeString() [5/6]
|
inlineoverridevirtual |
Translate from the error code value to its string representation.
Reimplemented from CBlastException.
Definition at line 72 of file pssm_engine.hpp.
References CException::GetErrCodeString().
◆ GetErrCodeString() [6/6]
|
inlineoverridevirtual |
Translate from the error code value to its string representation.
Reimplemented from CBlastException.
Definition at line 74 of file remote_blast.hpp.
References CRemoteBlastException::eIncompleteConfig, CRemoteBlastException::eServiceNotAvailable, CException::GetErrCode(), and CException::GetErrCodeString().
◆ GetErrors() [1/2]
| TQueryMessages CSearchResults::GetErrors | ( | int | min_severity = eBlastSevError | ) | const |
Accessor for the error/warning messsages for this query.
- Parameters
-
min_severity minimum severity to report errors [in]
Definition at line 244 of file blast_results.cpp.
References ITERATE, and CSearchResults::m_Errors.
Referenced by CBlastAligner::GenerateAlignments(), CRemoteBlastAligner::GenerateAlignments(), CIgBlast::s_AppendResults(), and CIgBlast::x_ConvertResultType().
◆ GetErrors() [2/2]
| string CRemoteBlast::GetErrors | ( | void | ) |
This returns a string containing any errors that were produced by the search.
A successful search should return an empty string here.
- Returns
- An empty string or a newline seperated list of errors.
Definition at line 1208 of file remote_blast.cpp.
References i, CRemoteBlast::m_Errs, and string.
Referenced by BOOST_AUTO_TEST_CASE(), CRemoteBlast::CheckStatus(), CRemoteBlast::GetSearchStrategy(), CBlastFormatterApp::Run(), CBlastFormatterVdbApp::Run(), and CRemoteBlast::x_IsUnknownRID().
◆ GetErrorStrings()
| string CSearchResults::GetErrorStrings | ( | ) | const |
Retrieve a string with the query identifier followed by the errors produced, returns a empty string if HasErrors() returns false.
Definition at line 258 of file blast_results.cpp.
References eBlastSevError, TQueryMessages::GetQueryId(), ITERATE, CSearchResults::m_Errors, and string.
Referenced by CBlastAligner::GenerateAlignments(), and CRemoteBlastAligner::GenerateAlignments().
◆ GetErrorVector()
This returns any errors encountered as a vector of strings.
- See also
- CRemoteBlast::GetErrors
- Returns
- Reference to a vector of errors.
Definition at line 1245 of file remote_blast.cpp.
References CRemoteBlast::m_Errs.
Referenced by CRemoteBlast::GetResultSet(), and s_BuildResultsRemote().
◆ GetEvalueThreshold() [1/3]
| double CBlastOptions::GetEvalueThreshold | ( | ) | const |
Definition at line 1906 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetEvalueThreshold(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CBlastOptionsHandle::GetEvalueThreshold(), LogBlastOptions(), and CIgBlast::x_SetupVSearch().
◆ GetEvalueThreshold() [2/3]
|
inline |
Returns EvalueThreshold.
Definition at line 247 of file blast_options_handle.hpp.
References CBlastOptions::GetEvalueThreshold(), and CBlastOptionsHandle::m_Opts.
Referenced by BOOST_AUTO_TEST_CASE(), and BOOST_FIXTURE_TEST_CASE().
◆ GetEvalueThreshold() [3/3]
|
inline |
Definition at line 1432 of file blast_options_local_priv.hpp.
References BlastHitSavingOptions::expect_value, and CBlastOptionsLocal::m_HitSaveOpts.
Referenced by CBlastOptions::GetEvalueThreshold().
◆ GetExtnOpts() [1/2]
|
private |
Returns BlastExtensionOptions for eLocal objects, NULL for eRemote.
Definition at line 2664 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetExtnOpts(), and CBlastOptions::m_Local.
Referenced by CTracebackSearchTestFixture::x_GetSampleHspStream(), CTracebackSearchTestFixture::x_GetSelfHitHspStream(), CTracebackTestFixture::x_MakeStream(), and CTracebackTestFixture::x_SetupGapAlign().
◆ GetExtnOpts() [2/2]
|
inlineprivate |
Definition at line 432 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_ExtnOpts.
Referenced by CBlastOptions::GetExtnOpts(), and CBlastOptionsLocal::SetProgram().
◆ GetFilteredQueryRegions() [1/3]
| TSeqLocInfoVector CBl2Seq::GetFilteredQueryRegions | ( | ) | const |
Retrieves regions filtered on the query/queries.
Definition at line 216 of file bl2seq.cpp.
References CSearchResultSet::GetFilteredQueryRegions(), and CBl2Seq::m_Results.
◆ GetFilteredQueryRegions() [2/3]
| TSeqLocInfoVector CSearchResultSet::GetFilteredQueryRegions | ( | ) | const |
Retrieves the filtered query regions.
Definition at line 517 of file blast_results.cpp.
References CSearchResultSet::m_QueryMasks.
Referenced by CBl2Seq::GetFilteredQueryRegions().
◆ GetFilteredQueryRegions() [3/3]
|
inline |
Retrieve the filtered/masked query regions.
Definition at line 186 of file prelim_stage.hpp.
References CBlastPrelimSearch::m_MasksForAllQueries.
Referenced by CLocalBlast::Run().
◆ GetFilteredRedundantGis()
| void GetFilteredRedundantGis | ( | const IBlastSeqInfoSrc & | sisrc, |
| int | oid, | ||
| vector< TGi > & | gis | ||
| ) |
Get GIs for a sequence in a redundant database.
This function returns a list of GIs corresponding to the specified OID. This allows a GI list to be built for those GIs found by a search and included in the associated database; the returned GIs will be filtered by any OID and GI list filtering that is applied to the database (if any).
- Parameters
-
sisrc Source of sequence information. [in] oid OID for which to retrieve GIs. [in] gis GIs found for the specified oid. [out]
Definition at line 91 of file blast_seqinfosrc_aux.cpp.
References IBlastSeqInfoSrc::GetId(), IBlastSeqInfoSrc::HasGiList(), ITERATE, and ct::sort().
◆ GetFilteredRedundantSeqids()
| void GetFilteredRedundantSeqids | ( | const IBlastSeqInfoSrc & | sisrc, |
| int | oid, | ||
| vector< string > & | seqids, | ||
| bool | use_gis = true |
||
| ) |
Get Seqids for a sequence in a redundant database.
This function returns a list of GIs or Seqids corresponding to the specified OID. This allows a GI list to be built for those GIs found by a search and included in the associated database; the returned GIs will be filtered by any OID and GI list filtering that is applied to the database (if any).
- Parameters
-
sisrc Source of sequence information. [in] oid OID for which to retrieve GIs. [in] seqids SeqIds found for the specified oid. [out] use_gis Return only GIs seqids vector [in]
Definition at line 113 of file blast_seqinfosrc_aux.cpp.
References IBlastSeqInfoSrc::GetId(), IBlastSeqInfoSrc::HasGiList(), CTextseq_id_Base::IsSetAccession(), and ITERATE.
Referenced by BlastHitList2SeqAlign_OMF(), BLASTPrelminSearchHitListToStdSeg(), and s_BLAST_OneSubjectResults2CSeqAlign().
◆ GetFilteredSubjectRegions()
| void CBl2Seq::GetFilteredSubjectRegions | ( | vector< TSeqLocInfoVector > & | retval | ) | const |
Retrieves regions filtered on the subject sequence(s)
- Parameters
-
retval the return value of this method [in|out]
Definition at line 222 of file bl2seq.cpp.
References CSearchResultSet::empty(), CRef< C, Locker >::Empty(), ITERATE, and CBl2Seq::m_Results.
◆ GetFilteringAlgorithm() [1/2]
|
inline |
Retrieve the database filtering algorithm.
- Returns
- -1 if not none was used, otherwise the filtering algorithm ID
Definition at line 164 of file local_db_adapter.hpp.
References CRef< C, Locker >::Empty(), CSearchDatabase::GetFilteringAlgorithm(), and CLocalDbAdapter::m_DbInfo.
Referenced by CBlastnNode::Main(), CBlastpNode::Main(), CBlastxNode::Main(), CRPSBlastNode::Main(), CRPSTBlastnNode::Main(), CTblastnNode::Main(), CIgBlastnApp::CIgFormatter::Main(), CDeltaBlastApp::Run(), CPsiBlastApp::Run(), CTblastxApp::Run(), CIgBlastnApp::Run(), CIgBlastpApp::Run(), CRMBlastnApp::Run(), CBlastnApp::x_RunMTBySplitDB(), CBlastpApp::x_RunMTBySplitDB(), CBlastxApp::x_RunMTBySplitDB(), CRPSBlastApp::x_RunMTBySplitDB(), CRPSTBlastnApp::x_RunMTBySplitDB(), and CTblastnApp::x_RunMTBySplitDB().
◆ GetFilteringAlgorithm() [2/2]
| int CSearchDatabase::GetFilteringAlgorithm | ( | ) | const |
Accessor for the filtering algorithm ID.
Definition at line 196 of file uniform_search.cpp.
References eNoSubjMasking, CSearchDatabase::m_FilteringAlgorithmId, CSearchDatabase::m_MaskType, CSearchDatabase::m_NeedsFilteringTranslation, and CSearchDatabase::x_TranslateFilteringAlgorithm().
Referenced by CSetupFactory::CreateBlastSeqSrc(), CLocalDbAdapter::GetFilteringAlgorithm(), CLocalDbAdapter::MakeSeqInfoSrc(), CRemoteBlast::x_Init(), and CExportStrategy::x_Process_SearchDb().
◆ GetFilteringAlgorithmKey() [1/2]
| string CLocalDbAdapter::GetFilteringAlgorithmKey | ( | ) |
Retrieve the database filtering id from key.
- Returns
- kEmptyStr if not none was found, otherwise the filtering algorithm key
Definition at line 196 of file local_db_adapter.cpp.
References CRef< C, Locker >::Empty(), CSearchDatabase::GetFilteringAlgorithmKey(), kEmptyStr, and CLocalDbAdapter::m_DbInfo.
◆ GetFilteringAlgorithmKey() [2/2]
| string CSearchDatabase::GetFilteringAlgorithmKey | ( | ) | const |
Accessor for the filtering algorithm key.
Definition at line 210 of file uniform_search.cpp.
References eNoSubjMasking, CSearchDatabase::m_FilteringAlgorithmString, and CSearchDatabase::m_MaskType.
Referenced by CLocalDbAdapter::GetFilteringAlgorithmKey(), CRemoteBlast::x_Init(), and CExportStrategy::x_Process_SearchDb().
◆ GetFilterString() [1/3]
| char * CBlastOptions::GetFilterString | ( | ) | const |
Return the filtering string used.
- Returns
- copy of the filtering options string, caller must free() the return value
- Deprecated:
- Do not use this method, instead use the various methods to retrieve filtering options
- See also
- GetMaskAtHash, GetDustFiltering, GetDustFilteringLevel, GetDustFilteringWindow, GetDustFilteringWindow, GetSegFiltering, GetSegFilteringWindow, GetSegFilteringLocut, GetSegFilteringHicut GetRepeatFiltering, GetRepeatFilteringDB
Definition at line 1034 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetFilterString(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by BOOST_AUTO_TEST_CASE(), and CBlastOptionsHandle::GetFilterString().
◆ GetFilterString() [2/3]
| char * CBlastOptionsHandle::GetFilterString | ( | ) | const |
Returns FilterString.
Definition at line 98 of file blast_options_handle.cpp.
References CBlastOptions::GetFilterString(), and CBlastOptionsHandle::m_Opts.
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetFilterString() [3/3]
|
inline |
Definition at line 685 of file blast_options_local_priv.hpp.
References _ASSERT, BlastFilteringOptionsToString(), QuerySetUpOptions::filter_string, QuerySetUpOptions::filtering_options, CBlastOptionsLocal::m_QueryOpts, NULL, and strdup.
Referenced by CBlastOptions::GetFilterString().
◆ GetFinalDbSeq()
| int CBlastOptionsBuilder::GetFinalDbSeq | ( | ) |
Get the OID range end point.
Definition at line 722 of file blast_options_builder.cpp.
References CBlastOptionsBuilder::SOptional< T >::Get(), and CBlastOptionsBuilder::m_FinalDbSeq.
Referenced by CRemoteBlast::GetSearchOptions().
◆ GetFinalOid()
|
inline |
Returns last database ordinal id covered by this BlastSeqSrc.
Definition at line 588 of file seqsrc_seqdb.cpp.
Referenced by s_SeqDbSrcNew().
◆ GetFirstDbSeq()
| int CBlastOptionsBuilder::GetFirstDbSeq | ( | ) |
Get the OID range start point.
Definition at line 712 of file blast_options_builder.cpp.
References CBlastOptionsBuilder::SOptional< T >::Get(), and CBlastOptionsBuilder::m_FirstDbSeq.
Referenced by CRemoteBlast::GetSearchOptions().
◆ GetFirstId()
Get sequence id of the first segment of a paired read.
Definition at line 195 of file magicblast.hpp.
References CMagicBlastResults::GetQueryId().
◆ GetFirstInfo()
|
inline |
Get alignment flags for the query.
Definition at line 186 of file magicblast.hpp.
References CMagicBlastResults::m_FirstInfo.
◆ GetFirstOid()
|
inline |
Returns first database ordinal id covered by this BlastSeqSrc.
Definition at line 586 of file seqsrc_seqdb.cpp.
Referenced by s_SeqDbSrcNew().
◆ GetFlatResults()
| CRef< CSeq_align_set > CMagicBlastResultSet::GetFlatResults | ( | bool | no_discordant = false | ) |
Get all results as a single Seq-align-set object.
- Parameters
-
no_discordant Report only paires aligned concordantly [in]
Definition at line 732 of file magicblast.cpp.
References result, and CSeq_align_set_Base::Set().
◆ GetForceIndex() [1/2]
| bool CBlastOptions::GetForceIndex | ( | ) | const |
Definition at line 2583 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetForceIndex(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
◆ GetForceIndex() [2/2]
|
inline |
Definition at line 1834 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_ForceMBIndex.
Referenced by CBlastOptions::GetForceIndex().
◆ GetFrameOffset()
Definition at line 155 of file igblast.hpp.
References map_checker< Container >::end(), map_checker< Container >::find(), and CIgAnnotationInfo::m_FrameOffset.
Referenced by CIgBlast::x_AnnotateD(), CIgBlast::x_AnnotateDJ(), CIgBlast::x_AnnotateDomain(), and CIgBlast::x_AnnotateJ().
◆ GetFrameShiftPenalty() [1/4]
| int CBlastOptions::GetFrameShiftPenalty | ( | ) | const |
Definition at line 2293 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetFrameShiftPenalty(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
◆ GetFrameShiftPenalty() [2/4]
|
inline |
Returns FrameShiftPenalty.
Definition at line 88 of file blastx_options.hpp.
◆ GetFrameShiftPenalty() [3/4]
|
inline |
Returns FrameShiftPenalty.
Definition at line 71 of file tblastn_options.hpp.
◆ GetFrameShiftPenalty() [4/4]
|
inline |
Definition at line 1670 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_ScoringOpts, and BlastScoringOptions::shift_pen.
Referenced by CBlastOptions::GetFrameShiftPenalty().
◆ GetFreqRatios()
|
static |
Returns matrix of BLASTAA_SIZE by query size (dimensions are opposite of what is stored in the BlastScoreBlk) containing frequency ratios.
- Parameters
-
pssm PSSM to extract data from [in]
- Exceptions
-
std::runtime_error if frequency ratios are not available
Definition at line 264 of file psiblast_aux_priv.cpp.
References _ASSERT, BLASTAA_SIZE, Convert2Matrix(), CPssm_Base::GetByRow(), CPssmIntermediateData_Base::GetFreqRatios(), CPssm_Base::GetIntermediateData(), CPssm_Base::GetNumColumns(), and CPssm_Base::GetNumRows().
Referenced by PsiBlastComputePssmScores(), PsiBlastSetupScoreBlock(), CMakeProfileDBApp::x_RPSUpdateStatistics(), and CMakeProfileDBApp::x_UpdateFreqRatios().
◆ GetFwr4EndOffset()
Definition at line 171 of file igblast.hpp.
References map_checker< Container >::end(), map_checker< Container >::find(), and CIgAnnotationInfo::m_Fwr4EndOffset.
Referenced by CIgBlast::x_FillJDomain().
◆ GetGapExistence() [1/5]
|
inlinevirtual |
Obtain the gap existence value to use when building the PSSM.
Reimplemented from IPssmInput_Base.
Definition at line 111 of file msa_pssm_input.hpp.
References IPssmInput_Base::GetGapExistence().
◆ GetGapExistence() [2/5]
|
inlinevirtual |
Obtain the gap existence value to use when building the PSSM.
Reimplemented from IPssmInput_Base.
Definition at line 110 of file psi_pssm_input.hpp.
References IPssmInput_Base::GetGapExistence().
◆ GetGapExistence() [3/5]
|
inlinevirtual |
Obtain the gap existence value to use when building the PSSM.
Reimplemented from IPssmInput_Base.
Definition at line 209 of file psi_pssm_input.hpp.
References IPssmInput_Base::GetGapExistence(), and CPsiBlastInputData::m_GapExistence.
◆ GetGapExistence() [4/5]
|
inlinevirtual |
Obtain the gap existence value for the underlying matrix used to build the PSSM.
Reimplemented in CCddInputData, CPsiBlastInputData, CPsiBlastInputFreqRatios, and CPsiBlastInputClustalW.
Definition at line 73 of file pssm_input.hpp.
References BLAST_GAP_OPEN_PROT.
Referenced by CPsiBlastInputClustalW::GetGapExistence(), CPsiBlastInputFreqRatios::GetGapExistence(), CPsiBlastInputData::GetGapExistence(), CCddInputData::GetGapExistence(), and CPssmEngine::x_GetGapExistence().
◆ GetGapExistence() [5/5]
|
inlinevirtual |
Get gap existence to use when building PSSM.
- Returns
- Gap existence
Reimplemented from IPssmInput_Base.
Definition at line 189 of file cdd_pssm_input.hpp.
References IPssmInput_Base::GetGapExistence(), and CCddInputData::m_GapExistence.
◆ GetGapExtension() [1/5]
|
inlinevirtual |
Obtain the gap extension value to use when building the PSSM.
Reimplemented from IPssmInput_Base.
Definition at line 118 of file msa_pssm_input.hpp.
References IPssmInput_Base::GetGapExtension().
◆ GetGapExtension() [2/5]
|
inlinevirtual |
Obtain the gap extension value to use when building the PSSM.
Reimplemented from IPssmInput_Base.
Definition at line 117 of file psi_pssm_input.hpp.
References IPssmInput_Base::GetGapExtension().
◆ GetGapExtension() [3/5]
|
inlinevirtual |
Obtain the gap extension value to use when building the PSSM.
Reimplemented from IPssmInput_Base.
Definition at line 216 of file psi_pssm_input.hpp.
References IPssmInput_Base::GetGapExtension(), and CPsiBlastInputData::m_GapExtension.
◆ GetGapExtension() [4/5]
|
inlinevirtual |
Obtain the gap extension value for the underlying matrix used to build the PSSM.
Reimplemented in CCddInputData, CPsiBlastInputData, CPsiBlastInputFreqRatios, and CPsiBlastInputClustalW.
Definition at line 78 of file pssm_input.hpp.
References BLAST_GAP_EXTN_PROT.
Referenced by CPsiBlastInputClustalW::GetGapExtension(), CPsiBlastInputFreqRatios::GetGapExtension(), CPsiBlastInputData::GetGapExtension(), CCddInputData::GetGapExtension(), and CPssmEngine::x_GetGapExtension().
◆ GetGapExtension() [5/5]
|
inlinevirtual |
Get gap extension to use when building PSSM.
- Returns
- Gap extension
Reimplemented from IPssmInput_Base.
Definition at line 195 of file cdd_pssm_input.hpp.
References IPssmInput_Base::GetGapExtension(), and CCddInputData::m_GapExtension.
◆ GetGapExtensionCost() [1/7]
|
inline |
Returns GapExtensionCost.
Definition at line 207 of file blast_nucl_options.hpp.
Referenced by BOOST_FIXTURE_TEST_CASE().
◆ GetGapExtensionCost() [2/7]
| int CBlastOptions::GetGapExtensionCost | ( | ) | const |
Definition at line 2274 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetGapExtensionCost(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by PsiBlastComputePssmScores(), CPsiBlastArgs::x_CreatePssmFromMsa(), and CScoreBuilder::x_Initialize().
◆ GetGapExtensionCost() [3/7]
|
inline |
Returns GapExtensionCost.
Definition at line 124 of file blast_prot_options.hpp.
Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), PsiBlastComputePssmFromAlignment(), and CDeltaBlast::Run().
◆ GetGapExtensionCost() [4/7]
|
inline |
Returns GapExtensionCost.
Definition at line 118 of file blast_rps_options.hpp.
◆ GetGapExtensionCost() [5/7]
|
inline |
Return gap extension cost.
Definition at line 167 of file magicblast_options.hpp.
◆ GetGapExtensionCost() [6/7]
| int CBlastRPSInfo::GetGapExtensionCost | ( | ) | const |
Returns the gap extension cost associated with the scoring matrix above.
Definition at line 639 of file rps_aux.cpp.
References CBlastRPSInfo::m_RpsInfo.
Referenced by CSetupFactory::CreateRpsStructures().
◆ GetGapExtensionCost() [7/7]
|
inline |
Definition at line 1658 of file blast_options_local_priv.hpp.
References BlastScoringOptions::gap_extend, and CBlastOptionsLocal::m_ScoringOpts.
Referenced by CBlastOptions::GetGapExtensionCost().
◆ GetGapExtnAlgorithm() [1/3]
|
inline |
Returns GapExtnAlgorithm.
Definition at line 168 of file blast_nucl_options.hpp.
Referenced by BOOST_FIXTURE_TEST_CASE().
◆ GetGapExtnAlgorithm() [2/3]
| EBlastPrelimGapExt CBlastOptions::GetGapExtnAlgorithm | ( | ) | const |
Definition at line 1606 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetGapExtnAlgorithm(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
◆ GetGapExtnAlgorithm() [3/3]
|
inline |
Definition at line 1166 of file blast_options_local_priv.hpp.
References BlastExtensionOptions::ePrelimGapExt, and CBlastOptionsLocal::m_ExtnOpts.
Referenced by CBlastOptions::GetGapExtnAlgorithm().
◆ GetGaplessColumnWeights()
|
static |
Returns the relative gapless PSSM column weights to pseudocounts for the provided PSSM.
- Parameters
-
pssm PSSM to extract data from [in] retval vector containing the gapless column weights or an empty vector if this data is not available [in|out]
Definition at line 355 of file psiblast_aux_priv.cpp.
References copy(), ctll::empty(), CPssmIntermediateData_Base::GetGaplessColumnWeights(), and CPssm_Base::GetIntermediateData().
◆ GetGapOpeningCost() [1/7]
|
inline |
Returns GapOpeningCost.
Definition at line 201 of file blast_nucl_options.hpp.
Referenced by BOOST_FIXTURE_TEST_CASE().
◆ GetGapOpeningCost() [2/7]
| int CBlastOptions::GetGapOpeningCost | ( | ) | const |
Definition at line 2255 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetGapOpeningCost(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by PsiBlastComputePssmScores(), CPsiBlastArgs::x_CreatePssmFromMsa(), and CScoreBuilder::x_Initialize().
◆ GetGapOpeningCost() [3/7]
|
inline |
Returns GapOpeningCost.
Definition at line 118 of file blast_prot_options.hpp.
Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), PsiBlastComputePssmFromAlignment(), and CDeltaBlast::Run().
◆ GetGapOpeningCost() [4/7]
|
inline |
Returns GapOpeningCost.
Definition at line 116 of file blast_rps_options.hpp.
◆ GetGapOpeningCost() [5/7]
|
inline |
Return gap opening cost.
Definition at line 160 of file magicblast_options.hpp.
◆ GetGapOpeningCost() [6/7]
| int CBlastRPSInfo::GetGapOpeningCost | ( | ) | const |
Returns the gap opening cost associated with the scoring matrix above.
Definition at line 633 of file rps_aux.cpp.
References CBlastRPSInfo::m_RpsInfo.
Referenced by CSetupFactory::CreateRpsStructures().
◆ GetGapOpeningCost() [7/7]
|
inline |
Definition at line 1646 of file blast_options_local_priv.hpp.
References BlastScoringOptions::gap_open, and CBlastOptionsLocal::m_ScoringOpts.
Referenced by CBlastOptions::GetGapOpeningCost().
◆ GetGappedKarlinBlk()
|
inline |
Retrieve gapped Karlin parameters.
Definition at line 102 of file blast_results.hpp.
Referenced by s_BuildArchiveAll().
◆ GetGappedMode() [1/3]
| bool CBlastOptions::GetGappedMode | ( | ) | const |
Returns true if gapped BLAST is set, false otherwise.
Definition at line 2075 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetGappedMode(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CBlastOptionsHandle::GetGappedMode(), CBlastTracebackSearch::Run(), CBlastAppArgs::SetOptions(), CBlastAppArgs::SetOptionsForSavedStrategy(), CQuerySplitter::Split(), and CBlastPrelimSearch::x_BuildStdSegList().
◆ GetGappedMode() [2/3]
|
inline |
Returns GappedMode.
Definition at line 276 of file blast_options_handle.hpp.
References CBlastOptions::GetGappedMode(), and CBlastOptionsHandle::m_Opts.
Referenced by BOOST_AUTO_TEST_CASE(), and BOOST_FIXTURE_TEST_CASE().
◆ GetGappedMode() [3/3]
|
inline |
Returns true if gapped BLAST is set, false otherwise.
Definition at line 1544 of file blast_options_local_priv.hpp.
References BlastScoringOptions::gapped_calculation, CBlastOptionsLocal::m_ScoringOpts, and true.
Referenced by CBlastOptions::GetGappedMode().
◆ GetGapTracebackAlgorithm() [1/3]
|
inline |
Returns GapTracebackAlgorithm.
Definition at line 175 of file blast_nucl_options.hpp.
Referenced by BOOST_FIXTURE_TEST_CASE().
◆ GetGapTracebackAlgorithm() [2/3]
| EBlastTbackExt CBlastOptions::GetGapTracebackAlgorithm | ( | ) | const |
Definition at line 1625 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetGapTracebackAlgorithm(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
◆ GetGapTracebackAlgorithm() [3/3]
|
inline |
Definition at line 1178 of file blast_options_local_priv.hpp.
References BlastExtensionOptions::eTbackExt, and CBlastOptionsLocal::m_ExtnOpts.
Referenced by CBlastOptions::GetGapTracebackAlgorithm().
◆ GetGapTrigger() [1/3]
| double CBlastOptions::GetGapTrigger | ( | ) | const |
Definition at line 1587 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetGapTrigger(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CBlastOptionsHandle::GetGapTrigger().
◆ GetGapTrigger() [2/3]
|
inline |
Returns GapTrigger.
Definition at line 210 of file blast_options_handle.hpp.
References CBlastOptions::GetGapTrigger(), and CBlastOptionsHandle::m_Opts.
Referenced by BOOST_FIXTURE_TEST_CASE().
◆ GetGapTrigger() [3/3]
|
inline |
Definition at line 1129 of file blast_options_local_priv.hpp.
References BlastInitialWordOptions::gap_trigger, and CBlastOptionsLocal::m_InitWordOpts.
Referenced by CBlastOptions::GetGapTrigger().
◆ GetGapXDropoff() [1/4]
| double CBlastOptions::GetGapXDropoff | ( | ) | const |
Definition at line 1549 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetGapXDropoff(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CBlastOptionsHandle::GetGapXDropoff().
◆ GetGapXDropoff() [2/4]
|
inline |
Returns GapXDropoff.
Definition at line 204 of file blast_options_handle.hpp.
References CBlastOptions::GetGapXDropoff(), and CBlastOptionsHandle::m_Opts.
Referenced by BOOST_FIXTURE_TEST_CASE().
◆ GetGapXDropoff() [3/4]
|
inline |
Return x-dropoff parameter for gapped alignment.
Definition at line 144 of file magicblast_options.hpp.
◆ GetGapXDropoff() [4/4]
|
inline |
Definition at line 1142 of file blast_options_local_priv.hpp.
References BlastExtensionOptions::gap_x_dropoff, and CBlastOptionsLocal::m_ExtnOpts.
Referenced by CBlastOptions::GetGapXDropoff().
◆ GetGapXDropoffFinal() [1/3]
| double CBlastOptions::GetGapXDropoffFinal | ( | ) | const |
Definition at line 1568 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetGapXDropoffFinal(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CBlastOptionsHandle::GetGapXDropoffFinal().
◆ GetGapXDropoffFinal() [2/3]
|
inline |
Returns GapXDropoffFinal.
Definition at line 216 of file blast_options_handle.hpp.
References CBlastOptions::GetGapXDropoffFinal(), and CBlastOptionsHandle::m_Opts.
Referenced by BOOST_FIXTURE_TEST_CASE().
◆ GetGapXDropoffFinal() [3/3]
|
inline |
Definition at line 1154 of file blast_options_local_priv.hpp.
References BlastExtensionOptions::gap_x_dropoff_final, and CBlastOptionsLocal::m_ExtnOpts.
Referenced by CBlastOptions::GetGapXDropoffFinal().
◆ GetGeneticCodeId() [1/3]
Retrieve the genetic code associated with a sequence.
- Parameters
-
index index of the sequence in the sequence container [in]
Implements IBlastQuerySource.
Definition at line 294 of file bioseq_extract_data_priv.cpp.
References Get(), ITERATE, CBlastQuerySourceBioseqSet::m_Bioseqs, CBlastQuerySourceBioseqSet::m_IsProt, and max().
◆ GetGeneticCodeId() [2/3]
Retrieve the genetic code associated with a sequence.
- Parameters
-
index index of the sequence in the sequence container [in]
Implements IBlastQuerySource.
Definition at line 298 of file blast_objmgr_tools.cpp.
References CBlastQueryVector::GetBlastSearchQuery(), i, CBlastQuerySourceOM::m_QueryVector, CBlastQuerySourceOM::m_TSeqLocVector, and CRef< C, Locker >::NotEmpty().
◆ GetGeneticCodeId() [3/3]
Retrieve the genetic code associated with a sequence.
- Parameters
-
index index of the sequence in the sequence container [in]
Implemented in CBlastQuerySourceOM, and CBlastQuerySourceBioseqSet.
Referenced by SetupQueries_OMF(), and SetupSubjects_OMF().
◆ GetGiList() [1/2]
| list< TGi > CBlastOptionsBuilder::GetGiList | ( | ) |
Get the GI list.
Definition at line 732 of file blast_options_builder.cpp.
References CBlastOptionsBuilder::m_GiList.
Referenced by CRemoteBlast::GetSearchOptions(), and s_ImportDatabase().
◆ GetGiList() [2/2]
| const CRef< CSeqDBGiList > & CSearchDatabase::GetGiList | ( | ) | const |
Accessor for the gi list.
Definition at line 109 of file uniform_search.cpp.
References CSearchDatabase::m_GiList.
Referenced by CBlastKmerThread::Main(), CMagicBlastThread::Main(), CMagicBlastApp::x_LogBlastSearchInfo(), and CExportStrategy::x_Process_SearchDb().
◆ GetGiListLimitation()
| const CSearchDatabase::TGiList CSearchDatabase::GetGiListLimitation | ( | ) | const |
Definition at line 115 of file uniform_search.cpp.
References CSeqDBGiList::Empty(), CRef< C, Locker >::Empty(), CSeqDBGiList::GetGiList(), and CSearchDatabase::m_GiList.
Referenced by CRemoteBlast::x_Init(), CExportStrategy::x_Process_SearchDb(), CRemoteSeqSearch::x_RemoteBlast(), and CRemotePssmSearch::x_RemoteBlast().
◆ GetGumbelBlk()
|
inline |
Retrieve gumbel parameters.
Definition at line 92 of file blast_results.hpp.
◆ GetHitlistSize() [1/3]
| int CBlastOptions::GetHitlistSize | ( | ) | const |
Definition at line 1772 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetHitlistSize(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CFormattingArgs::ExtractAlgorithmOptions(), CBlastOptionsHandle::GetHitlistSize(), LogBlastOptions(), CLocalVDBBlast::Run(), CVDBThread::RunTandemSearches(), and CLocalVDBBlast::RunThreadedSearch().
◆ GetHitlistSize() [2/3]
|
inline |
Returns HitlistSize.
Definition at line 225 of file blast_options_handle.hpp.
References CBlastOptions::GetHitlistSize(), and CBlastOptionsHandle::m_Opts.
Referenced by BOOST_AUTO_TEST_CASE(), and BOOST_FIXTURE_TEST_CASE().
◆ GetHitlistSize() [3/3]
|
inline |
Definition at line 1269 of file blast_options_local_priv.hpp.
References BlastHitSavingOptions::hitlist_size, and CBlastOptionsLocal::m_HitSaveOpts.
Referenced by CBlastOptions::GetHitlistSize().
◆ GetHitSaveOpts() [1/2]
|
private |
Returns BlastHitSavingOptions for eLocal objects, NULL for eRemote.
Definition at line 2670 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetHitSaveOpts(), and CBlastOptions::m_Local.
Referenced by CTracebackSearchTestFixture::x_GetSampleHspStream(), CTracebackSearchTestFixture::x_GetSelfHitHspStream(), CTracebackTestFixture::x_MakeStream(), and CTracebackTestFixture::x_SetupGapAlign().
◆ GetHitSaveOpts() [2/2]
|
inlineprivate |
Definition at line 438 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_HitSaveOpts.
Referenced by CBlastOptions::GetHitSaveOpts(), and CBlastOptionsLocal::SetProgram().
◆ GetHTMLFreeString()
|
static |
Reference for requested publication without umlaut.
Definition at line 118 of file version.cpp.
References CReference::GetString(), and offset.
◆ GetId() [1/4]
Retrieve a sequence identifier given its index in the vector.
- Parameters
-
index the ordinal number to retrieve [in]
Implements IBlastSeqInfoSrc.
Definition at line 61 of file seqinfosrc_seqvec.cpp.
References GetId(), CSeqVecSeqInfoSrc::m_SeqVec, NCBI_THROW, and CRef< C, Locker >::Reset().
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetId() [2/4]
Retrieve a sequence identifier given its index in the vector.
- Parameters
-
index the ordinal number to retrieve [in]
Implements IBlastSeqInfoSrc.
Definition at line 63 of file seqinfosrc_bioseq.cpp.
References _ASSERT, CSeq_loc::GetId(), CBlastQuerySourceBioseqSet::GetSeqLoc(), CBioseqSeqInfoSrc::m_DataSource, CRef< C, Locker >::NotEmpty(), and CConstRef< C, Locker >::NotEmpty().
Referenced by CBioseqSeqInfoSrc::GetSeqLoc().
◆ GetId() [3/4]
Method to retrieve a sequence identifier given its ordinal number.
- Parameters
-
index the ordinal number to retrieve [in]
Implemented in CSeqDbSeqInfoSrc, CBioseqSeqInfoSrc, and CSeqVecSeqInfoSrc.
Referenced by GetFilteredRedundantGis(), and GetFilteredRedundantSeqids().
◆ GetId() [4/4]
Retrieve a sequence identifier given its ordinal number.
- Parameters
-
index the ordinal number to retrieve [in]
Implements IBlastSeqInfoSrc.
Definition at line 67 of file seqinfosrc_seqdb.cpp.
References CSeqDB::GetSeqIDs(), and CSeqDbSeqInfoSrc::m_iSeqDb.
Referenced by BOOST_AUTO_TEST_CASE(), CSeqDbSeqInfoSrc::GetMasks(), and CSeqDbSeqInfoSrc::GetSeqLoc().
◆ GetIgAnnotation()
|
inline |
Definition at line 206 of file igblast.hpp.
References CIgBlastResults::m_Annotation.
◆ GetIgnoreMsaMaster() [1/2]
| bool CBlastOptions::GetIgnoreMsaMaster | ( | ) | const |
Definition at line 2493 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetIgnoreMsaMaster(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
◆ GetIgnoreMsaMaster() [2/2]
|
inline |
Definition at line 1790 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_PSIBlastOpts, PSIBlastOptions::nsg_compatibility_mode, and true.
Referenced by CBlastOptions::GetIgnoreMsaMaster().
◆ GetImpalaScaleFactor() [1/2]
|
inlinevirtual |
Obtain the IMPALA Scale Factor value to use when building the PSSM.
Reimplemented from IPssmInputFreqRatios.
Definition at line 124 of file psi_pssm_input.hpp.
References IPssmInputFreqRatios::GetImpalaScaleFactor().
◆ GetImpalaScaleFactor() [2/2]
|
inlinevirtual |
Reimplemented in CPsiBlastInputFreqRatios.
Definition at line 144 of file pssm_input.hpp.
References kPSSM_NoImpalaScaling.
Referenced by CPsiBlastInputFreqRatios::GetImpalaScaleFactor(), and CPssmEngine::x_CreatePssmFromFreqRatios().
◆ GetInclusionThreshold() [1/3]
| double CBlastOptions::GetInclusionThreshold | ( | ) | const |
Definition at line 2455 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetInclusionThreshold(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
◆ GetInclusionThreshold() [2/3]
|
inline |
Returns InclusionThreshold.
Definition at line 66 of file psiblast_options.hpp.
Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), and PsiBlastComputePssmFromAlignment().
◆ GetInclusionThreshold() [3/3]
|
inline |
Definition at line 1766 of file blast_options_local_priv.hpp.
References PSIBlastOptions::inclusion_ethresh, and CBlastOptionsLocal::m_PSIBlastOpts.
Referenced by CBlastOptions::GetInclusionThreshold().
◆ GetIndexName() [1/2]
Definition at line 2610 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetIndexName(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CSetupFactory::InitializeMegablastDbIndex().
◆ GetIndexName() [2/2]
Definition at line 1844 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_MBIndexName.
Referenced by CBlastOptions::GetIndexName().
◆ GetInformationContent()
|
static |
Returns the information content per position of the PSSM.
- Parameters
-
pssm PSSM to extract data from [in] retval vector containing the information content or an empty vector if this data is not available [in|out]
Definition at line 337 of file psiblast_aux_priv.cpp.
References copy(), ctll::empty(), CPssmIntermediateData_Base::GetInformationContent(), and CPssm_Base::GetIntermediateData().
◆ GetInitWordOpts() [1/2]
|
private |
Returns BlastInitialWordOptions for eLocal objects, NULL for eRemote.
Definition at line 2658 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetInitWordOpts(), and CBlastOptions::m_Local.
◆ GetInitWordOpts() [2/2]
|
inlineprivate |
Definition at line 426 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_InitWordOpts.
Referenced by CBlastOptions::GetInitWordOpts(), and CBlastOptionsLocal::SetProgram().
◆ GetIntervalSizes()
|
static |
Length of the aligned regions per position of the query sequence.
- Parameters
-
pssm PSSM to extract data from [in] retval vector containing the interval sizes or an empty vector if this data is not available [in|out]
Definition at line 390 of file psiblast_aux_priv.cpp.
References copy(), ctll::empty(), CPssm_Base::GetIntermediateData(), and CPssmIntermediateData_Base::GetIntervalSizes().
◆ GetIsOldStyleMBIndex() [1/2]
| bool CBlastOptions::GetIsOldStyleMBIndex | ( | ) | const |
Definition at line 2592 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetIsOldStyleMBIndex(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CSetupFactory::InitializeMegablastDbIndex().
◆ GetIsOldStyleMBIndex() [2/2]
|
inline |
Definition at line 1854 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_OldStyleMBIndex.
Referenced by CBlastOptions::GetIsOldStyleMBIndex().
◆ GetIsProtein() [1/2]
|
inline |
Answers whether sequences in this object are protein or nucleotide.
Definition at line 109 of file seqsrc_multiseq.cpp.
References CMultiSeqInfo::m_ibIsProt.
◆ GetIsProtein() [2/2]
|
inline |
Answers whether sequences in this object are protein or nucleotide.
Definition at line 186 of file seqsrc_query_factory.cpp.
References CQueryFactoryInfo::m_IsProt.
◆ GetIterationNumber()
| unsigned int CPsiBlastIterationState::GetIterationNumber | ( | ) | const |
Return the number of the current iteration.
Definition at line 129 of file psiblast_iteration.cpp.
References CPsiBlastIterationState::m_IterationsDone.
Referenced by BOOST_AUTO_TEST_CASE(), CDeltaBlastApp::DoPsiBlastIterations(), CPsiBlastApp::SavePssmToFile(), and CPsiBlastApp::x_RunLocalPsiBlastIterations().
◆ GetJDomain()
Definition at line 163 of file igblast.hpp.
References map_checker< Container >::end(), map_checker< Container >::find(), and CIgAnnotationInfo::m_JDomainInfo.
Referenced by CIgBlast::x_FillJDomain().
◆ GetKABlocks()
| list< CRef< objects::CBlast4_ka_block > > CRemoteBlast::GetKABlocks | ( | void | ) |
Get the Karlin/Altschul parameter blocks produced by the search.
- Returns
- List of references to KA blocks.
Definition at line 561 of file remote_blast.cpp.
References CRemoteBlast::x_GetGSRR().
Referenced by CRemoteBlast::GetResultSet().
◆ GetLastChunk() [1/2]
get the last chunk where query identified with global_query_index is found
- Parameters
-
global_query_index index of the query in the context of the full,non-split query [in]
- Returns
- chunk number where query is last found
Definition at line 371 of file split_query_aux_priv.cpp.
References i, CQueryDataPerChunk::kUninitialized, CQueryDataPerChunk::m_LastChunkForQueryCache, and CQueryDataPerChunk::m_QueryIndicesPerChunk.
Referenced by CQueryDataPerChunk::GetLastChunk(), and CQuerySplitter::x_ComputeContextOffsets_TranslatedQueries().
◆ GetLastChunk() [2/2]
get the last chunk where query identified with global_query_index is found
- Parameters
-
chunk_num chunk number where query is found [in] context_in_chunk which context within this chunk contains query [in]
- Returns
- chunk number where query is last found
Definition at line 362 of file split_query_aux_priv.cpp.
References _ASSERT, CQueryDataPerChunk::GetLastChunk(), CQueryDataPerChunk::m_QueryIndicesPerChunk, ncbi::grid::netcache::search::fields::size, and CQueryDataPerChunk::x_ContextInChunkToQueryIndex().
◆ GetLastId()
Get sequence id of the last sequence of a paired read.
Definition at line 198 of file magicblast.hpp.
References CMagicBlastResults::m_MateId.
◆ GetLastInfo()
|
inline |
Get alignment flags for the mate.
Definition at line 189 of file magicblast.hpp.
References CMagicBlastResults::m_LastInfo.
◆ GetLength() [1/9]
Return the length of a sequence.
- Parameters
-
i index of the sequence in the sequence container [in]
Implements IBlastQuerySource.
Definition at line 324 of file blast_objmgr_tools.cpp.
References GetLength(), CBlastQueryVector::GetQuerySeqLoc(), CBlastQueryVector::GetScope(), CBlastQuerySourceOM::GetSeqId(), i, NStr::IntToString(), CBlastQuerySourceOM::m_QueryVector, CBlastQuerySourceOM::m_TSeqLocVector, max(), NCBI_THROW, and CRef< C, Locker >::NotEmpty().
◆ GetLength() [2/9]
Return the length of a sequence.
- Parameters
-
index index of the sequence in the sequence container [in]
Implements IBlastQuerySource.
Definition at line 332 of file bioseq_extract_data_priv.cpp.
References NStr::IntToString(), CBlastQuerySourceBioseqSet::m_Bioseqs, and NCBI_THROW.
Referenced by CBioseqSeqInfoSrc::GetLength().
◆ GetLength() [3/9]
Return the length of a sequence.
- Parameters
-
index index of the sequence in the sequence container [in]
Implemented in CBlastQuerySourceBioseqSet, and CBlastQuerySourceOM.
Referenced by CObjMgr_LocalQueryData::GetSeqLength(), CObjMgrFree_LocalQueryData::GetSeqLength(), SetupQueries_OMF(), SetupQueryInfo_OMF(), and SetupSubjects_OMF().
◆ GetLength() [4/9]
Retrieve sequence length given its index in the vector.
- Parameters
-
index the ordinal number to retrieve [in]
Implements IBlastSeqInfoSrc.
Definition at line 88 of file seqinfosrc_seqvec.cpp.
References GetLength(), CSeqVecSeqInfoSrc::m_SeqVec, and NCBI_THROW.
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetLength() [5/9]
Retrieve sequence length given its index in the vector.
- Parameters
-
index the ordinal number to retrieve [in]
Implements IBlastSeqInfoSrc.
Definition at line 79 of file seqinfosrc_bioseq.cpp.
References CBlastQuerySourceBioseqSet::GetLength(), and CBioseqSeqInfoSrc::m_DataSource.
◆ GetLength() [6/9]
Method to retrieve a sequence length given its ordinal number.
- Parameters
-
index the ordinal number to retrieve [in]
Implemented in CSeqDbSeqInfoSrc, CBioseqSeqInfoSrc, and CSeqVecSeqInfoSrc.
◆ GetLength() [7/9]
Retrieve sequence length given its ordinal number.
- Parameters
-
index the ordinal number to retrieve [in]
Implements IBlastSeqInfoSrc.
Definition at line 77 of file seqinfosrc_seqdb.cpp.
References CSeqDB::GetSeqLength(), and CSeqDbSeqInfoSrc::m_iSeqDb.
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetLength() [8/9]
|
inline |
Get length of the hit segment in residues.
- Returns
- Segment length
Definition at line 248 of file cdd_pssm_input.hpp.
References COpenRange< Position >::GetLength(), and CCddInputData::CHitSegment::m_QueryRange.
◆ GetLength() [9/9]
| int CCddInputData::CHit::GetLength | ( | void | ) | const |
Get hit length in residues, counts number of matching residues, gaps are not counted.
- Returns
- Length
Definition at line 402 of file cdd_pssm_input.cpp.
◆ GetLengthAdjustment()
|
inline |
Retrieve the length adjustment for boundary conditions.
Definition at line 122 of file blast_results.hpp.
Referenced by s_BuildArchiveAll().
◆ GetLocality()
| CBlastOptions::EAPILocality CBlastOptions::GetLocality | ( | void | ) | const |
Return the locality used when the object was created.
Definition at line 334 of file blast_options_cxx.cpp.
References CBlastOptions::eBoth, CBlastOptions::eLocal, CBlastOptions::eRemote, CBlastOptions::m_Local, and CBlastOptions::m_Remote.
Referenced by CBlastOptions::Clone(), CBlastOptionsHandle::SetDefaults(), CBlastNucleotideOptionsHandle::SetTraditionalBlastnDefaults(), CBlastNucleotideOptionsHandle::SetTraditionalMegablastDefaults(), and CBlastNucleotideOptionsHandle::SetVecScreenDefaults().
◆ GetLongestIntronLength() [1/5]
| int CBlastOptions::GetLongestIntronLength | ( | void | ) | const |
for linking HSPs with uneven gaps
Definition at line 2055 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetLongestIntronLength(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
◆ GetLongestIntronLength() [2/5]
|
inline |
Returns LongestIntronLength.
Definition at line 94 of file blastx_options.hpp.
◆ GetLongestIntronLength() [3/5]
|
inline |
Returns LongestIntronLength.
Definition at line 77 of file tblastn_options.hpp.
◆ GetLongestIntronLength() [4/5]
|
inline |
Definition at line 1532 of file blast_options_local_priv.hpp.
References BlastHitSavingOptions::longest_intron, and CBlastOptionsLocal::m_HitSaveOpts.
Referenced by CBlastOptions::GetLongestIntronLength().
◆ GetLongestIntronLength() [5/5]
|
inline |
Get max intron length.
- Returns
- Max intron length
Definition at line 215 of file magicblast_options.hpp.
◆ GetLookupDbFilter() [1/3]
|
inline |
Return db filtering option for the lookup table.
The filtering removes from lookup table words that are frequent in the database.
- Returns
- If true, words that are frequent in the dabase will be removed
Definition at line 79 of file magicblast_options.hpp.
◆ GetLookupDbFilter() [2/3]
| bool CBlastOptions::GetLookupDbFilter | ( | void | ) | const |
Definition at line 947 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetLookupDbFilter(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CMagicBlastApp::Run().
◆ GetLookupDbFilter() [3/3]
|
inline |
Definition at line 658 of file blast_options_local_priv.hpp.
References LookupTableOptions::db_filter, and CBlastOptionsLocal::m_LutOpts.
Referenced by CBlastOptions::GetLookupDbFilter().
◆ GetLookupTableStride() [1/3]
| Uint4 CBlastOptions::GetLookupTableStride | ( | ) | const |
Definition at line 932 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetLookupTableStride(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
◆ GetLookupTableStride() [2/3]
|
inline |
Return number of words skipped betweem collected ones when creating a lookup table.
Definition at line 99 of file magicblast_options.hpp.
◆ GetLookupTableStride() [3/3]
|
inline |
Skip words after each collected one while creating a lookup table (currently only for megablast)
Definition at line 622 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_LutOpts, and LookupTableOptions::stride.
Referenced by CBlastOptions::GetLookupTableStride().
◆ GetLookupTableType() [1/3]
|
inline |
Returns LookupTableType.
Definition at line 74 of file blast_nucl_options.hpp.
Referenced by BOOST_FIXTURE_TEST_CASE().
◆ GetLookupTableType() [2/3]
| ELookupTableType CBlastOptions::GetLookupTableType | ( | ) | const |
Definition at line 895 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetLookupTableType(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetLookupTableType() [3/3]
|
inline |
Definition at line 591 of file blast_options_local_priv.hpp.
References LookupTableOptions::lut_type, and CBlastOptionsLocal::m_LutOpts.
Referenced by CBlastOptions::GetLookupTableType().
◆ GetLowestEvalue()
Returns the lowest score from the list of scores in CDense_seg::TScores.
- Parameters
-
scores list of scores [in] bit_score If not NULL, returns the bit score corresponding to the lowest evalue found [in|out]
Definition at line 529 of file psiblast_aux_priv.cpp.
References BLAST_EXPECT_VALUE, i, ITERATE, s_GetBitScore(), s_GetEvalue(), and tmp.
Referenced by CPsiBlastAlignmentProcessor::operator()(), and CPsiBlastInputData::x_ExtractAlignmentData().
◆ GetLowScorePerc() [1/3]
| double CBlastOptions::GetLowScorePerc | ( | ) | const |
Sets a low score to drop ungapped alignments if hit list is full.
Definition at line 2138 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetLowScorePerc(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CBlastOptionsHandle::GetLowScorePerc().
◆ GetLowScorePerc() [2/3]
|
inline |
Returns low score percentage for ungapped alignments.
Definition at line 300 of file blast_options_handle.hpp.
References CBlastOptions::GetLowScorePerc(), and CBlastOptionsHandle::m_Opts.
◆ GetLowScorePerc() [3/3]
|
inline |
Sets low score percentages.
Definition at line 1570 of file blast_options_local_priv.hpp.
References BlastHitSavingOptions::low_score_perc, and CBlastOptionsLocal::m_HitSaveOpts.
Referenced by CBlastOptions::GetLowScorePerc().
◆ GetLutOpts() [1/2]
|
private |
Returns LookupTableOptions for eLocal objects, NULL for eRemote.
Definition at line 2652 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetLutOpts(), and CBlastOptions::m_Local.
◆ GetLutOpts() [2/2]
|
inlineprivate |
Definition at line 420 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_LutOpts.
Referenced by CBlastOptions::GetLutOpts(), and CBlastOptionsLocal::SetProgram().
◆ GetMask() [1/3]
Return the filtered (masked) regions for a sequence.
- Parameters
-
i index of the sequence in the sequence container [in]
Implements IBlastQuerySource.
Definition at line 264 of file blast_objmgr_tools.cpp.
References CBlastQueryVector::GetMaskedRegions(), i, CBlastQuerySourceOM::m_QueryVector, CBlastQuerySourceOM::m_TSeqLocVector, MaskedQueryRegionsToPackedSeqLoc(), CRef< C, Locker >::NotEmpty(), and CBlastQuerySourceOM::x_CalculateMasks().
◆ GetMask() [2/3]
Return the filtered (masked) regions for a sequence.
- Parameters
-
index index of the sequence in the sequence container [in]
Implements IBlastQuerySource.
Definition at line 266 of file bioseq_extract_data_priv.cpp.
◆ GetMask() [3/3]
Return the filtered (masked) regions for a sequence.
- Parameters
-
index index of the sequence in the sequence container [in]
Implemented in CBlastQuerySourceBioseqSet, and CBlastQuerySourceOM.
Referenced by SetupSubjects_OMF().
◆ GetMaskAlgoId()
|
inline |
Returns the default filtering algorithm to use with sequence data extracted from this BlastSeqSrc.
Definition at line 591 of file seqsrc_seqdb.cpp.
Referenced by s_SeqDbSrcNew().
◆ GetMaskAtHash() [1/3]
| bool CBlastOptions::GetMaskAtHash | ( | ) | const |
Definition at line 1133 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetMaskAtHash(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CBlastOptionsHandle::GetMaskAtHash().
◆ GetMaskAtHash() [2/3]
|
inline |
Returns whether masking should only be done for lookup table creation.
Definition at line 198 of file blast_options_handle.hpp.
References CBlastOptions::GetMaskAtHash(), and CBlastOptionsHandle::m_Opts.
Referenced by BOOST_AUTO_TEST_CASE(), and BOOST_FIXTURE_TEST_CASE().
◆ GetMaskAtHash() [3/3]
|
inline |
Definition at line 734 of file blast_options_local_priv.hpp.
References QuerySetUpOptions::filtering_options, CBlastOptionsLocal::m_QueryOpts, and SBlastFilterOptions::mask_at_hash.
Referenced by CBlastOptions::GetMaskAtHash(), and CBlastOptions::SetFilterString().
◆ GetMaskedQueryRegions()
| void CSearchResults::GetMaskedQueryRegions | ( | TMaskedQueryRegions & | flt_query_regions | ) | const |
Retrieve the query regions which were masked by BLAST.
- Parameters
-
flt_query_regions the return value [in|out]
Definition at line 228 of file blast_results.cpp.
References CSearchResults::m_Masks.
◆ GetMaskedRegions() [1/3]
|
virtual |
Return the filtered (masked) regions for a sequence.
- Parameters
-
i index of the sequence in the sequence container [in]
Implements IBlastQuerySource.
Definition at line 251 of file blast_objmgr_tools.cpp.
References CBlastQueryVector::GetMaskedRegions(), i, CBlastQuerySourceOM::m_Program, CBlastQuerySourceOM::m_QueryVector, CBlastQuerySourceOM::m_TSeqLocVector, mask, CRef< C, Locker >::NotEmpty(), PackedSeqLocToMaskedQueryRegions(), and CBlastQuerySourceOM::x_CalculateMasks().
◆ GetMaskedRegions() [2/3]
|
virtual |
Return the filtered (masked) regions for a sequence.
- Parameters
-
index index of the sequence in the sequence container [in]
Implements IBlastQuerySource.
Definition at line 272 of file bioseq_extract_data_priv.cpp.
◆ GetMaskedRegions() [3/3]
|
pure virtual |
Return the filtered (masked) regions for a sequence.
- Parameters
-
index index of the sequence in the sequence container [in]
Implemented in CBlastQuerySourceBioseqSet, and CBlastQuerySourceOM.
Referenced by s_GetRestrictedBlastSeqLocs().
◆ GetMaskLevel() [1/3]
| int CBlastOptions::GetMaskLevel | ( | ) | const |
Masklevel filtering option -RMH-.
Definition at line 2095 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetMaskLevel(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CBlastOptionsHandle::GetMaskLevel().
◆ GetMaskLevel() [2/3]
|
inline |
Returns MaskLevel -RMH-.
Definition at line 288 of file blast_options_handle.hpp.
References CBlastOptions::GetMaskLevel(), and CBlastOptionsHandle::m_Opts.
◆ GetMaskLevel() [3/3]
|
inline |
Masklevel filtering option -RMH-.
Definition at line 1557 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_HitSaveOpts, and BlastHitSavingOptions::mask_level.
Referenced by CBlastOptions::GetMaskLevel().
◆ GetMasks() [1/9]
|
virtual |
Retrieves the subject masks for the corresponding index.
- Parameters
-
index the ordinal number to retrieve [in] target_range range for which to return masks for. Empty ranges indicate that no masks should be retrieved, whole ranges mean that masks for the whole sequence should be retrieved [in] retval the masks will be returned through this parameter [out]
- Returns
- true if there were masks returned in retval, otherwise false.
Implements IBlastSeqInfoSrc.
Definition at line 97 of file seqinfosrc_seqdb.cpp.
References COpenRange< TSeqPos >::GetEmpty(), and CSeqDbSeqInfoSrc::m_FilteringAlgoId.
◆ GetMasks() [2/9]
|
virtual |
Retrieves the subject masks for the corresponding index.
- Parameters
-
index the ordinal number to retrieve [in] target_range range for which to return masks for. Empty ranges indicate that no masks should be retrieved, whole ranges mean that masks for the whole sequence should be retrieved [in] retval the masks will be returned through this parameter [out]
- Returns
- true if there were masks returned in retval, otherwise false.
Implements IBlastSeqInfoSrc.
Definition at line 127 of file seqinfosrc_seqvec.cpp.
References COpenRange< TSeqPos >::GetEmpty().
◆ GetMasks() [3/9]
|
virtual |
Retrieves the subject masks for the corresponding index.
- Parameters
-
index the ordinal number to retrieve [in] target_range range for which to return masks for. Empty ranges indicate that no masks should be retrieved, whole ranges mean that masks for the whole sequence should be retrieved [in] retval the masks will be returned through this parameter [out]
- Returns
- true if there were masks returned in retval, otherwise false.
Implements IBlastSeqInfoSrc.
Definition at line 94 of file seqinfosrc_bioseq.cpp.
◆ GetMasks() [4/9]
|
pure virtual |
Retrieves the subject masks for the corresponding index.
- Parameters
-
index the ordinal number to retrieve [in] target_range range for which to return masks for. Empty ranges indicate that no masks should be retrieved, whole ranges mean that masks for the whole sequence should be retrieved [in] retval the masks will be returned through this parameter [out]
- Returns
- true if there were masks returned in retval, otherwise false.
Implemented in CBioseqSeqInfoSrc, CSeqVecSeqInfoSrc, and CSeqDbSeqInfoSrc.
Referenced by BlastHitList2SeqAlign_OMF(), and s_BLAST_OneSubjectResults2CSeqAlign().
◆ GetMasks() [5/9]
|
virtual |
Retrieves the subject masks for the corresponding index.
- Parameters
-
index the ordinal number to retrieve [in] target_ranges ranges for which to return masks for. Empty ranges indicate that no masks should be retrieved, whole ranges mean that masks for the whole sequence should be retrieved [in] retval the masks will be returned through this parameter [out]
- Returns
- true if there were masks returned in retval, otherwise false.
Implements IBlastSeqInfoSrc.
Definition at line 109 of file seqinfosrc_seqdb.cpp.
References CSeqLocInfo::eFrameNotSet, ctll::front(), COpenRange< TSeqPos >::GetEmpty(), CSeqDbSeqInfoSrc::GetId(), CSeqDB::GetMaskData(), ITERATE, CSeqDbSeqInfoSrc::m_FilteringAlgoId, CSeqDbSeqInfoSrc::m_iSeqDb, and si.
◆ GetMasks() [6/9]
|
virtual |
Retrieves the subject masks for the corresponding index.
- Parameters
-
index the ordinal number to retrieve [in] target_ranges range for which to return masks for. Empty ranges indicate that no masks should be retrieved, whole ranges mean that masks for the whole sequence should be retrieved [in] retval the masks will be returned through this parameter [out]
- Returns
- true if there were masks returned in retval, otherwise false.
Implements IBlastSeqInfoSrc.
Definition at line 139 of file seqinfosrc_seqvec.cpp.
References CSeqLocInfo::eFrameNotSet, ITERATE, CSeqVecSeqInfoSrc::m_SeqVec, mask, NCBI_THROW, and s_SeqIntervalToSeqLocInfo().
◆ GetMasks() [7/9]
|
virtual |
Retrieves the subject masks for the corresponding index.
- Parameters
-
index the ordinal number to retrieve [in] target_ranges range for which to return masks for. Empty ranges indicate that no masks should be retrieved, whole ranges mean that masks for the whole sequence should be retrieved [in] retval the masks will be returned through this parameter [out]
- Returns
- true if there were masks returned in retval, otherwise false.
Implements IBlastSeqInfoSrc.
Definition at line 101 of file seqinfosrc_bioseq.cpp.
◆ GetMasks() [8/9]
|
pure virtual |
Retrieves the subject masks for the corresponding index.
- Parameters
-
index the ordinal number to retrieve [in] target_ranges ranges for which to return masks for. Empty ranges indicate that no masks should be retrieved, whole ranges mean that masks for the whole sequence should be retrieved [in] retval the masks will be returned through this parameter [out]
- Returns
- true if there were masks returned in retval, otherwise false.
Implemented in CBioseqSeqInfoSrc, CSeqVecSeqInfoSrc, and CSeqDbSeqInfoSrc.
◆ GetMasks() [9/9]
| TSeqLocInfoVector CRemoteBlast::GetMasks | ( | void | ) |
Get the queries' masked locations.
Definition at line 489 of file remote_blast.cpp.
References _ASSERT, CSeq_id::Compare(), CSeq_id::e_YES, CConstRef< C, Locker >::Empty(), CPacked_seqint_Base::Get(), CSeq_loc_Base::GetPacked_int(), CRemoteBlast::GetQueries(), CSeq_loc_Base::IsPacked_int(), ITERATE, CRemoteBlast::m_Program, CRemoteBlast::m_Service, mask, NetworkFrame2FrameNumber(), NetworkProgram2BlastProgramType(), NULL, si, and CRemoteBlast::x_GetMasks().
Referenced by BOOST_AUTO_TEST_CASE(), and CRemoteBlast::GetResultSet().
◆ GetMaskType() [1/2]
| ESubjectMaskingType CSearchDatabase::GetMaskType | ( | ) | const |
Definition at line 217 of file uniform_search.cpp.
References CSearchDatabase::m_MaskType.
Referenced by CBlastFormat::CBlastFormat(), CSetupFactory::CreateBlastSeqSrc(), and CExportStrategy::x_Process_SearchDb().
◆ GetMaskType() [2/2]
|
inline |
Definition at line 592 of file seqsrc_seqdb.cpp.
Referenced by s_SeqDbSrcNew().
◆ GetMatchReward() [1/3]
|
inline |
Returns MatchReward.
Definition at line 183 of file blast_nucl_options.hpp.
Referenced by BOOST_AUTO_TEST_CASE(), and BOOST_FIXTURE_TEST_CASE().
◆ GetMatchReward() [2/3]
| int CBlastOptions::GetMatchReward | ( | ) | const |
Definition at line 2217 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetMatchReward(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CScoreBuilder::x_Initialize().
◆ GetMatchReward() [3/3]
|
inline |
Definition at line 1622 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_ScoringOpts, and BlastScoringOptions::reward.
Referenced by CBlastOptions::GetMatchReward().
◆ GetMatrixName() [1/10]
|
inlinevirtual |
Obtain the name of the underlying matrix to use when building the PSSM.
Reimplemented from IPssmInput_Base.
Definition at line 104 of file msa_pssm_input.hpp.
References IPssmInput_Base::GetMatrixName().
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetMatrixName() [2/10]
|
inlinevirtual |
Obtain the name of the underlying matrix to use when building the PSSM.
Reimplemented from IPssmInput_Base.
Definition at line 104 of file psi_pssm_input.hpp.
References IPssmInput_Base::GetMatrixName().
◆ GetMatrixName() [3/10]
|
inlinevirtual |
Obtain the name of the underlying matrix to use when building the PSSM.
Reimplemented from IPssmInput_Base.
Definition at line 219 of file psi_pssm_input.cpp.
References IPssmInput_Base::GetMatrixName(), and CPsiBlastInputData::m_MatrixName.
◆ GetMatrixName() [4/10]
|
inlinevirtual |
Obtain the name of the underlying matrix to use when building the PSSM.
Reimplemented in SU_PSSMInput, CCddInputData, CPssmInputUnsupportedMatrix, CNullPssmInput, CdPssmInput, CPsiBlastInputData, CPsiBlastInputFreqRatios, and CPsiBlastInputClustalW.
Definition at line 68 of file pssm_input.hpp.
References BLAST_DEFAULT_MATRIX.
Referenced by CPsiBlastInputClustalW::GetMatrixName(), CPsiBlastInputFreqRatios::GetMatrixName(), CPsiBlastInputData::GetMatrixName(), CPssmEngine::x_CreatePssmFromCDD(), CPssmEngine::x_CreatePssmFromFreqRatios(), CPssmEngine::x_CreatePssmFromMsa(), and CPssmEngine::x_GetMatrixName().
◆ GetMatrixName() [5/10]
|
inline |
Returns MatrixName.
Definition at line 195 of file blast_nucl_options.hpp.
Referenced by BOOST_FIXTURE_TEST_CASE().
◆ GetMatrixName() [6/10]
| const char * CBlastOptions::GetMatrixName | ( | void | ) | const |
Definition at line 2198 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetMatrixName(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by BOOST_AUTO_TEST_CASE(), CWindowSizeArg::ExtractAlgorithmOptions(), CWordThresholdArg::ExtractAlgorithmOptions(), CBlastnNode::Main(), CBlastpNode::Main(), CBlastxNode::Main(), CRPSBlastNode::Main(), CRPSTBlastnNode::Main(), CTblastnNode::Main(), CIgBlastnApp::CIgFormatter::Main(), CBlastFormatterApp::PrintFormattedOutput(), PsiBlastComputePssmScores(), CDeltaBlastApp::Run(), CPsiBlastApp::Run(), CTblastxApp::Run(), CIgBlastnApp::Run(), CIgBlastpApp::Run(), CRMBlastnApp::Run(), CPsiBlastArgs::x_CreatePssmFromMsa(), CScoreBuilder::x_Initialize(), CBlastnApp::x_RunMTBySplitDB(), CBlastpApp::x_RunMTBySplitDB(), CBlastxApp::x_RunMTBySplitDB(), CRPSBlastApp::x_RunMTBySplitDB(), CRPSTBlastnApp::x_RunMTBySplitDB(), and CTblastnApp::x_RunMTBySplitDB().
◆ GetMatrixName() [7/10]
|
inline |
Returns MatrixName.
Definition at line 112 of file blast_prot_options.hpp.
Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), PsiBlastComputePssmFromAlignment(), and CDeltaBlast::Run().
◆ GetMatrixName() [8/10]
| const char * CBlastRPSInfo::GetMatrixName | ( | void | ) | const |
Returns the name of the scoring matrix used to build the RPS-BLAST database.
Definition at line 627 of file rps_aux.cpp.
References CBlastRPSInfo::m_RpsInfo.
Referenced by CSetupFactory::CreateRpsStructures().
◆ GetMatrixName() [9/10]
|
inline |
Definition at line 563 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_ScoringOpts, and BlastScoringOptions::matrix.
Referenced by CBlastOptions::GetMatrixName().
◆ GetMatrixName() [10/10]
|
inlinevirtual |
Get scoring matrix name.
- Returns
- Scoring matrix name
Reimplemented from IPssmInput_Base.
Definition at line 149 of file cdd_pssm_input.hpp.
References CCddInputData::m_MatrixName.
◆ GetMaxDbWordCount() [1/3]
| Uint1 CBlastOptions::GetMaxDbWordCount | ( | void | ) | const |
Get maximum word count for lookup table word masking by database frequency.
Definition at line 963 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetMaxDbWordCount(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
◆ GetMaxDbWordCount() [2/3]
|
inline |
Get maximum word count for lookup table word masking by database frequency.
Definition at line 91 of file magicblast_options.hpp.
◆ GetMaxDbWordCount() [3/3]
|
inline |
Definition at line 670 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_LutOpts, and LookupTableOptions::max_db_word_count.
Referenced by CBlastOptions::GetMaxDbWordCount().
◆ GetMaxEditDistance() [1/3]
| int CBlastOptions::GetMaxEditDistance | ( | ) | const |
Definition at line 1980 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetMaxEditDistance(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
◆ GetMaxEditDistance() [2/3]
|
inline |
Definition at line 191 of file magicblast_options.hpp.
◆ GetMaxEditDistance() [3/3]
|
inline |
Definition at line 1484 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_HitSaveOpts, and BlastHitSavingOptions::max_edit_distance.
Referenced by CBlastOptions::GetMaxEditDistance().
◆ GetMaxFractionAmbiguous()
|
inline |
Get maximum fraction of ambiguous bases for query quality filtering.
Definition at line 118 of file magicblast_options.hpp.
◆ GetMaxHspsPerSubject() [1/3]
| int CBlastOptions::GetMaxHspsPerSubject | ( | ) | const |
Definition at line 1810 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetMaxHspsPerSubject(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CBlastOptionsHandle::GetMaxHspsPerSubject().
◆ GetMaxHspsPerSubject() [2/3]
|
inline |
Returns MaxHspsPerSubjectQueryPair.
Definition at line 239 of file blast_options_handle.hpp.
References CBlastOptions::GetMaxHspsPerSubject(), and CBlastOptionsHandle::m_Opts.
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetMaxHspsPerSubject() [3/3]
|
inline |
Definition at line 1293 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_HitSaveOpts, and BlastHitSavingOptions::max_hsps_per_subject.
Referenced by CBlastOptions::GetMaxHspsPerSubject().
◆ GetMaxLength() [1/2]
|
inline |
Setter and getter functions for the private fields.
Returns maximal length of a set of sequences.
Definition at line 79 of file seqsrc_multiseq.cpp.
References CMultiSeqInfo::m_iMaxLength.
◆ GetMaxLength() [2/2]
|
inline |
Setter and getter functions for the private fields.
Returns maximal length of a set of sequences.
Definition at line 162 of file seqsrc_query_factory.cpp.
References CQueryFactoryInfo::m_MaxLength.
◆ GetMaxMismatches() [1/2]
| int CBlastOptions::GetMaxMismatches | ( | ) | const |
Definition at line 1706 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetMaxMismatches(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
◆ GetMaxMismatches() [2/2]
|
inline |
Definition at line 1232 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_ExtnOpts, and BlastExtensionOptions::max_mismatches.
Referenced by CBlastOptions::GetMaxMismatches().
◆ GetMaxNumHspPerSequence() [1/3]
| int CBlastOptions::GetMaxNumHspPerSequence | ( | ) | const |
Definition at line 1791 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetMaxNumHspPerSequence(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CBlastOptionsHandle::GetMaxNumHspPerSequence().
◆ GetMaxNumHspPerSequence() [2/3]
|
inline |
Returns MaxNumHspPerSequence.
Definition at line 231 of file blast_options_handle.hpp.
References CBlastOptions::GetMaxNumHspPerSequence(), and CBlastOptionsHandle::m_Opts.
Referenced by BOOST_FIXTURE_TEST_CASE().
◆ GetMaxNumHspPerSequence() [3/3]
|
inline |
Definition at line 1281 of file blast_options_local_priv.hpp.
References BlastHitSavingOptions::hsp_num_max, and CBlastOptionsLocal::m_HitSaveOpts.
Referenced by CBlastOptions::GetMaxNumHspPerSequence().
◆ GetMBIndexLoaded() [1/2]
| bool CBlastOptions::GetMBIndexLoaded | ( | ) | const |
Definition at line 2601 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetMBIndexLoaded(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CSetupFactory::InitializeMegablastDbIndex(), CBlastnNode::Main(), CIgBlastnApp::CIgFormatter::Main(), CBlastFormatterApp::PrintFormattedOutput(), CIgBlastnApp::Run(), CRMBlastnApp::Run(), s_CreateRepeatsSearchOptions(), and CBlastnApp::x_RunMTBySplitDB().
◆ GetMBIndexLoaded() [2/2]
|
inline |
Definition at line 1839 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_MBIndexLoaded.
Referenced by CBlastOptions::GetMBIndexLoaded().
◆ GetMBTemplateLength() [1/2]
| unsigned char CBlastOptions::GetMBTemplateLength | ( | ) | const |
Megablast only lookup table options.
Definition at line 982 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetMBTemplateLength(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CSetupFactory::InitializeMegablastDbIndex().
◆ GetMBTemplateLength() [2/2]
|
inline |
Megablast only lookup table options.
Definition at line 634 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_LutOpts, and LookupTableOptions::mb_template_length.
Referenced by CBlastOptions::GetMBTemplateLength().
◆ GetMBTemplateType() [1/2]
| unsigned char CBlastOptions::GetMBTemplateType | ( | ) | const |
Definition at line 1001 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetMBTemplateType(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
◆ GetMBTemplateType() [2/2]
|
inline |
Definition at line 646 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_LutOpts, and LookupTableOptions::mb_template_type.
Referenced by CBlastOptions::GetMBTemplateType().
◆ GetMessages() [1/3]
|
inline |
Returns error messages/warnings.
Definition at line 296 of file bl2seq.hpp.
References CBl2Seq::m_Messages.
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetMessages() [2/3]
| void ILocalQueryData::GetMessages | ( | TSearchMessages & | messages | ) | const |
Retrieve all error/warning messages.
Definition at line 142 of file query_data.cpp.
References ILocalQueryData::m_Messages.
Referenced by BlastSetupPreliminarySearchEx(), and CBlastTracebackSearch::x_Init().
◆ GetMessages() [3/3]
|
inline |
Return list of saved diag messages.
Definition at line 262 of file blast_aux.hpp.
References CBlastAppDiagHandler::m_messages.
Referenced by CPsiBlastApp::DoIterations(), CDeltaBlastApp::DoPsiBlastIterations(), CBlastnNode::Main(), CBlastpNode::Main(), CBlastxNode::Main(), CRPSBlastNode::Main(), CRPSTBlastnNode::Main(), CTblastnNode::Main(), CBlastnApp::Run(), CBlastpApp::Run(), CBlastxApp::Run(), CDeltaBlastApp::Run(), CPsiBlastApp::Run(), CTblastnApp::Run(), CTblastxApp::Run(), CPsiBlastApp::x_RunLocalPsiBlastIterations(), CBlastnApp::x_RunMTBySplitDB(), CBlastpApp::x_RunMTBySplitDB(), CBlastxApp::x_RunMTBySplitDB(), CRPSBlastApp::x_RunMTBySplitDB(), CRPSTBlastnApp::x_RunMTBySplitDB(), CTblastnApp::x_RunMTBySplitDB(), CBlastnApp::x_RunMTBySplitQuery(), CBlastpApp::x_RunMTBySplitQuery(), CBlastxApp::x_RunMTBySplitQuery(), CRPSBlastApp::x_RunMTBySplitQuery(), CRPSTBlastnApp::x_RunMTBySplitQuery(), and CTblastnApp::x_RunMTBySplitQuery().
◆ GetMinDiagSeparation() [1/3]
| int CBlastOptions::GetMinDiagSeparation | ( | ) | const |
Definition at line 2019 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetMinDiagSeparation(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CBlastOptionsHandle::GetMinDiagSeparation().
◆ GetMinDiagSeparation() [2/3]
|
inline |
Returns MinDiagSeparation.
Definition at line 270 of file blast_options_handle.hpp.
References CBlastOptions::GetMinDiagSeparation(), and CBlastOptionsHandle::m_Opts.
◆ GetMinDiagSeparation() [3/3]
|
inline |
Definition at line 1508 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_HitSaveOpts, and BlastHitSavingOptions::min_diag_separation.
Referenced by CBlastOptions::GetMinDiagSeparation().
◆ GetMinDimerEntropy()
|
inline |
Get mininum dimer entropy for query quality filtering.
Definition at line 126 of file magicblast_options.hpp.
◆ GetMinHits()
|
inline |
Returns the number of hits to initiate calculation of Jaccard distance.
Definition at line 73 of file blastp_kmer_options.hpp.
Referenced by BOOST_AUTO_TEST_CASE(), CBlastKmerThread::Main(), and CBlastKmerSearch::Run().
◆ GetMinLength()
|
inline |
Returns minimal length of a set of sequences.
Definition at line 168 of file seqsrc_query_factory.cpp.
References CQueryFactoryInfo::m_MinLength.
◆ GetMismatchPenalty() [1/4]
|
inline |
Returns MismatchPenalty.
Definition at line 189 of file blast_nucl_options.hpp.
Referenced by BOOST_AUTO_TEST_CASE(), and BOOST_FIXTURE_TEST_CASE().
◆ GetMismatchPenalty() [2/4]
| int CBlastOptions::GetMismatchPenalty | ( | ) | const |
Definition at line 2236 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetMismatchPenalty(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CScoreBuilder::x_Initialize().
◆ GetMismatchPenalty() [3/4]
|
inline |
Returns mismatch penalty.
Definition at line 153 of file magicblast_options.hpp.
◆ GetMismatchPenalty() [4/4]
|
inline |
Definition at line 1634 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_ScoringOpts, and BlastScoringOptions::penalty.
Referenced by CBlastOptions::GetMismatchPenalty().
◆ GetMismatchWindow() [1/2]
| int CBlastOptions::GetMismatchWindow | ( | ) | const |
Definition at line 1728 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetMismatchWindow(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
◆ GetMismatchWindow() [2/2]
|
inline |
Definition at line 1244 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_ExtnOpts, and BlastExtensionOptions::mismatch_window.
Referenced by CBlastOptions::GetMismatchWindow().
◆ GetMoleculeType()
| CSearchDatabase::EMoleculeType CSearchDatabase::GetMoleculeType | ( | ) | const |
Accessor for the molecule type.
Definition at line 82 of file uniform_search.cpp.
References CSearchDatabase::m_MolType.
Referenced by CSearchDatabase::IsProtein().
◆ GetNegativeGiList() [1/2]
| list< TGi > CBlastOptionsBuilder::GetNegativeGiList | ( | ) |
Get the negative GI list.
Definition at line 773 of file blast_options_builder.cpp.
References CBlastOptionsBuilder::m_NegativeGiList.
Referenced by CRemoteBlast::GetSearchOptions(), and s_ImportDatabase().
◆ GetNegativeGiList() [2/2]
| const CRef< CSeqDBGiList > & CSearchDatabase::GetNegativeGiList | ( | ) | const |
Accessor for the negative gi list.
Definition at line 134 of file uniform_search.cpp.
References CSearchDatabase::m_NegativeGiList.
Referenced by CBlastKmerThread::Main(), CMagicBlastThread::Main(), CMagicBlastApp::x_LogBlastSearchInfo(), and CExportStrategy::x_Process_SearchDb().
◆ GetNegativeGiListLimitation()
| const CSearchDatabase::TGiList CSearchDatabase::GetNegativeGiListLimitation | ( | ) | const |
Definition at line 140 of file uniform_search.cpp.
References CSeqDBGiList::Empty(), CRef< C, Locker >::Empty(), CSeqDBGiList::GetGiList(), and CSearchDatabase::m_NegativeGiList.
Referenced by CRemoteBlast::x_Init(), and CExportStrategy::x_Process_SearchDb().
◆ GetNegativeTaxidList() [1/3]
| list< TTaxId > CBlastOptionsBuilder::GetNegativeTaxidList | ( | ) |
Get the negative tax id list.
Definition at line 809 of file blast_options_builder.cpp.
References CBlastOptionsBuilder::SOptional< T >::Get(), and CBlastOptionsBuilder::m_NegativeTaxidList.
Referenced by CRemoteBlast::GetSearchOptions(), and s_ImportDatabase().
◆ GetNegativeTaxidList() [2/3]
Definition at line 491 of file remote_blast.hpp.
References CRemoteBlast::m_NegativeTaxidList.
Referenced by CBlastFormatterApp::PrintFormattedOutput().
◆ GetNegativeTaxidList() [3/3]
Definition at line 289 of file search_strategy.cpp.
References eBlastOpt_NegativeTaxidList, set< Key, Compare >::insert(), and CImportStrategy::x_GetProgramOptionIntegerList().
◆ GetNextUnusedOID()
|
private |
Auxiliary function thet returns the oid value that is one more than the largest oid used so far.
Definition at line 654 of file blast_dbindex.cpp.
References CIndexedDb_New::SVolumeDescriptor::n_oids, CIndexedDb_New::SVolumeDescriptor::start_oid, and CIndexedDb_New::volumes_.
Referenced by CIndexedDb_New::AddIndexInfo().
◆ GetNumAlignedSequences()
|
private |
Returns the number of sequences that make up the multiple sequence alignment.
- Exceptions
-
CBlastException if this number hasn't been calculated yet (need to invoke Process() first!)
Definition at line 187 of file psi_pssm_input.cpp.
References _ASSERT, CPsiBlastInputData::m_MsaDimensions, and PSIMsaDimensions::num_seqs.
Referenced by CPsiBlastInputData::x_ExtractAlignmentData().
◆ GetNumberOfChunks()
|
inline |
Returns the number of chunks the query/queries will be split into.
Definition at line 85 of file split_query.hpp.
References CQuerySplitter::m_NumChunks.
Referenced by BOOST_AUTO_TEST_CASE(), CQuerySplitter::IsQuerySplit(), operator<<(), CSplitQueryTestFixture::QuerySplitter_BlastnMultiQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastnSingleQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastxMultiQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastxSingleQueryMultiChunk(), CBlastPrelimSearch::Run(), CSplitQueryTestFixture::x_TestCContextTranslator(), and CSplitQueryTestFixture::x_ValidateLocalQueryData().
◆ GetNumberOfContexts()
| unsigned int GetNumberOfContexts | ( | EBlastProgramType | p | ) |
Returns the number of contexts for a given BLAST program.
- See also
- BLAST_GetNumberOfContexts
- Parameters
-
p program
Definition at line 1453 of file blast_setup_cxx.cpp.
References BLAST_GetNumberOfContexts(), Blast_ProgramNameFromType(), NStr::IntToString(), msg(), and NCBI_THROW.
Referenced by Blast_GetSeqLocInfoVector(), BOOST_AUTO_TEST_CASE(), s_AddMask(), s_GetBlastnMask(), SetupQueries_OMF(), SetupQueryInfo_OMF(), CQuerySplitter::x_ComputeQueryContextsForChunks(), and x_TestGetSeqLocInfoVector().
◆ GetNumberOfThreads()
|
inline |
Accessor for the number of threads to use.
Definition at line 373 of file setup_factory.hpp.
References ASSERT, CThreadable::kMinNumThreads, and CThreadable::m_NumThreads.
Referenced by BOOST_AUTO_TEST_CASE(), CDeltaBlast::Run(), CLocalBlast::Run(), CBlastPrelimSearch::Run(), CPsiBlast::Run(), CPsiBlastImpl::Run(), CBlastPrelimSearch::x_LaunchMultiThreadedSearch(), CMagicBlast::x_Run(), and CBlastKmer::x_SearchMultipleQueries().
◆ GetNumChunks()
| size_t CSplitQueryBlk::GetNumChunks | ( | ) | const |
Retrieve the number of chunks.
Definition at line 60 of file split_query_blk.cpp.
References CSplitQueryBlk::m_SplitQueryBlk, and SSplitQueryBlk::num_chunks.
Referenced by BOOST_AUTO_TEST_CASE(), CContextTranslator::CContextTranslator(), CQueryDataPerChunk::CQueryDataPerChunk(), operator<<(), CSplitQueryTestFixture::QuerySplitter_BlastnMultiQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastnSingleQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastxMultiQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastxSingleQueryMultiChunk(), CSplitQueryTestFixture::x_ValidateChunkBounds(), CSplitQueryTestFixture::x_ValidateContextOffsetsPerChunkAssignment(), CSplitQueryTestFixture::x_ValidateQueriesPerChunkAssignment(), and CSplitQueryTestFixture::x_ValidateQueryContextsPerChunkAssignment().
◆ GetNumExtensions()
| Int4 CLocalBlast::GetNumExtensions | ( | ) |
Retrieve the number of extensions performed during the search.
Definition at line 296 of file local_blast.cpp.
References BlastUngappedStats::good_init_extends, SInternalData::m_Diagnostics, CLocalBlast::m_InternalData, and BlastDiagnostics::ungapped_stat.
Referenced by CBlastnNode::Main(), s_RunLocalVDBSearch(), and CBlastnApp::x_RunMTBySplitDB().
◆ GetNumFrames()
|
inline |
Definition at line 497 of file blast_setup.hpp.
References BLAST_GetNumberOfContexts(), and CBlastQueryFilteredFrames::m_Program.
Referenced by BOOST_AUTO_TEST_CASE(), and s_RestrictSeqLocs_Multiframe().
◆ GetNumMatchingSeqs()
|
static |
Gets the number of matching sequences per position of the PSSM.
- Parameters
-
pssm PSSM to extract data from [in] retval vector containing the number of matching sequences or an empty vector if this data is not available [in|out]
Definition at line 408 of file psiblast_aux_priv.cpp.
References copy(), ctll::empty(), CPssm_Base::GetIntermediateData(), and CPssmIntermediateData_Base::GetNumMatchingSeqs().
◆ GetNumQueries() [1/4]
|
virtual |
Get the number of queries.
Implements ILocalQueryData.
Definition at line 235 of file objmgr_query_data.cpp.
References _ASSERT, CObjMgr_LocalQueryData::GetQueryInfo(), CObjMgr_LocalQueryData::m_QuerySource, and IBlastQuerySource::Size().
◆ GetNumQueries() [2/4]
|
virtual |
Get the number of queries.
Implements ILocalQueryData.
Definition at line 135 of file objmgrfree_query_data.cpp.
References _ASSERT, CObjMgrFree_LocalQueryData::GetQueryInfo(), CObjMgrFree_LocalQueryData::m_QuerySource, and IBlastQuerySource::Size().
◆ GetNumQueries() [3/4]
|
inline |
Return the number of unique query ID's represented by this object.
Definition at line 410 of file blast_results.hpp.
References CSearchResultSet::m_NumQueries.
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetNumQueries() [4/4]
|
pure virtual |
Get the number of queries.
Implemented in CObjMgrFree_LocalQueryData, and CObjMgr_LocalQueryData.
Referenced by BlastSetupPreliminarySearchEx(), ILocalQueryData::GetSumOfSequenceLengths(), ILocalQueryData::IsAtLeastOneQueryValid(), operator<<(), CPsiBlastValidate::QueryFactory(), CDeltaBlast::Run(), CLocalBlast::Run(), CBlastTracebackSearch::Run(), s_BLAST_OneSubjectResults2CSeqAlign(), s_BlastResults2SeqAlignSequenceCmp_OMF(), s_LocalQueryData2Packed_seqint(), s_MakeEmptyResults(), CMagicBlast::x_BuildResultSet(), CMagicBlast::x_BuildSeqAlignSet(), CQuerySplitter::x_ComputeQueryIndicesForChunks(), CQuerySplitter::x_ExtractCScopesAndMasks(), CMagicBlast::x_Run(), ILocalQueryData::x_ValidateIndex(), and CSplitQueryTestFixture::x_ValidateLocalQueryData().
◆ GetNumQueriesForChunk()
| size_t CSplitQueryBlk::GetNumQueriesForChunk | ( | size_t | chunk_num | ) | const |
Get the number of queries in a given chunk.
- Parameters
-
chunk_num desired chunk [in]
Definition at line 66 of file split_query_blk.cpp.
References CSplitQueryBlk::m_SplitQueryBlk, and SplitQueryBlk_GetNumQueriesForChunk().
Referenced by BOOST_AUTO_TEST_CASE(), and CSplitQueryTestFixture::x_ValidateLocalQueryData().
◆ GetNumResults()
|
inline |
Return the number of results contained by this object.
- Note
- this returns the number of queries for results of type eDatabaseSearch and (number of queries * number of subjects) for results of type eSequenceComparison
Definition at line 404 of file blast_results.hpp.
References CSearchResultSet::m_Results.
Referenced by BOOST_AUTO_TEST_CASE(), CBl2Seq::CSearchResultSet2TSeqAlignVector(), CSimpleB2SWrapper::DoBlast2Seqs(), CSearchResultSet::GetResults(), CdBlaster::processBlastHits(), CdBlaster::psiBlast(), CSearchResultSet::size(), and CTracebackSearchTestFixture::x_Traceback().
◆ GetNumSeqs() [1/2]
|
inline |
Returns number of sequences.
Definition at line 115 of file seqsrc_multiseq.cpp.
References CMultiSeqInfo::m_ivSeqBlkVec.
◆ GetNumSeqs() [2/2]
|
inline |
Returns number of sequences.
Definition at line 192 of file seqsrc_query_factory.cpp.
References CQueryFactoryInfo::m_NumSeqs.
Referenced by CQueryFactoryInfo::GetSeqBlk().
◆ GetOffDiagonalRange() [1/3]
| int CBlastOptions::GetOffDiagonalRange | ( | ) | const |
Definition at line 1510 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetOffDiagonalRange(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CBlastOptionsHandle::GetOffDiagonalRange().
◆ GetOffDiagonalRange() [2/3]
|
inline |
Definition at line 185 of file blast_options_handle.hpp.
References CBlastOptions::GetOffDiagonalRange(), and CBlastOptionsHandle::m_Opts.
◆ GetOffDiagonalRange() [3/3]
|
inline |
Definition at line 1105 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_InitWordOpts, and BlastInitialWordOptions::scan_range.
Referenced by CBlastOptions::GetOffDiagonalRange().
◆ GetOptions() [1/9]
|
inlinevirtual |
Obtain the options for the PSSM engine.
Implements IPssmInputData.
Definition at line 99 of file msa_pssm_input.hpp.
◆ GetOptions() [2/9]
|
inlinevirtual |
Obtain the options for the PSSM engine.
Implements IPssmInputData.
Definition at line 213 of file psi_pssm_input.cpp.
References CPsiBlastInputData::m_Opts.
◆ GetOptions() [3/9]
|
inline |
Return the object which this object is a handle for.
This method is intended to be used when one wants to INSPECT the values of options which are not exposed by the classes derived from CBlastOptionsHandle.
Definition at line 160 of file blast_options_handle.hpp.
References CBlastOptionsHandle::m_Opts.
Referenced by Blast_FindWindowMaskerLoc_Fwd(), BOOST_AUTO_TEST_CASE(), CheckForFreqRatioFile(), CLocalDbAdapter::CLocalDbAdapter(), CPsiBl2SeqTestFixture::CPsiBl2SeqTestFixture(), CPsiBlastTestFixture::CPsiBlastTestFixture(), CVecscreenRun::CFormatter::FormatResults(), CLocalDbAdapter::IsProtein(), CBlastKmerThread::Main(), CBlastnNode::Main(), CBlastpNode::Main(), CBlastxNode::Main(), CRPSBlastNode::Main(), CRPSTBlastnNode::Main(), CTblastnNode::Main(), CMagicBlastThread::Main(), CLocalDbAdapter::MakeSeqInfoSrc(), CLocalDbAdapter::MakeSeqSrc(), CPsiBlastValidate::QueryFactory(), CDeltaBlast::Run(), CLocalVDBBlast::Run(), CPsiBlastImpl::Run(), CBlastnApp::Run(), CBlastpApp::Run(), CBlastxApp::Run(), CDeltaBlastApp::Run(), CPsiBlastApp::Run(), CTblastnApp::Run(), CTblastxApp::Run(), CIgBlastnApp::Run(), CIgBlastpApp::Run(), CMagicBlastApp::Run(), CRMBlastnApp::Run(), CBlastKmerSearch::Run(), CBlastKmerApplication::Run(), CVDBBlastnApp::Run(), CVDBTblastnApp::Run(), CBlastDemoApplication::Run(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), CVDBThread::RunTandemSearches(), CLocalVDBBlast::RunThreadedSearch(), s_CreateRepeatsSearchOptions(), setupQueryInfoForOffsetTranslation(), CLocalVDBBlast::x_AdjustDbSize(), CBLASTSeqToolJob::x_CreateProjectItems(), CPsiBlastImpl::x_CreatePssmScoresFromFrequencyRatios(), CRemoteBlast::x_Init(), CSequenceDataTester::x_Init(), CScoreBuilder::x_Initialize(), CBlastAppArgs::x_IssueWarningsForIgnoredOptions(), CSplitQueryTestFixture::x_PrepareBlastQueryStructures(), CLocalVDBBlast::x_PrepareQuery(), CExportStrategy::x_Process_BlastOptions(), CPsiBlastApp::x_RunLocalPsiBlastIterations(), CBlastnApp::x_RunMTBySplitDB(), CBlastpApp::x_RunMTBySplitDB(), CBlastxApp::x_RunMTBySplitDB(), CRPSBlastApp::x_RunMTBySplitDB(), CRPSTBlastnApp::x_RunMTBySplitDB(), CTblastnApp::x_RunMTBySplitDB(), CBlastnApp::x_RunMTBySplitQuery(), CBlastpApp::x_RunMTBySplitQuery(), CBlastxApp::x_RunMTBySplitQuery(), CRPSBlastApp::x_RunMTBySplitQuery(), CRPSTBlastnApp::x_RunMTBySplitQuery(), CTblastnApp::x_RunMTBySplitQuery(), CIgBlast::x_SetupVSearch(), and CTracebackSearchTestFixture::x_Traceback().
◆ GetOptions() [4/9]
|
pure virtual |
Obtain the options for the PSSM engine.
Implemented in SU_PSSMInput, CNullPssmInput, CPssmInputFlankingGaps, CdPssmInput, CPsiBlastInputData, and CPsiBlastInputClustalW.
Referenced by s_CheckAgainstNullData(), s_Validate(), and CPssmEngine::x_CreatePssmFromMsa().
◆ GetOptions() [5/9]
|
pure virtual |
Create a CBlastOptionsHandle.
This creates a CBlastOptionsHandle for the specified program value. The options can be used to configure a search created by the GetSeqSearch() or GetPssmSearch() methods. The search object and the CBlastOptionsHandle object should be created by the same ISearchFactory subclass.
- Parameters
-
program The program type for this search.
- Returns
- An options handle object for this program and factory type.
Implemented in CRemoteSearchFactory, and CLocalSearchFactory.
Referenced by RunMultipleProteinSearch().
◆ GetOptions() [6/9]
|
virtual |
Get an options handle for a search of the specified type.
Implements ISearchFactory.
Definition at line 81 of file local_search.cpp.
References CBlastOptionsFactory::Create().
◆ GetOptions() [7/9]
|
virtual |
Get an options handle for a search of the specified type.
Implements ISearchFactory.
Definition at line 70 of file remote_search.cpp.
References CBlastOptionsFactory::Create(), and CBlastOptions::eRemote.
◆ GetOptions() [8/9]
|
inlinevirtual |
Get CDD-related PSSM engine options.
- Returns
- CDD-related PSSM engine options
Implements IPssmInputCdd.
Definition at line 165 of file cdd_pssm_input.hpp.
References CCddInputData::m_Opts.
◆ GetOptions() [9/9]
|
pure virtual |
Get CDD-related PSI-BLAST options.
Implemented in CPssmInputWithNoCDs, and CCddInputData.
Referenced by s_Validate(), and CPssmEngine::x_CreatePssmFromCDD().
◆ GetOptionsBuilder()
|
inline |
Return the BlastOptions builder used in this class.
Definition at line 158 of file search_strategy.hpp.
References _ASSERT, CImportStrategy::FetchData(), CImportStrategy::m_OptionsBuilder, and NULL.
◆ GetOptionsHandle() [1/2]
| CRef< blast::CBlastOptionsHandle > CImportStrategy::GetOptionsHandle | ( | ) |
Builds and returns the OptionsHandle.
Definition at line 132 of file search_strategy.cpp.
References CImportStrategy::FetchData(), and CImportStrategy::m_Data.
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetOptionsHandle() [2/2]
|
inline |
Retrieve the options handle.
Definition at line 285 of file bl2seq.hpp.
References CBl2Seq::m_OptsHandle.
Referenced by BOOST_AUTO_TEST_CASE(), and CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest().
◆ GetOrganismSpecificRepeatsDatabases()
| vector< CRef< objects::CBlast4_database_info > > CBlastServices::GetOrganismSpecificRepeatsDatabases | ( | ) |
Retrieve organism specific repeats databases.
Definition at line 389 of file blast_services.cpp.
References ITERATE, CBlastServices::m_AvailableDatabases, NPOS, and CBlastServices::x_GetAvailableDatabases().
◆ GetOutOfFrameMode() [1/4]
| bool CBlastOptions::GetOutOfFrameMode | ( | ) | const |
Definition at line 2312 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetOutOfFrameMode(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CBlastTracebackSearch::Run().
◆ GetOutOfFrameMode() [2/4]
|
inline |
Returns OutOfFrameMode.
Definition at line 82 of file blastx_options.hpp.
◆ GetOutOfFrameMode() [3/4]
|
inline |
Returns OutOfFrameMode.
Definition at line 65 of file tblastn_options.hpp.
◆ GetOutOfFrameMode() [4/4]
|
inline |
Definition at line 1682 of file blast_options_local_priv.hpp.
References BlastScoringOptions::is_ooframe, CBlastOptionsLocal::m_ScoringOpts, and true.
Referenced by CBlastOptions::GetOutOfFrameMode().
◆ GetPaired() [1/3]
| bool CBlastOptions::GetPaired | ( | ) | const |
Definition at line 2155 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetPaired(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
◆ GetPaired() [2/3]
|
inline |
Are the mapping reads assumed paired.
- Returns
- True if reads are assumed paired, false otherwise
Definition at line 199 of file magicblast_options.hpp.
Referenced by CMagicBlastThread::Main().
◆ GetPaired() [3/3]
|
inline |
Definition at line 1582 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_HitSaveOpts, and BlastHitSavingOptions::paired.
Referenced by CBlastOptions::GetPaired().
◆ GetPercentIdentity() [1/3]
| double CBlastOptions::GetPercentIdentity | ( | ) | const |
Definition at line 1961 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetPercentIdentity(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CBlastOptionsHandle::GetPercentIdentity().
◆ GetPercentIdentity() [2/3]
|
inline |
Returns PercentIdentity.
Definition at line 258 of file blast_options_handle.hpp.
References CBlastOptions::GetPercentIdentity(), and CBlastOptionsHandle::m_Opts.
Referenced by BOOST_AUTO_TEST_CASE(), and BOOST_FIXTURE_TEST_CASE().
◆ GetPercentIdentity() [3/3]
|
inline |
Definition at line 1472 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_HitSaveOpts, and BlastHitSavingOptions::percent_identity.
Referenced by CBlastOptions::GetPercentIdentity().
◆ GetPhiAlignments()
| CRef< objects::CBlast4_phi_alignments > CRemoteBlast::GetPhiAlignments | ( | void | ) |
Get the results of a PHI-Align request, if PHI pattern was set.
- Returns
- Reference to PHI alignment set.
Definition at line 471 of file remote_blast.cpp.
References CRemoteBlast::x_GetGSRR().
◆ GetPHIPattern() [1/4]
| const char * CBlastOptions::GetPHIPattern | ( | ) | const |
Definition at line 2423 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetPHIPattern(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by BOOST_AUTO_TEST_CASE(), CPHIBlastNuclOptionsHandle::GetPHIPattern(), CPHIBlastProtOptionsHandle::GetPHIPattern(), and CPsiBlastApp::x_RunLocalPsiBlastIterations().
◆ GetPHIPattern() [2/4]
|
inline |
Retrieves the pattern string option.
- Returns
- Pattern string satisfying PROSITE rules.
Definition at line 74 of file phiblast_nucl_options.hpp.
References CBlastOptions::GetPHIPattern(), and CBlastOptionsHandle::m_Opts.
◆ GetPHIPattern() [3/4]
|
inline |
Retrieves the pattern string option.
- Returns
- Pattern string satisfying PROSITE rules.
Definition at line 75 of file phiblast_prot_options.hpp.
References CBlastOptions::GetPHIPattern(), and CBlastOptionsHandle::m_Opts.
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetPHIPattern() [4/4]
|
inline |
Definition at line 1760 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_LutOpts, and LookupTableOptions::phi_pattern.
Referenced by CBlastOptions::GetPHIPattern().
◆ GetPhiQueryInfo()
|
inline |
Retrieves PHI-BLAST information about pattern on query.
Definition at line 253 of file blast_results.hpp.
References CSearchResults::m_PhiQueryInfo.
Referenced by CBlastFormat::PrintPhiResult().
◆ GetPointer()
|
inline |
The a pointer to the wrapped object.
Definition at line 120 of file setup_factory.hpp.
References CStructWrapper< TData >::m_Data.
◆ GetPreviouslyFoundSeqIds()
| CPsiBlastIterationState::TSeqIds CPsiBlastIterationState::GetPreviouslyFoundSeqIds | ( | ) | const |
Retrieve the set of Seq-id's found in the previous iteration.
Definition at line 113 of file psiblast_iteration.cpp.
References CPsiBlastIterationState::m_CurrentData.
Referenced by CDeltaBlastApp::DoPsiBlastIterations(), and CPsiBlastApp::x_RunLocalPsiBlastIterations().
◆ GetProgram() [1/4]
| string CRemoteBlast::GetProgram | ( | ) |
Get the program used for this search.
- Returns
- The value of the program parameter.
Definition at line 1885 of file remote_blast.cpp.
References CRemoteBlast::m_Program, and CRemoteBlast::x_GetRequestInfo().
Referenced by BOOST_AUTO_TEST_CASE(), and CRemoteBlast::GetSearchOptions().
◆ GetProgram() [2/4]
| EProgram CBlastOptions::GetProgram | ( | ) | const |
Accessors/Mutators for individual options.
Returns the task this object is best suited for
Definition at line 833 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetProgram(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CLocalDbAdapter::CLocalDbAdapter(), CWordThresholdArg::ExtractAlgorithmOptions(), CGappedArgs::ExtractAlgorithmOptions(), CGeneticCodeArgs::ExtractAlgorithmOptions(), CBlastOptions::IsIterativeSearch(), CBlastnNode::Main(), CPsiBlastApp::Run(), CVDBBlastnApp::Run(), s_SetCompositionBasedStats(), CScoreBuilder::x_Initialize(), CBlastnApp::x_RunMTBySplitDB(), CBlastnApp::x_RunMTBySplitQuery(), CBlastpApp::x_RunMTBySplitQuery(), CBlastxApp::x_RunMTBySplitQuery(), CRPSBlastApp::x_RunMTBySplitQuery(), CRPSTBlastnApp::x_RunMTBySplitQuery(), and CTblastnApp::x_RunMTBySplitQuery().
◆ GetProgram() [3/4]
| string CImportStrategy::GetProgram | ( | ) | const |
Fetches program, one of blastn, blastp, blastx, tblastn, tblastx.
Definition at line 159 of file search_strategy.cpp.
References CImportStrategy::m_Request.
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetProgram() [4/4]
|
inline |
Accessors/Mutators for individual options.
Definition at line 536 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_Program.
Referenced by CBlastOptions::GetProgram().
◆ GetProgramOptions()
| objects::CBlast4_parameters * CImportStrategy::GetProgramOptions | ( | ) |
Options for controlling program execution and database filtering.
- Returns
- the program options or NULL if unavailable
Definition at line 242 of file search_strategy.cpp.
References CBlast4_queue_search_request_Base::CanGetProgram_options(), CImportStrategy::m_Request, NULL, and CBlast4_queue_search_request_Base::SetProgram_options().
Referenced by BOOST_AUTO_TEST_CASE(), and CImportStrategy::x_GetProgramOptionIntegerList().
◆ GetProgramType() [1/2]
| EBlastProgramType CBlastOptions::GetProgramType | ( | ) | const |
Returns the CORE BLAST notion of program type.
Definition at line 842 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetProgramType(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by BlastSetupPreliminarySearchEx(), BOOST_AUTO_TEST_CASE(), CBlastTracebackSearch::CBlastTracebackSearch(), CObjMgrFree_LocalQueryData::CObjMgrFree_LocalQueryData(), CVDBThread::CVDBThread(), CBlastDatabaseArgs::ExtractAlgorithmOptions(), CWindowSizeArg::ExtractAlgorithmOptions(), CWordThresholdArg::ExtractAlgorithmOptions(), CPhiBlastArgs::ExtractAlgorithmOptions(), CQueryOptionsArgs::ExtractAlgorithmOptions(), CIgBlastArgs::ExtractAlgorithmOptions(), CSetupFactory::InitializeMegablastDbIndex(), CLocalDbAdapter::IsProtein(), LogBlastOptions(), CLocalDbAdapter::MakeSeqInfoSrc(), CLocalDbAdapter::MakeSeqSrc(), CBlastFormatterApp::PrintFormattedOutput(), CBlastFormatterVdbApp::PrintFormattedOutput(), CSplitQueryTestFixture::QuerySplitter_BlastnMultiQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastnSingleQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastxMultiQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastxSingleQueryMultiChunk(), CBlastDemoApplication::Run(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), SafeSetupQueries(), SafeSetupQueryInfo(), CBlastOptions::SetFilterString(), setupQueryInfoForOffsetTranslation(), setupQueryStructures(), CBlastQuerySourceOM::x_CalculateMasks(), CQuerySplitter::x_ComputeChunkRanges(), CQuerySplitter::x_ComputeContextOffsets_NonTranslatedQueries(), CQuerySplitter::x_ComputeContextOffsets_TranslatedQueries(), CQuerySplitter::x_ComputeContextOffsetsForChunks(), CQuerySplitter::x_ComputeQueryContextsForChunks(), CQuerySplitter::x_ComputeQueryIndicesForChunks(), CTracebackTestFixture::x_ComputeTracebak(), CTracebackSearchTestFixture::x_GetSampleHspStream(), CTracebackSearchTestFixture::x_GetSelfHitHspStream(), CBlastTracebackSearch::x_Init(), CSequenceDataTester::x_IsProtein(), CBlastAppArgs::x_IssueWarningsForIgnoredOptions(), CTracebackTestFixture::x_MakeStream(), CSplitQueryTestFixture::x_PrepareBlastQueryStructures(), CBlastOptionsBuilder::x_ProcessOneOption(), CTracebackTestFixture::x_SetupGapAlign(), and CTracebackTestFixture::x_SetupMain().
◆ GetProgramType() [2/2]
| EBlastProgramType CBlastOptionsLocal::GetProgramType | ( | ) | const |
Definition at line 353 of file blast_options_local_priv.cpp.
References EProgramToEBlastProgramType(), and CBlastOptionsLocal::m_Program.
Referenced by CBlastOptionsMemento::CBlastOptionsMemento(), CBlastOptions::GetProgramType(), CBlastOptionsLocal::SetFilterString(), and CBlastOptionsLocal::Validate().
◆ GetPseudoCount() [1/3]
| int CBlastOptions::GetPseudoCount | ( | ) | const |
Definition at line 2474 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetPseudoCount(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
◆ GetPseudoCount() [2/3]
|
inline |
Returns PseudoCount.
Definition at line 72 of file psiblast_options.hpp.
Referenced by BOOST_AUTO_TEST_CASE(), and PsiBlastComputePssmFromAlignment().
◆ GetPseudoCount() [3/3]
|
inline |
Definition at line 1778 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_PSIBlastOpts, and PSIBlastOptions::pseudo_count.
Referenced by CBlastOptions::GetPseudoCount().
◆ GetPSIBlastOpts() [1/2]
|
private |
Returns PSIBlastOptions for eLocal objects, NULL for eRemote.
Definition at line 2676 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetPSIBlastOpts(), and CBlastOptions::m_Local.
◆ GetPSIBlastOpts() [2/2]
|
inlineprivate |
Definition at line 444 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_PSIBlastOpts.
Referenced by CBlastOptions::GetPSIBlastOpts().
◆ GetPsiGappedKarlinBlk()
|
inline |
Retrieve PSI-BLAST gapped Karlin parameters.
Definition at line 112 of file blast_results.hpp.
Referenced by s_BuildArchiveAll(), and CPssmEngine::SetUngappedStatisticalParams().
◆ GetPSIInclusionThreshold()
|
inline |
Get e-value threshold for including sequences in Pssm calculation.
- Returns
- E-value cutoff for sequences
Same as GetInclusionThreshold().It was added for clear distinction between Psi and Delta Blast inclusion thresholds
Definition at line 78 of file deltablast_options.hpp.
◆ GetPsiNumberOfIterations()
| unsigned int CRemoteBlast::GetPsiNumberOfIterations | ( | void | ) |
Definition at line 2645 of file remote_blast.cpp.
References eBlastOpt_Web_StepNumber, CRef< C, Locker >::Empty(), CBlast4Field::GetName(), CRemoteBlast::m_FormatOpts, CRemoteBlast::m_RID, CRef< C, Locker >::NotEmpty(), and CRemoteBlast::x_GetPsiIterationsFromServer().
Referenced by CBlastFormatterApp::PrintFormattedOutput(), and CBlastFormatterVdbApp::PrintFormattedOutput().
◆ GetPsiNumOfIterations()
| unsigned int CImportStrategy::GetPsiNumOfIterations | ( | ) |
Get number of iteration for psi blast, return 0 if num of iterations not available.
Definition at line 141 of file search_strategy.cpp.
References CImportStrategy::FetchData(), and CImportStrategy::m_Data.
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetPsiUngappedKarlinBlk()
|
inline |
Retrieve PSI-BLAST ungapped Karlin parameters.
Definition at line 107 of file blast_results.hpp.
Referenced by s_BuildArchiveAll(), and CPssmEngine::SetUngappedStatisticalParams().
◆ GetPssm() [1/4]
| CConstRef< objects::CPssmWithParameters > CPsiBlast::GetPssm | ( | ) | const |
Accessor for the most recently used PSSM.
Definition at line 89 of file psiblast.cpp.
References CPsiBlastImpl::GetPssm(), and CPsiBlast::m_Impl.
◆ GetPssm() [2/4]
| CConstRef< CPssmWithParameters > CPsiBlastImpl::GetPssm | ( | void | ) | const |
Accessor for the most recently used PSSM.
Definition at line 190 of file psiblast_impl.cpp.
References CPsiBlastImpl::m_Pssm.
Referenced by CPsiBlast::GetPssm().
◆ GetPssm() [3/4]
| CRef< CPssmWithParameters > CDeltaBlast::GetPssm | ( | int | index = 0 | ) |
Accessor for PSSM computd from CDD hits and used in protein search.
- Parameters
-
index PSSM index corresponding to query
- Returns
- PSSM
Definition at line 186 of file deltablast.cpp.
References CDeltaBlast::m_Pssm, and NCBI_THROW.
◆ GetPssm() [4/4]
| CConstRef< CPssmWithParameters > CDeltaBlast::GetPssm | ( | int | index = 0 | ) | const |
Accessor for PSSM computd from CDD hits and used in protein search.
- Parameters
-
index PSSM index corresponding to query
- Returns
- PSSM
Definition at line 177 of file deltablast.cpp.
References CDeltaBlast::m_Pssm, and NCBI_THROW.
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetPSSM()
| CRef< objects::CPssmWithParameters > CRemoteBlast::GetPSSM | ( | void | ) |
Get the PSSM produced by the search.
- Returns
- Reference to a Score-matrix-parameters object.
Definition at line 587 of file remote_blast.cpp.
References CRemoteBlast::x_GetGSRR().
Referenced by CPsiBlastApp::DoIterations(), CBlastFormatterApp::PrintFormattedOutput(), and CDeltaBlastApp::Run().
◆ GetPssmSearch() [1/3]
|
virtual |
Get an object to manage a remote PSSM search.
Implements ISearchFactory.
Definition at line 75 of file local_search.cpp.
◆ GetPssmSearch() [2/3]
|
virtual |
Get an object to manage a remote PSSM search.
Implements ISearchFactory.
Definition at line 64 of file remote_search.cpp.
◆ GetPssmSearch() [3/3]
|
pure virtual |
Create a new search object with a pssm-based query.
A search object will be constructed and configured for a search using a PSSM query.
- Returns
- A search object for a PSSM search.
Implemented in CRemoteSearchFactory, and CLocalSearchFactory.
◆ GetPubmedUrl()
|
static |
Get Pubmed url for requested publication.
Definition at line 129 of file version.cpp.
References int, and kPubMedUrls.
Referenced by BOOST_AUTO_TEST_CASE(), and s_DoTestReference().
◆ GetQueries() [1/3]
| CRef< CBlast4_queries > CRemoteBlast::GetQueries | ( | ) |
Get the queries used for this search.
The queries specified for this search will be returned. The returned object will include either a list of seq-locs, a CBioseq, or a PSSM query.
- Returns
- The queries used for this search.
Definition at line 1921 of file remote_blast.cpp.
References CRef< C, Locker >::Empty(), CRemoteBlast::m_Queries, and CRemoteBlast::x_GetRequestInfo().
Referenced by BOOST_AUTO_TEST_CASE(), CRemoteBlast::GetMasks(), CBlastFormatterApp::x_ExtractQueries(), CBlastFormatterVdbApp::x_ExtractQueries(), and CRemoteBlast::x_ExtractQueryIds().
◆ GetQueries() [2/3]
| CRef< objects::CBlast4_queries > CImportStrategy::GetQueries | ( | ) |
The queries either as Bioseq, seqloc, or pssm.
Definition at line 215 of file search_strategy.cpp.
References CImportStrategy::m_Request, and CBlast4_queue_search_request_Base::SetQueries().
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetQueries() [3/3]
|
inline |
Retrieve a vector of query sequences.
Definition at line 244 of file bl2seq.hpp.
References CBl2Seq::m_tQueries.
Referenced by BOOST_AUTO_TEST_CASE(), and CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest().
◆ GetQuery() [1/6]
|
inlinevirtual |
Get the query sequence used as master for the multiple sequence alignment in ncbistdaa encoding.
Implements IPssmInput_Base.
Definition at line 90 of file msa_pssm_input.hpp.
◆ GetQuery() [2/6]
|
inlinevirtual |
◆ GetQuery() [3/6]
|
inlinevirtual |
Get the query sequence used as master for the multiple sequence alignment in ncbistdaa encoding.
Implements IPssmInput_Base.
Definition at line 201 of file psi_pssm_input.cpp.
References CPsiBlastInputData::m_Query.
◆ GetQuery() [4/6]
Retrieve the query sequence.
Definition at line 230 of file bl2seq.hpp.
References CBl2Seq::m_tQueries.
◆ GetQuery() [5/6]
|
pure virtual |
Get the query sequence used as master for the multiple sequence alignment in ncbistdaa encoding.
Implemented in SU_PSSMInput, CPssmInputWithNoCDs, CCddInputData, CNullPssmInput, CPssmInputFlankingGaps, CdPssmInput, CPsiBlastInputData, CPsiBlastInputFreqRatios, and CPsiBlastInputClustalW.
Referenced by s_CheckAgainstNullData(), CPssmEngine::x_CreatePssmFromFreqRatios(), and CPssmEngine::x_GetQuery().
◆ GetQuery() [6/6]
|
inlinevirtual |
Get query sequence.
- Returns
- Query sequence
Implements IPssmInput_Base.
Definition at line 139 of file cdd_pssm_input.hpp.
References CCddInputData::m_QueryData.
◆ GetQueryContexts()
| vector< int > CSplitQueryBlk::GetQueryContexts | ( | size_t | chunk_num | ) | const |
Get the contexts of the queries contained in a given chunk.
- Parameters
-
chunk_num desired chunk [in]
Definition at line 97 of file split_query_blk.cpp.
References i, CSplitQueryBlk::m_SplitQueryBlk, NULL, sfree, and SplitQueryBlk_GetQueryContextsForChunk().
Referenced by CContextTranslator::CContextTranslator(), operator<<(), and CSplitQueryTestFixture::x_ValidateQueryContextsPerChunkAssignment().
◆ GetQueryCovHspPerc() [1/3]
| double CBlastOptions::GetQueryCovHspPerc | ( | ) | const |
Definition at line 1999 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetQueryCovHspPerc(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by BOOST_AUTO_TEST_CASE(), and CBlastOptionsHandle::GetQueryCovHspPerc().
◆ GetQueryCovHspPerc() [2/3]
|
inline |
Returns QueryCovHspPerc.
Definition at line 264 of file blast_options_handle.hpp.
References CBlastOptions::GetQueryCovHspPerc(), and CBlastOptionsHandle::m_Opts.
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetQueryCovHspPerc() [3/3]
|
inline |
Definition at line 1496 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_HitSaveOpts, and BlastHitSavingOptions::query_cov_hsp_perc.
Referenced by CBlastOptions::GetQueryCovHspPerc().
◆ GetQueryEncoding()
| EBlastEncoding GetQueryEncoding | ( | EBlastProgramType | program | ) |
Returns the encoding for the sequence data used in BLAST for the query.
- Parameters
-
program program type [in]
- Exceptions
-
CBlastException in case of unsupported program
Definition at line 1090 of file blast_setup_cxx.cpp.
References abort(), eBlastEncodingError, eBlastEncodingNcbi4na, eBlastEncodingNucleotide, eBlastEncodingProtein, eBlastTypeBlastn, eBlastTypeBlastp, eBlastTypeBlastx, eBlastTypeMapping, eBlastTypePhiBlastn, eBlastTypePhiBlastp, eBlastTypePsiBlast, eBlastTypePsiTblastn, eBlastTypeRpsBlast, eBlastTypeRpsTblastn, eBlastTypeTblastn, and eBlastTypeTblastx.
Referenced by SetupQueries_OMF().
◆ GetQueryFactoryForChunk()
| CRef< IQueryFactory > CQuerySplitter::GetQueryFactoryForChunk | ( | Uint4 | chunk_num | ) |
Returns a IQueryFactory suitable to be executed by a BLAST search class.
- Parameters
-
chunk_num chunk number to retrieve (< GetNumberOfChunks())
Definition at line 892 of file split_query_cxx.cpp.
References CRef< C, Locker >::Empty(), NStr::IntToString(), CQuerySplitter::m_NumChunks, CQuerySplitter::m_QueryChunkFactories, CQuerySplitter::m_SplitBlk, msg(), and CQuerySplitter::Split().
Referenced by BOOST_AUTO_TEST_CASE(), CBlastPrelimSearch::Run(), CSplitQueryTestFixture::x_TestCContextTranslator(), and CSplitQueryTestFixture::x_ValidateLocalQueryData().
◆ GetQueryForPssm() [1/4]
|
inlinevirtual |
◆ GetQueryForPssm() [2/4]
|
inlinevirtual |
@inheritDoc
Reimplemented from IPssmInput_Base.
Definition at line 226 of file psi_pssm_input.hpp.
References CPsiBlastInputData::m_QueryBioseq.
◆ GetQueryForPssm() [3/4]
|
inlinevirtual |
Get a CBioseq object for attachment into the CPssmWithParameters that CPssmEngine produces (only attached if it's not NULL).
This is required for any PSSM which is intended to be used as a starting point for a PSI-BLAST iteration
Reimplemented in CCddInputData, CPsiBlastInputData, and CPsiBlastInputClustalW.
Definition at line 88 of file pssm_input.hpp.
References NULL.
Referenced by CPssmEngine::x_CreatePssmFromCDD(), CPssmEngine::x_CreatePssmFromFreqRatios(), and CPssmEngine::x_CreatePssmFromMsa().
◆ GetQueryForPssm() [4/4]
|
inlinevirtual |
Get query as Bioseq.
- Returns
- Query as bioseq
Reimplemented from IPssmInput_Base.
Definition at line 184 of file cdd_pssm_input.hpp.
References CCddInputData::m_QueryBioseq.
◆ GetQueryGeneticCode() [1/4]
| int CBlastOptions::GetQueryGeneticCode | ( | ) | const |
Definition at line 1470 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetQueryGeneticCode(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CBlastnNode::Main(), CBlastpNode::Main(), CBlastxNode::Main(), CRPSBlastNode::Main(), CRPSTBlastnNode::Main(), CTblastnNode::Main(), CIgBlastnApp::CIgFormatter::Main(), CBlastFormatterApp::PrintFormattedOutput(), CDeltaBlastApp::Run(), CPsiBlastApp::Run(), CTblastxApp::Run(), CIgBlastnApp::Run(), CIgBlastpApp::Run(), CRMBlastnApp::Run(), CBlastQuerySourceOM::x_AutoDetectGeneticCodes(), CBlastnApp::x_RunMTBySplitDB(), CBlastpApp::x_RunMTBySplitDB(), CBlastxApp::x_RunMTBySplitDB(), CRPSBlastApp::x_RunMTBySplitDB(), CRPSTBlastnApp::x_RunMTBySplitDB(), and CTblastnApp::x_RunMTBySplitDB().
◆ GetQueryGeneticCode() [2/4]
|
inline |
Returns QueryGeneticCode.
Definition at line 74 of file blastx_options.hpp.
◆ GetQueryGeneticCode() [3/4]
|
inline |
Returns QueryGeneticCode.
Definition at line 87 of file tblastx_options.hpp.
◆ GetQueryGeneticCode() [4/4]
|
inline |
Definition at line 1013 of file blast_options_local_priv.hpp.
References QuerySetUpOptions::genetic_code, and CBlastOptionsLocal::m_QueryOpts.
Referenced by CBlastOptions::GetQueryGeneticCode().
◆ GetQueryId() [1/2]
| string TQueryMessages::GetQueryId | ( | void | ) | const |
Get the query id as a string.
- Returns
- The query id.
Definition at line 972 of file blast_aux.cpp.
References TQueryMessages::m_IdString.
Referenced by CBlastKmerResults::GetErrors(), CSearchResults::GetErrorStrings(), and CSearchResults::GetWarningStrings().
◆ GetQueryId() [2/2]
Get query sequence id.
Definition at line 192 of file magicblast.hpp.
References CMagicBlastResults::m_QueryId.
Referenced by CMagicBlastResults::GetFirstId().
◆ GetQueryIndices()
| vector< size_t > CSplitQueryBlk::GetQueryIndices | ( | size_t | chunk_num | ) | const |
Get the indices of the queries contained in a given chunk.
- Parameters
-
chunk_num desired chunk [in]
Definition at line 79 of file split_query_blk.cpp.
References i, CSplitQueryBlk::m_SplitQueryBlk, NULL, sfree, SplitQueryBlk_GetQueryIndicesForChunk(), and UINT4_MAX.
Referenced by CQueryDataPerChunk::CQueryDataPerChunk(), operator<<(), CQuerySplitter::x_ComputeQueryContextsForChunks(), and CSplitQueryTestFixture::x_ValidateQueriesPerChunkAssignment().
◆ GetQueryInfo() [1/4]
|
virtual |
Accessor for the BlastQueryInfo structure.
Implements ILocalQueryData.
Definition at line 222 of file objmgr_query_data.cpp.
References abort(), CBlastQueryInfo::Get(), CObjMgr_LocalQueryData::m_Options, ILocalQueryData::m_QueryInfo, CObjMgr_LocalQueryData::m_QuerySource, NULL, CBlastQueryInfo::Reset(), and SafeSetupQueryInfo().
Referenced by CObjMgr_LocalQueryData::GetNumQueries(), and CObjMgr_LocalQueryData::GetSequenceBlk().
◆ GetQueryInfo() [2/4]
|
virtual |
Accessor for the BlastQueryInfo structure.
Implements ILocalQueryData.
Definition at line 120 of file objmgrfree_query_data.cpp.
References CBlastQueryInfo::Get(), CObjMgrFree_LocalQueryData::m_BioseqSet, CObjMgrFree_LocalQueryData::m_Options, ILocalQueryData::m_QueryInfo, CObjMgrFree_LocalQueryData::m_QuerySource, NCBI_CURRENT_FUNCTION, NCBI_THROW, CConstRef< C, Locker >::NotEmpty(), NULL, CBlastQueryInfo::Reset(), and SafeSetupQueryInfo().
Referenced by CObjMgrFree_LocalQueryData::GetNumQueries(), and CObjMgrFree_LocalQueryData::GetSequenceBlk().
◆ GetQueryInfo() [3/4]
| BlastQueryInfo * CEffectiveSearchSpaceCalculator::GetQueryInfo | ( | ) | const |
Retrieve the BlastQueryInfo structure that stores the effective search spaces for all queries.
This function is intended only for internal use by Blast routines.
Definition at line 146 of file effsearchspace_calc.cpp.
References CEffectiveSearchSpaceCalculator::m_QueryInfo.
◆ GetQueryInfo() [4/4]
|
pure virtual |
Accessor for the BlastQueryInfo structure.
Implemented in CObjMgrFree_LocalQueryData, and CObjMgr_LocalQueryData.
Referenced by BlastSetupPreliminarySearchEx(), CContextTranslator::CContextTranslator(), CEffectiveSearchSpaceCalculator::CEffectiveSearchSpaceCalculator(), CSetupFactory::CreateLookupTable(), CSetupFactory::CreateScoreBlock(), ILocalQueryData::IsValidQuery(), LocalBlastResults2SeqAlign(), CMagicBlastThread::Main(), CDeltaBlast::Run(), CQuerySplitter::x_ComputeContextOffsets_NonTranslatedQueries(), CQuerySplitter::x_ComputeContextOffsets_TranslatedQueries(), CBlastTracebackSearch::x_Init(), CSplitQueryTestFixture::x_TestCContextTranslator(), and CSequenceDataTester::x_TestSingleSequence_Local().
◆ GetQueryLength() [1/7]
|
inlinevirtual |
Get the query's length.
Implements IPssmInput_Base.
Definition at line 93 of file msa_pssm_input.hpp.
Referenced by BOOST_AUTO_TEST_CASE(), CPsiBlastInputClustalW::x_CopyQueryToMsa(), CPsiBlastInputClustalW::x_ExtractQueryForPssm(), and CPsiBlastInputClustalW::x_ValidateQueryInMsa().
◆ GetQueryLength() [2/7]
|
inlinevirtual |
Get the query's length.
Implements IPssmInput_Base.
Definition at line 101 of file psi_pssm_input.hpp.
◆ GetQueryLength() [3/7]
|
inlinevirtual |
Get the query's length.
Implements IPssmInput_Base.
Definition at line 207 of file psi_pssm_input.cpp.
References CPsiBlastInputData::m_MsaDimensions, and PSIMsaDimensions::query_length.
Referenced by CPsiBlastInputData::x_CopyQueryToMsa(), CPsiBlastInputData::x_ExtractQueryForPssm(), and CPsiBlastInputData::x_ProcessDenseg().
◆ GetQueryLength() [4/7]
|
pure virtual |
Get the query's length.
Implemented in SU_PSSMInput, CPssmInputWithNoCDs, CCddInputData, CNullPssmInput, CPssmInputQueryLength0, CPssmInputFlankingGaps, CdPssmInput, CPsiBlastInputData, CPsiBlastInputFreqRatios, and CPsiBlastInputClustalW.
Referenced by s_CheckAgainstNullData(), CPssmEngine::x_CreatePssmFromFreqRatios(), and CPssmEngine::x_GetQueryLength().
◆ GetQueryLength() [5/7]
| size_t CQueryDataPerChunk::GetQueryLength | ( | int | global_query_index | ) | const |
Get the length of the query.
- Parameters
-
global_query_index index of the query in the context of the full,non-split query [in]
- Returns
- length of query
Definition at line 338 of file split_query_aux_priv.cpp.
References _ASSERT, and CQueryDataPerChunk::m_QueryLengths.
◆ GetQueryLength() [6/7]
| size_t CQueryDataPerChunk::GetQueryLength | ( | size_t | chunk_num, |
| int | context_in_chunk | ||
| ) | const |
Get the length of the query.
- Parameters
-
chunk_num chunk number where query is found [in] context_in_chunk which context within this chunk contains query [in]
- Returns
- length of query
Definition at line 345 of file split_query_aux_priv.cpp.
References _ASSERT, CQueryDataPerChunk::m_QueryIndicesPerChunk, ncbi::grid::netcache::search::fields::size, and CQueryDataPerChunk::x_ContextInChunkToQueryIndex().
Referenced by CQuerySplitter::x_ComputeContextOffsets_TranslatedQueries().
◆ GetQueryLength() [7/7]
|
inlinevirtual |
Get query length.
- Returns
- Query length
Implements IPssmInput_Base.
Definition at line 144 of file cdd_pssm_input.hpp.
References CCddInputData::m_QueryData.
Referenced by CCddInputData::x_ExtractQueryForPssm().
◆ GetQueryMasks() [1/2]
| CBlastOptionsBuilder::TMaskList CBlastOptionsBuilder::GetQueryMasks | ( | void | ) |
Get the query masks.
Definition at line 784 of file blast_options_builder.cpp.
References CBlastOptionsBuilder::SOptional< T >::Get(), and CBlastOptionsBuilder::m_QueryMasks.
◆ GetQueryMasks() [2/2]
|
inline |
Return query masks.
Definition at line 133 of file prelim_stage.hpp.
Referenced by CMagicBlast::x_BuildResultSet().
◆ GetQueryMessages()
| void ILocalQueryData::GetQueryMessages | ( | size_t | index, |
| TQueryMessages & | qmsgs | ||
| ) |
Retrieve error/warning messages for a specific query.
Definition at line 135 of file query_data.cpp.
References ILocalQueryData::m_Messages, and ILocalQueryData::x_ValidateIndex().
Referenced by CLocalBlast::Run(), CMagicBlast::x_Run(), and CSequenceDataTester::x_TestSingleSequence_Local().
◆ GetQueryOpts() [1/2]
|
private |
Returns QuerySetUpOptions for eLocal objects, NULL for eRemote.
Definition at line 2646 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetQueryOpts(), and CBlastOptions::m_Local.
Referenced by CTracebackTestFixture::x_SetupMain().
◆ GetQueryOpts() [2/2]
|
inlineprivate |
Definition at line 414 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_QueryOpts.
Referenced by CBlastOptions::GetQueryOpts().
◆ GetQueryRange()
| TSeqRange CImportStrategy::GetQueryRange | ( | ) |
The start and stop on the query (if applicable)
Definition at line 171 of file search_strategy.cpp.
References CImportStrategy::FetchData(), and CImportStrategy::m_Data.
◆ GetReadMaxFractionAmbiguous() [1/2]
| double CBlastOptions::GetReadMaxFractionAmbiguous | ( | void | ) | const |
Get maximum fraction of ambiguous bases for next-generation read quality filtering.
Definition at line 1411 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetReadMaxFractionAmbiguous(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
◆ GetReadMaxFractionAmbiguous() [2/2]
|
inline |
Definition at line 1049 of file blast_options_local_priv.hpp.
References QuerySetUpOptions::filtering_options, SReadQualityOptions::frac_ambig, CBlastOptionsLocal::m_QueryOpts, NULL, and SBlastFilterOptions::readQualityOptions.
Referenced by CBlastOptions::GetReadMaxFractionAmbiguous().
◆ GetReadMinDimerEntropy() [1/2]
| int CBlastOptions::GetReadMinDimerEntropy | ( | void | ) | const |
Get minimum dimer entropy for next-generation read quality filtering.
Definition at line 1431 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetReadMinDimerEntropy(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
◆ GetReadMinDimerEntropy() [2/2]
|
inline |
Definition at line 1070 of file blast_options_local_priv.hpp.
References SReadQualityOptions::entropy, QuerySetUpOptions::filtering_options, CBlastOptionsLocal::m_QueryOpts, NULL, and SBlastFilterOptions::readQualityOptions.
Referenced by CBlastOptions::GetReadMinDimerEntropy().
◆ GetReadQualityFiltering() [1/3]
| bool CBlastOptions::GetReadQualityFiltering | ( | void | ) | const |
Returns true if next-generation read quality filtering is turned on.
Definition at line 1391 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetReadQualityFiltering(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
◆ GetReadQualityFiltering() [2/3]
|
inline |
Return true if query quality filtering is on.
Definition at line 110 of file magicblast_options.hpp.
◆ GetReadQualityFiltering() [3/3]
|
inline |
Definition at line 1025 of file blast_options_local_priv.hpp.
References QuerySetUpOptions::filtering_options, CBlastOptionsLocal::m_QueryOpts, and SBlastFilterOptions::readQualityOptions.
Referenced by CBlastOptions::GetReadQualityFiltering().
◆ GetRef()
|
inline |
Get the reference to the stored value.
Definition at line 231 of file blast_options_builder.hpp.
Referenced by CBlastOptionsBuilder::x_ProcessOneOption().
◆ GetRepeatFiltering() [1/3]
|
inline |
Is repeat filtering enabled?
Definition at line 127 of file blast_nucl_options.hpp.
Referenced by Blast_FindRepeatFilterLoc(), BOOST_AUTO_TEST_CASE(), and BOOST_FIXTURE_TEST_CASE().
◆ GetRepeatFiltering() [2/3]
| bool CBlastOptions::GetRepeatFiltering | ( | ) | const |
Returns true if repeat filtering is on.
Definition at line 1305 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetRepeatFiltering(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CBlastQuerySourceOM::x_CalculateMasks().
◆ GetRepeatFiltering() [3/3]
|
inline |
Definition at line 917 of file blast_options_local_priv.hpp.
References QuerySetUpOptions::filtering_options, CBlastOptionsLocal::m_QueryOpts, and SBlastFilterOptions::repeatFilterOptions.
Referenced by CBlastOptions::GetRepeatFiltering(), and CBlastOptions::SetFilterString().
◆ GetRepeatFilteringDB() [1/3]
|
inline |
Get the repeat filtering database.
Definition at line 133 of file blast_nucl_options.hpp.
Referenced by Blast_FindRepeatFilterLoc(), BOOST_AUTO_TEST_CASE(), and BOOST_FIXTURE_TEST_CASE().
◆ GetRepeatFilteringDB() [2/3]
| const char * CBlastOptions::GetRepeatFilteringDB | ( | ) | const |
Returns the name of the repeat filtering database to use.
Definition at line 1324 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetRepeatFilteringDB(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CBlastQuerySourceOM::x_CalculateMasks().
◆ GetRepeatFilteringDB() [3/3]
|
inline |
Definition at line 942 of file blast_options_local_priv.hpp.
References SRepeatFilterOptions::database, QuerySetUpOptions::filtering_options, CBlastOptionsLocal::m_QueryOpts, NULL, and SBlastFilterOptions::repeatFilterOptions.
Referenced by CBlastOptions::GetRepeatFilteringDB(), and CBlastOptions::SetFilterString().
◆ GetResidueFrequencies()
|
static |
Returns matrix of BLASTAA_SIZE by query size (dimensions are opposite of what is stored in the BlastScoreBlk) containing the residue frequencies per position of the PSSM.
- Parameters
-
pssm PSSM to extract data from [in]
- Returns
- NULL if residue frequencies are not available
Definition at line 287 of file psiblast_aux_priv.cpp.
References _ASSERT, BLASTAA_SIZE, Convert2Matrix(), CPssm_Base::GetByRow(), CPssm_Base::GetIntermediateData(), CPssm_Base::GetNumColumns(), CPssm_Base::GetNumRows(), CPssmIntermediateData_Base::GetResFreqsPerPos(), and NULL.
◆ GetRestrictedQueryRange()
|
inline |
Return the range that was used to restrict the query sequence(s) (returns TSeqRange::GetEmpty() if not applicable)
Definition at line 159 of file blast_options_builder.hpp.
◆ GetResults() [1/5]
|
virtual |
Return results corresponding to a given subject sequence and chunk.
- Note
- Overrides CIndexedDb::GetResults().
- Parameters
-
oid [I] The subject sequence id. chunk [I] The chunk number. init_hitlist [I/O] The results are returned here.
- Returns
- Word size used for search.
Implements CIndexedDb.
Definition at line 1069 of file blast_dbindex.cpp.
References BlastInitHitListMove(), BlastInitHitListReset(), i, CIndexedDb_Old::LocateIndex(), results, CIndexedDb_Old::results_, and CIndexedDb_Old::seqmap_.
◆ GetResults() [2/5]
|
virtual |
Return results corresponding to a given subject sequence and chunk.
- Note
- Overrides CIndexedDb::GetResults().
- Parameters
-
oid [I] The subject sequence id. chunk [I] The chunk number. init_hitlist [I/O] The results are returned here.
- Returns
- Word size used for search.
Implements CIndexedDb.
Definition at line 903 of file blast_dbindex.cpp.
References ASSERT, BlastInitHitListMove(), BlastInitHitListReset(), CIndexedDb_New::FindVolume(), CDbIndex::CSearchResults::GetResults(), CDbIndex::CSearchResults::GetWordSize(), CIndexedDb_New::results_holder_, and CIndexedDb_New::volumes_.
◆ GetResults() [3/5]
|
pure virtual |
Return results corresponding to a given subject sequence and chunk.
- Parameters
-
oid [I] The subject sequence id. chunk [I] The chunk number. init_hitlist [I/O] The results are returned here.
- Returns
- Word size used for search.
Implemented in CIndexedDb_New, and CIndexedDb_Old.
Referenced by s_MB_IdbGetResults().
◆ GetResults() [4/5]
| CSearchResults & CSearchResultSet::GetResults | ( | size_type | qi, |
| size_type | si | ||
| ) |
Retrieve results for a query-subject pair contained by this object.
- Parameters
-
qi query sequence index [in] si subject sequence index [in]
- Note
- it only works for results of type eSequenceComparison
Definition at line 401 of file blast_results.cpp.
References eSequenceComparison, CSearchResultSet::GetNumResults(), CSearchResultSet::m_NumQueries, CSearchResultSet::m_Results, CSearchResultSet::m_ResultType, NCBI_THROW, and si.
Referenced by BOOST_AUTO_TEST_CASE(), CSearchResultSet::GetResults(), and CMultiAligner::x_AlignClusterQueries().
◆ GetResults() [5/5]
| const CSearchResults & CSearchResultSet::GetResults | ( | size_type | qi, |
| size_type | si | ||
| ) | const |
Retrieve results for a query-subject pair.
- Parameters
-
qi query sequence index [in] si subject sequence index [in]
- Note
- it only works for results of type eSequenceComparison
Definition at line 410 of file blast_results.cpp.
References CSearchResultSet::GetResults(), and si.
◆ GetResultSet()
| CRef< CSearchResultSet > CRemoteBlast::GetResultSet | ( | ) |
Submit the search (if necessary) and return the results.
Submit the search and return the results.
- Returns
- Search results.
Definition at line 2120 of file remote_blast.cpp.
References E, eBlastSevError, eBlastSevWarning, CRemoteBlast::eDebug, NStr::fConvErr_NoThrow, NStr::Find(), CRemoteBlast::GetErrorVector(), CRemoteBlast::GetKABlocks(), CRemoteBlast::GetMasks(), CException::GetMsg(), CRemoteBlast::GetRID(), CRemoteBlast::GetSearchStats(), CRemoteBlast::GetSeqAlignSets(), CRemoteBlast::GetWarningVector(), ITERATE, kBlastMessageNoContext, kEmptyStr, kNoRIDSpecified(), CRemoteBlast::m_CBOH, CRemoteBlast::m_ReadFile, CRemoteBlast::m_Service, CRemoteBlast::m_Task, CRemoteBlast::m_Verbose, NcbiCout, NON_CONST_ITERATE, NPOS, NStr::ReplaceInPlace(), CRef< C, Locker >::Reset(), CBlastAncillaryData::SetLengthAdjustment(), CSearchResultSet::SetRID(), NStr::StringToInt8(), CRemoteBlast::SubmitSync(), TSearchMessages::ToString(), W, and CRemoteBlast::x_ExtractQueryIds().
Referenced by BOOST_AUTO_TEST_CASE(), CPsiBlastApp::DoIterations(), CRemoteBlastAligner::GenerateAlignments(), CBlastnNode::Main(), CBlastpNode::Main(), CBlastxNode::Main(), CRPSBlastNode::Main(), CRPSTBlastnNode::Main(), CTblastnNode::Main(), CBlastFormatterApp::PrintFormattedOutput(), CBlastFormatterVdbApp::PrintFormattedOutput(), CIgBlast::Run(), CDeltaBlastApp::Run(), CTblastxApp::Run(), CRMBlastnApp::Run(), CBlastnApp::x_RunMTBySplitDB(), CBlastpApp::x_RunMTBySplitDB(), CBlastxApp::x_RunMTBySplitDB(), CRPSBlastApp::x_RunMTBySplitDB(), CRPSTBlastnApp::x_RunMTBySplitDB(), and CTblastnApp::x_RunMTBySplitDB().
◆ GetResultType()
|
inline |
Get the type of results contained in this object.
Definition at line 456 of file blast_results.hpp.
References CSearchResultSet::m_ResultType.
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetRid()
|
inline |
Definition at line 293 of file igblast.hpp.
References CIgBlast::m_RID.
◆ GetRID() [1/2]
|
inline |
Returns the RID for these results (if applicable), otherwise returns an empty string.
Definition at line 190 of file blast_results.hpp.
References CSearchResults::m_RID.
Referenced by CBlastFormat::PrintPhiResult().
◆ GetRID() [2/2]
Gets the request id (RID) associated with the search.
If the search was not successfully submitted, this will be empty.
Definition at line 1624 of file remote_blast.cpp.
References CRemoteBlast::m_RID.
Referenced by BOOST_AUTO_TEST_CASE(), CRemoteBlast::GetResultSet(), and CIgBlast::Run().
◆ GetScalingFactor()
| double CBlastRPSInfo::GetScalingFactor | ( | ) | const |
Returns the scaling factor used to build RPS-BLAST database.
Definition at line 621 of file rps_aux.cpp.
References CBlastRPSInfo::m_RpsInfo.
Referenced by CSetupFactory::CreateScoreBlock().
◆ GetScores()
|
static |
Returns matrix of BLASTAA_SIZE by query size (dimensions are opposite of what is stored in the BlastScoreBlk) containing scores.
- Parameters
-
pssm PSSM to extract data from [in]
- Exceptions
-
std::runtime_error if scores are not available
Definition at line 240 of file psiblast_aux_priv.cpp.
References _ASSERT, BLAST_SCORE_MIN, BLASTAA_SIZE, Convert2Matrix(), CPssm_Base::GetByRow(), CPssm_Base::GetFinalData(), CPssm_Base::GetNumColumns(), CPssm_Base::GetNumRows(), and CPssmFinalData_Base::GetScores().
Referenced by BOOST_AUTO_TEST_CASE(), and PsiBlastSetupScoreBlock().
◆ GetScoringOpts() [1/2]
|
private |
Returns BlastScoringOptions for eLocal objects, NULL for eRemote.
Definition at line 2688 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetScoringOpts(), and CBlastOptions::m_Local.
Referenced by CBlastSetupTestFixture::s_GetScoringOpts(), CTracebackSearchTestFixture::x_GetSampleHspStream(), CTracebackSearchTestFixture::x_GetSelfHitHspStream(), CTracebackTestFixture::x_MakeStream(), CTracebackTestFixture::x_SetupGapAlign(), and CTracebackTestFixture::x_SetupMain().
◆ GetScoringOpts() [2/2]
|
inlineprivate |
Definition at line 456 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_ScoringOpts.
Referenced by CBlastOptions::GetScoringOpts(), and CBlastOptionsLocal::SetProgram().
◆ GetSearchDatabase()
|
inline |
Definition at line 129 of file local_db_adapter.hpp.
References CLocalDbAdapter::m_DbInfo.
Referenced by PrintSAMHeader(), and CMagicBlastApp::x_LogBlastSearchInfo().
◆ GetSearchMessages() [1/4]
|
inline |
Retrieve any error/warning messages that occurred during the search.
Definition at line 155 of file local_blast.hpp.
References CLocalBlast::m_Messages.
Referenced by CBl2Seq::RunEx().
◆ GetSearchMessages() [2/4]
|
inline |
Retrieve any error/warning messages that occurred during the search.
Definition at line 180 of file prelim_stage.hpp.
References CBlastPrelimSearch::m_Messages.
Referenced by CLocalBlast::Run(), CPsiBlastImpl::Run(), and CMagicBlast::x_Run().
◆ GetSearchMessages() [3/4]
|
inline |
Retrieve any error/warning messages that occurred during the search.
Definition at line 139 of file traceback_stage.hpp.
References CBlastTracebackSearch::m_Messages.
Referenced by CLocalBlast::Run().
◆ GetSearchMessages() [4/4]
|
inline |
Definition at line 81 of file magicblast.hpp.
References CMagicBlast::m_Messages.
◆ GetSearchOptions() [1/2]
| CRef< CBlastOptionsHandle > CRemoteBlast::GetSearchOptions | ( | ) |
Get the search options used for this search.
This returns the CBlastOptionsHandle for this search. If this object was constructed with an RID, a CBlastOptionsHandle will be constructed from the search options stored on the remote server. In this case the returned CBlastOptionsHandle will have a concrete type that corresponds to the program+service, and a locality of "eLocal".
Definition at line 2018 of file remote_blast.cpp.
References set< Key, Compare >::clear(), CRef< C, Locker >::Empty(), CBlastOptions::eRemote, CBlastOptionsBuilder::GetDbFilteringAlgorithmId(), CBlastOptionsBuilder::GetDbFilteringAlgorithmKey(), CBlastOptionsBuilder::GetEntrezQuery(), CBlastOptionsBuilder::GetFinalDbSeq(), CBlastOptionsBuilder::GetFirstDbSeq(), CBlastOptionsBuilder::GetGiList(), CBlastOptionsBuilder::GetNegativeGiList(), CBlastOptionsBuilder::GetNegativeTaxidList(), CRemoteBlast::GetProgram(), CBlastOptionsBuilder::GetSearchOptions(), CRemoteBlast::GetService(), CBlastOptionsBuilder::GetTaxidList(), CBlastOptionsBuilder::HasDbFilteringAlgorithmId(), CBlastOptionsBuilder::HasDbFilteringAlgorithmKey(), CBlastOptionsBuilder::HaveEntrezQuery(), CBlastOptionsBuilder::HaveFinalDbSeq(), CBlastOptionsBuilder::HaveFirstDbSeq(), CBlastOptionsBuilder::HaveGiList(), CBlastOptionsBuilder::HaveNegativeGiList(), CBlastOptionsBuilder::HaveNegativeTaxidList(), CBlastOptionsBuilder::HaveTaxidList(), set< Key, Compare >::insert(), kEmptyStr, CRemoteBlast::m_AlgoOpts, CRemoteBlast::m_CBOH, CRemoteBlast::m_DbFilteringAlgorithmId, CRemoteBlast::m_DbFilteringAlgorithmKey, CRemoteBlast::m_EntrezQuery, CRemoteBlast::m_FinalDbSeq, CRemoteBlast::m_FirstDbSeq, CRemoteBlast::m_FormatOpts, CRemoteBlast::m_GiList, CRemoteBlast::m_NegativeGiList, CRemoteBlast::m_NegativeTaxidList, CRemoteBlast::m_ProgramOpts, CRemoteBlast::m_Task, and CRemoteBlast::m_TaxidList.
Referenced by BOOST_AUTO_TEST_CASE(), CBlastFormatterApp::PrintFormattedOutput(), CBlastFormatterVdbApp::PrintFormattedOutput(), and CRemoteBlast::x_GetRequestInfoFromFile().
◆ GetSearchOptions() [2/2]
| CRef< CBlastOptionsHandle > CBlastOptionsBuilder::GetSearchOptions | ( | const objects::CBlast4_parameters * | aopts, |
| const objects::CBlast4_parameters * | popts, | ||
| const objects::CBlast4_parameters * | fopts, | ||
| string * | task_name = NULL |
||
| ) |
Build and return options as a CBlastOptionsHandle.
A CBlastOptionsHandle is constructed and returned.
- Parameters
-
aopts List of algorithm options [in]. popts List of program options [in]. fopts List of formatting options [in]. task_name name of the task deduced from the arguments [in|out]
Definition at line 667 of file blast_options_builder.cpp.
References CBlastOptionsBuilder::AdjustProgram(), CBlastOptionsBuilder::ComputeProgram(), CBlastOptionsFactory::Create(), EProgramToTaskName(), CBlastOptionsBuilder::SOptional< T >::Have(), CBlastOptionsBuilder::m_IgnoreQueryMasks, CBlastOptionsBuilder::m_Locality, CBlastOptionsBuilder::m_Program, CBlastOptionsBuilder::m_QueryMasks, CBlastOptionsBuilder::m_Service, NULL, s_MergeCBlast4_parameters(), CBlastOptionsBuilder::x_ApplyInteractions(), and CBlastOptionsBuilder::x_ProcessOptions().
Referenced by CRemoteBlast::GetSearchOptions().
◆ GetSearchSpace()
|
inline |
Retrieve the search space for this query sequence.
If the results correspond to a blastx search, the search space will refer to protein letters
Definition at line 118 of file blast_results.hpp.
Referenced by s_BuildArchiveAll().
◆ GetSearchStats()
| list< string > CRemoteBlast::GetSearchStats | ( | void | ) |
Get the search statistics block as a list of strings.
Search statistics describe the data flow during each step of a BLAST search. They are subject to change, and are not formally defined, but can sometimes provide insight when investigating software problems.
- Returns
- List of strings, each contains one line of search stats block.
Definition at line 574 of file remote_blast.cpp.
References CRemoteBlast::x_GetGSRR().
Referenced by CRemoteBlast::GetResultSet().
◆ GetSearchStrategy() [1/2]
| CRef< objects::CBlast4_request > CRemoteBlast::GetSearchStrategy | ( | void | ) |
Fetch the search strategy for this object without submitting the search.
Definition at line 182 of file remote_blast.cpp.
References CRemoteBlast::GetErrors(), CRemoteBlast::m_ClientId, NCBI_THROW, CBlast4_request_Base::SetBody(), CBlast4_request_Base::SetIdent(), CRemoteBlast::x_CheckConfig(), and CRemoteBlast::x_GetBlast4SearchRequestBody().
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetSearchStrategy() [2/2]
| CRef< objects::CBlast4_request > CExportStrategy::GetSearchStrategy | ( | void | ) |
Definition at line 352 of file search_strategy.cpp.
References CExportStrategy::m_ClientId, CExportStrategy::m_QueueSearchRequest, CBlast4_request_Base::SetBody(), CBlast4_request_Base::SetIdent(), and CBlast4_request_body_Base::SetQueue_search().
Referenced by BOOST_AUTO_TEST_CASE(), and CExportStrategy::ExportSearchStrategy_ASN1().
◆ GetSegFiltering() [1/4]
| bool CBlastOptions::GetSegFiltering | ( | ) | const |
Definition at line 1229 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetSegFiltering(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by BOOST_AUTO_TEST_CASE(), CBlastAdvancedProteinOptionsHandle::SetGappedExtensionDefaults(), and CBlastxOptionsHandle::SetGappedExtensionDefaults().
◆ GetSegFiltering() [2/4]
|
inline |
Is SEG filtering enabled?
Definition at line 86 of file blast_prot_options.hpp.
Referenced by BOOST_FIXTURE_TEST_CASE().
◆ GetSegFiltering() [3/4]
|
inline |
Is SEG filtering enabled?
Definition at line 79 of file blast_rps_options.hpp.
◆ GetSegFiltering() [4/4]
|
inline |
Definition at line 832 of file blast_options_local_priv.hpp.
References QuerySetUpOptions::filtering_options, CBlastOptionsLocal::m_QueryOpts, and SBlastFilterOptions::segOptions.
Referenced by CBlastOptions::GetSegFiltering(), and CBlastOptions::SetFilterString().
◆ GetSegFilteringHicut() [1/4]
| double CBlastOptions::GetSegFilteringHicut | ( | ) | const |
Definition at line 1286 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetSegFilteringHicut(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
◆ GetSegFilteringHicut() [2/4]
|
inline |
Get hicut parameter for seg.
Definition at line 104 of file blast_prot_options.hpp.
Referenced by BOOST_FIXTURE_TEST_CASE().
◆ GetSegFilteringHicut() [3/4]
|
inline |
Get hicut parameter for seg.
Definition at line 97 of file blast_rps_options.hpp.
◆ GetSegFilteringHicut() [4/4]
|
inline |
Definition at line 897 of file blast_options_local_priv.hpp.
References QuerySetUpOptions::filtering_options, SSegOptions::hicut, kInvalidFilterValue, CBlastOptionsLocal::m_QueryOpts, NULL, and SBlastFilterOptions::segOptions.
Referenced by CBlastOptions::GetSegFilteringHicut(), and CBlastOptions::SetFilterString().
◆ GetSegFilteringLocut() [1/4]
| double CBlastOptions::GetSegFilteringLocut | ( | ) | const |
Definition at line 1267 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetSegFilteringLocut(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
◆ GetSegFilteringLocut() [2/4]
|
inline |
Get locut parameter for seg.
Definition at line 98 of file blast_prot_options.hpp.
Referenced by BOOST_FIXTURE_TEST_CASE().
◆ GetSegFilteringLocut() [3/4]
|
inline |
Get locut parameter for seg.
Definition at line 91 of file blast_rps_options.hpp.
◆ GetSegFilteringLocut() [4/4]
|
inline |
Definition at line 877 of file blast_options_local_priv.hpp.
References QuerySetUpOptions::filtering_options, kInvalidFilterValue, SSegOptions::locut, CBlastOptionsLocal::m_QueryOpts, NULL, and SBlastFilterOptions::segOptions.
Referenced by CBlastOptions::GetSegFilteringLocut(), and CBlastOptions::SetFilterString().
◆ GetSegFilteringWindow() [1/4]
| int CBlastOptions::GetSegFilteringWindow | ( | ) | const |
Definition at line 1248 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetSegFilteringWindow(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
◆ GetSegFilteringWindow() [2/4]
|
inline |
Get window parameter for seg.
Definition at line 92 of file blast_prot_options.hpp.
Referenced by BOOST_FIXTURE_TEST_CASE().
◆ GetSegFilteringWindow() [3/4]
|
inline |
Get window parameter for seg.
Definition at line 85 of file blast_rps_options.hpp.
◆ GetSegFilteringWindow() [4/4]
|
inline |
Definition at line 857 of file blast_options_local_priv.hpp.
References QuerySetUpOptions::filtering_options, kInvalidFilterValue, CBlastOptionsLocal::m_QueryOpts, NULL, SBlastFilterOptions::segOptions, and SSegOptions::window.
Referenced by CBlastOptions::GetSegFilteringWindow(), and CBlastOptions::SetFilterString().
◆ GetSegmentInfo() [1/3]
Get segment information (for mapping paired short reads)
Implements IBlastQuerySource.
Definition at line 382 of file bioseq_extract_data_priv.cpp.
References CBioseq_Base::CanGetDescr(), CSeqdesc_Base::e_User, CSeq_descr_Base::Get(), CUser_field_Base::GetData(), CBioseq_Base::GetDescr(), CUser_field::GetField(), CUser_field_Base::C_Data::GetInt(), CUser_field_Base::C_Data::IsInt(), ITERATE, and CBlastQuerySourceBioseqSet::m_Bioseqs.
Referenced by CBlastQuerySourceBioseqSet::IsFirstOfAPair().
◆ GetSegmentInfo() [2/3]
Get segment information (for mapping paired short reads)
Implements IBlastQuerySource.
Definition at line 159 of file blast_objmgr_priv.hpp.
References NCBI_THROW.
◆ GetSegmentInfo() [3/3]
Get segment information (for mapping paired short reads)
Implemented in CBlastQuerySourceOM, and CBlastQuerySourceBioseqSet.
Referenced by SetupQueryInfo_OMF().
◆ GetSegments() [1/2]
|
inline |
Get hit segments.
- Returns
- Reference to hit segments
Definition at line 344 of file cdd_pssm_input.hpp.
References CCddInputData::CHit::m_SegmentList.
Referenced by CCddInputData::CHit::IntersectWith(), and CCddInputData::CHit::Subtract().
◆ GetSegments() [2/2]
|
inline |
Get hit segments.
- Returns
- Reference to hit segments
Definition at line 348 of file cdd_pssm_input.hpp.
References CCddInputData::CHit::m_SegmentList.
◆ GetSentinelByte()
| Uint1 GetSentinelByte | ( | EBlastEncoding | encoding | ) |
Convenience function to centralize the knowledge of which sentinel bytes we use for supported encodings.
Note that only eBlastEncodingProtein, eBlastEncodingNucleotide, and eBlastEncodingNcbi4na support sentinel bytes, any other values for encoding will cause an exception to be thrown.
- Parameters
-
encoding Encoding for which a sentinel byte is needed [in]
- Returns
- sentinel byte
- Exceptions
-
CBlastException in case of unsupported encoding
Definition at line 1249 of file blast_setup_cxx.cpp.
References eBlastEncodingNcbi4na, eBlastEncodingNucleotide, eBlastEncodingProtein, kNuclSentinel, kProtSentinel, and NCBI_THROW.
Referenced by CompressedAalookupTestFixture::GetSeqBlk(), AalookupTestFixture::GetSeqBlk(), GetSequenceNucleotideBothStrands(), GetSequenceProtein(), GetSequenceSingleNucleotideStrand(), InitializeBlastScoreBlk(), and CPssmEngine::x_GuardProteinQuery().
◆ GetSeq_loc() [1/3]
Get the Seq_loc for the sequence indicated by index.
Implements ILocalQueryData.
Definition at line 243 of file objmgr_query_data.cpp.
References IBlastQuerySource::GetSeqLoc(), and CObjMgr_LocalQueryData::m_QuerySource.
◆ GetSeq_loc() [2/3]
Get the Seq_loc for the sequence indicated by index.
Implements ILocalQueryData.
Definition at line 143 of file objmgrfree_query_data.cpp.
References IBlastQuerySource::GetSeqLoc(), and CObjMgrFree_LocalQueryData::m_QuerySource.
◆ GetSeq_loc() [3/3]
|
pure virtual |
Get the Seq_loc for the sequence indicated by index.
Implemented in CObjMgrFree_LocalQueryData, and CObjMgr_LocalQueryData.
Referenced by operator<<(), CDeltaBlast::Run(), CLocalBlast::Run(), CBlastTracebackSearch::Run(), s_BLAST_OneSubjectResults2CSeqAlign(), s_CreateSeqAlign(), s_LocalQueryData2Packed_seqint(), s_MakeEmptyResults(), CMagicBlast::x_BuildResultSet(), CBlastPrelimSearch::x_BuildStdSegList(), CQuerySplitter::x_ComputeQueryContextsForChunks(), CQuerySplitter::x_ComputeQueryIndicesForChunks(), and CMagicBlast::x_Run().
◆ GetSeqAlign() [1/2]
|
inline |
Accessor for the Seq-align results.
Definition at line 193 of file blast_results.hpp.
References CSearchResults::m_Alignment.
Referenced by BOOST_AUTO_TEST_CASE(), CBlastAligner::GenerateAlignments(), CRemoteBlastAligner::GenerateAlignments(), CSimpleB2SWrapper::processBlastHits(), CMultiAligner::x_AlignClusterQueries(), CIgBlast::x_AnnotateC(), CIgBlast::x_AnnotateD(), CIgBlast::x_AnnotateDJ(), CIgBlast::x_AnnotateJ(), CIgBlast::x_ConvertResultType(), CIgBlast::x_FindDJ(), CIgBlast::x_ProcessCResult(), and CPsiBlastApp::x_RunLocalPsiBlastIterations().
◆ GetSeqAlign() [2/2]
|
inline |
Get alignments.
Definition at line 174 of file magicblast.hpp.
References CMagicBlastResults::m_Aligns.
◆ GetSeqAlignSets()
| TSeqAlignVector CRemoteBlast::GetSeqAlignSets | ( | ) |
Get the seqalign vector from the results.
This method returns the alignment data from the search as a TSeqAlignVector, which is a vector of CSeq_align_set objects. For multiple query searches, this method will normally return each alignment as a seperate element of the TSeqAlignVector. Note that in some cases, the TSeqAlignVector will not have an entry for some queries. If the vector contains fewer alignments than there were queries, it may be necessary for the calling code to match queries to alignments by comparing Seq_ids. This normally happens only if the same query is specified multiple times, or if one of the searches does not find any matches.
- Returns
- A seqalign vector.
Definition at line 405 of file remote_blast.cpp.
References CSeq_id::Compare(), CSeq_id::e_YES, CConstRef< C, Locker >::Empty(), CSeq_align_set_Base::Get(), CRemoteBlast::GetAlignments(), ITERATE, CRef< C, Locker >::NotEmpty(), CRef< C, Locker >::Reset(), CSeq_align_set_Base::Set(), and CRemoteBlast::x_ExtractQueryIds().
Referenced by BOOST_AUTO_TEST_CASE(), CRemoteBlast::GetResultSet(), s_BuildResultsRemote(), and x_CountHits().
◆ GetSeqBlk() [1/2]
|
inline |
Returns sequence block structure for one of the sequences.
- Parameters
-
index Which sequence to retrieve sequence block for? [in]
- Returns
- The sequence block.
Definition at line 123 of file seqsrc_multiseq.cpp.
References _ASSERT, and CMultiSeqInfo::m_ivSeqBlkVec.
◆ GetSeqBlk() [2/2]
|
inline |
Returns sequence block structure for one of the sequences.
- Parameters
-
index Which sequence to retrieve sequence block for? [in]
- Returns
- The sequence block.
Definition at line 200 of file seqsrc_query_factory.cpp.
References CQueryFactoryInfo::GetNumSeqs(), and CQueryFactoryInfo::m_SeqBlkVector.
◆ GetSeqDb()
Obtain a reference to the database.
Definition at line 242 of file uniform_search.cpp.
References CSearchDatabase::m_DbInitialized, CSearchDatabase::m_SeqDb, and CSearchDatabase::x_InitializeDb().
Referenced by CSetupFactory::CreateBlastSeqSrc(), CIgBlastArgs::ExtractAlgorithmOptions(), InitializeSubject(), CVectorScreen::IsDbAvailable(), LogCmdOptions(), CMagicBlastThread::Main(), CLocalDbAdapter::MakeSeqInfoSrc(), PrintSAMHeader(), CBlastnApp::Run(), CBlastpApp::Run(), CBlastxApp::Run(), CSeedTopApp::Run(), CTblastnApp::Run(), and s_InitializeSubject().
◆ GetSeqId() [1/4]
Accessor for the query's sequence identifier.
Definition at line 329 of file blast_results.cpp.
References CSearchResults::m_QueryId.
Referenced by CBlastFormat::PrintPhiResult(), and CIgBlast::x_ConvertResultType().
◆ GetSeqId() [2/4]
Return the sequence identifier associated with a sequence.
- Parameters
-
index index of the sequence in the sequence container [in]
Implements IBlastQuerySource.
Definition at line 288 of file bioseq_extract_data_priv.cpp.
References CBlastQuerySourceBioseqSet::m_Bioseqs.
◆ GetSeqId() [3/4]
Return the sequence identifier associated with a sequence.
- Parameters
-
index index of the sequence in the sequence container [in]
Implements IBlastQuerySource.
Definition at line 286 of file blast_objmgr_tools.cpp.
References GetId(), CBlastQueryVector::GetQuerySeqLoc(), CBlastQueryVector::GetScope(), i, CBlastQuerySourceOM::m_QueryVector, CBlastQuerySourceOM::m_TSeqLocVector, and CRef< C, Locker >::NotEmpty().
Referenced by CBlastQuerySourceOM::GetLength().
◆ GetSeqId() [4/4]
Return the sequence identifier associated with a sequence.
- Parameters
-
index index of the sequence in the sequence container [in]
Implemented in CBlastQuerySourceOM, and CBlastQuerySourceBioseqSet.
Referenced by SetupQueries_OMF(), and SetupSubjects_OMF().
◆ GetSeqIds()
|
static |
Extract the sequence ids from the sequence alignment which identify those sequences that will be used for PSSM construction.
- Parameters
-
seqalign Sequence alignment [in] opts options containing details for algorithm to select sequences from seqalign [in] retval List of sequence identifiers for those sequences from the seqalign which will participate in PSSM construction [out]
Definition at line 135 of file psiblast_iteration.cpp.
References set< Key, Compare >::clear(), and proc.
Referenced by BOOST_AUTO_TEST_CASE(), CDeltaBlastApp::DoPsiBlastIterations(), and CPsiBlastApp::x_RunLocalPsiBlastIterations().
◆ GetSeqLength() [1/3]
|
virtual |
Get the length of the sequence indicated by index.
Implements ILocalQueryData.
Definition at line 249 of file objmgr_query_data.cpp.
References IBlastQuerySource::GetLength(), and CObjMgr_LocalQueryData::m_QuerySource.
◆ GetSeqLength() [2/3]
|
virtual |
Get the length of the sequence indicated by index.
Implements ILocalQueryData.
Definition at line 149 of file objmgrfree_query_data.cpp.
References IBlastQuerySource::GetLength(), and CObjMgrFree_LocalQueryData::m_QuerySource.
◆ GetSeqLength() [3/3]
|
pure virtual |
Get the length of the sequence indicated by index.
Implemented in CObjMgrFree_LocalQueryData, and CObjMgr_LocalQueryData.
Referenced by CQueryDataPerChunk::CQueryDataPerChunk(), ILocalQueryData::GetSumOfSequenceLengths(), PsiBlastComputePssmScores(), s_BLAST_OneSubjectResults2CSeqAlign(), s_CreateSeqAlign(), s_LocalQueryData2Packed_seqint(), CBlastPrelimSearch::x_BuildStdSegList(), and CQuerySplitter::x_ComputeQueryIndicesForChunks().
◆ GetSeqLoc() [1/7]
Return the CSeq_loc associated with a sequence.
- Parameters
-
i index of the sequence in the sequence container [in]
Implements IBlastQuerySource.
Definition at line 276 of file blast_objmgr_tools.cpp.
References CBlastQueryVector::GetQuerySeqLoc(), i, CBlastQuerySourceOM::m_QueryVector, CBlastQuerySourceOM::m_TSeqLocVector, and CRef< C, Locker >::NotEmpty().
Referenced by CBlastQuerySourceOM::GetTitle().
◆ GetSeqLoc() [2/7]
Return the CSeq_loc associated with a sequence.
- Parameters
-
index index of the sequence in the sequence container [in]
Implements IBlastQuerySource.
Definition at line 278 of file bioseq_extract_data_priv.cpp.
References CBlastQuerySourceBioseqSet::m_Bioseqs.
Referenced by CBioseqSeqInfoSrc::GetId(), and s_ConstBioseqSetToSeqLocs().
◆ GetSeqLoc() [3/7]
Return the CSeq_loc associated with a sequence.
- Parameters
-
index index of the sequence in the sequence container [in]
Implemented in CBlastQuerySourceBioseqSet, and CBlastQuerySourceOM.
Referenced by CObjMgr_LocalQueryData::GetSeq_loc(), CObjMgrFree_LocalQueryData::GetSeq_loc(), s_GetRestrictedBlastSeqLocs(), s_RestrictSeqLocs_Multiframe(), and SetupSubjects_OMF().
◆ GetSeqLoc() [4/7]
Method to retrieve the sequence location given its ordinal number.
- Parameters
-
index the ordinal number to retrieve [in]
Implements IBlastSeqInfoSrc.
Definition at line 79 of file seqinfosrc_seqvec.cpp.
References CSeqVecSeqInfoSrc::m_SeqVec, and NCBI_THROW.
◆ GetSeqLoc() [5/7]
Retrieve a sequence identifier given its index in the vector.
- Parameters
-
index the ordinal number to retrieve [in]
Implements IBlastSeqInfoSrc.
Definition at line 74 of file seqinfosrc_bioseq.cpp.
References CreateWholeSeqLocFromIds(), and CBioseqSeqInfoSrc::GetId().
◆ GetSeqLoc() [6/7]
Method to retrieve the sequence location given its ordinal number.
- Parameters
-
index the ordinal number to retrieve [in]
Implemented in CSeqDbSeqInfoSrc, CBioseqSeqInfoSrc, and CSeqVecSeqInfoSrc.
Referenced by BlastHitList2SeqAlign_OMF(), and s_BLAST_OneSubjectResults2CSeqAlign().
◆ GetSeqLoc() [7/7]
Method to retrieve the sequence location given its ordinal number.
- Parameters
-
index the ordinal number to retrieve [in]
Implements IBlastSeqInfoSrc.
Definition at line 72 of file seqinfosrc_seqdb.cpp.
References CreateWholeSeqLocFromIds(), and CSeqDbSeqInfoSrc::GetId().
◆ GetSeqLocs() [1/3]
|
virtual |
Accessor for the TSeqLocs.
Implements IRemoteQueryData.
Definition at line 310 of file objmgr_query_data.cpp.
References abort(), CObjMgr_RemoteQueryData::m_Queries, CObjMgr_RemoteQueryData::m_QueryVector, IRemoteQueryData::m_SeqLocs, CRef< C, Locker >::NotEmpty(), s_QueryVectorToTSeqLocs(), and s_TSeqLocVectorToTSeqLocs().
◆ GetSeqLocs() [2/3]
|
virtual |
Accessor for the TSeqLocs.
Implements IRemoteQueryData.
Definition at line 218 of file objmgrfree_query_data.cpp.
References CObjMgrFree_RemoteQueryData::m_ClientBioseqSet, IRemoteQueryData::m_SeqLocs, NCBI_CURRENT_FUNCTION, NCBI_THROW, CConstRef< C, Locker >::NotEmpty(), and s_ConstBioseqSetToSeqLocs().
◆ GetSeqLocs() [3/3]
|
pure virtual |
Accessor for the TSeqLocs.
Implemented in CObjMgrFree_RemoteQueryData, and CObjMgr_RemoteQueryData.
Referenced by CRemoteBlast::x_InitQueries(), CExportStrategy::x_Process_Query(), CRemoteSeqSearch::x_RemoteBlast(), and CSequenceDataTester::x_TestSingleSequence_Remote().
◆ GetSeqSearch() [1/3]
|
virtual |
Get an object to manage a local sequence search.
Supporting elements.
Implements ISearchFactory.
Definition at line 69 of file local_search.cpp.
◆ GetSeqSearch() [2/3]
|
virtual |
Get an object to manage a remote sequence search.
Supporting elements.
Implements ISearchFactory.
Definition at line 58 of file remote_search.cpp.
◆ GetSeqSearch() [3/3]
|
pure virtual |
Create a new search object with a sequence-based query.
A search object will be constructed and configured for a search using a query that consists of one or more sequences.
- Returns
- A search object for a sequence search.
Implemented in CRemoteSearchFactory, and CLocalSearchFactory.
Referenced by RunMultipleProteinSearch().
◆ GetSequence()
| SBlastSequence GetSequence | ( | const objects::CSeq_loc & | sl, |
| EBlastEncoding | encoding, | ||
| objects::CScope * | scope, | ||
| objects::ENa_strand | strand = objects::eNa_strand_plus, |
||
| ESentinelType | sentinel = eSentinels, |
||
| std::string * | warnings = NULL |
||
| ) |
Retrieves a sequence using the object manager.
- Parameters
-
sl seqloc of the sequence to obtain [in] encoding encoding for the sequence retrieved. Supported encodings include: eBlastEncodingNcbi2na, eBlastEncodingNcbi4na, eBlastEncodingNucleotide, and eBlastEncodingProtein. [in] scope Scope from which the sequences are retrieved [in] strand strand to retrieve (applies to nucleotide only). N.B.: When requesting the eBlastEncodingNcbi2na, only the plus strand is retrieved, because BLAST only requires one strand on the subject sequences (as in BLAST databases). [in] sentinel Use eSentinels to guard nucleotide sequence with sentinel bytes (ignored for protein sequences, which always have sentinels) When using eBlastEncodingNcbi2na, this argument should be set to eNoSentinels as a sentinel byte cannot be represented in this encoding. [in] warnings Used to emit warnings when fetching sequence (e.g.: replacement of invalid characters). Parameter must be allocated by caller of this function and warnings will be appended. [out]
- Exceptions
-
CBlastException,CSeqVectorException,CException
- Returns
- pair containing the buffer and its length.
Definition at line 568 of file blast_objmgr_tools.cpp.
References GetSequence_OMF().
Referenced by AascanTestFixture::AascanTestFixture(), BOOST_AUTO_TEST_CASE(), CompressedAascanTestFixture::CompressedAascanTestFixture(), CPssmCddInputTest::CreatePssmInput(), CBlastQuerySourceOM::GetBlastSequence(), CompressedAalookupTestFixture::GetSeqBlk(), AalookupTestFixture::GetSeqBlk(), LinkHspTestFixture::setupLinkHspInputBlastn(), NtlookupTestFixture::SetUpQuery(), TestFixture::SetUpQuery(), NuclWordFinderTextFixture::setupSequences(), TestFixture::SetUpSubject(), CMultiAligner::x_FindPatternHits(), and CRandomlyFailMockBlastSeqSrc::x_PopulateBLAST_SequenceBlk().
◆ GetSequence_OMF()
| SBlastSequence GetSequence_OMF | ( | IBlastSeqVector & | sv, |
| EBlastEncoding | encoding, | ||
| objects::ENa_strand | strand, | ||
| ESentinelType | sentinel, | ||
| std::string * | warnings = 0 |
||
| ) |
Object manager free version of GetSequence.
Definition at line 1060 of file blast_setup_cxx.cpp.
References _ASSERT, eBlastEncodingNcbi2na, eBlastEncodingNcbi4na, eBlastEncodingNucleotide, eBlastEncodingProtein, eNa_strand_both, eNoSentinels, GetSequenceCompressedNucleotide(), GetSequenceNucleotideBothStrands(), GetSequenceProtein(), GetSequenceSingleNucleotideStrand(), and NCBI_THROW.
Referenced by CBlastQuerySourceBioseqSet::GetBlastSequence(), and GetSequence().
◆ GetSequenceBlk() [1/3]
|
virtual |
Accessor for the BLAST_SequenceBlk structure.
Implements ILocalQueryData.
Definition at line 206 of file objmgr_query_data.cpp.
References abort(), CBLAST_SequenceBlk::Get(), CObjMgr_LocalQueryData::GetQueryInfo(), ILocalQueryData::m_Messages, CObjMgr_LocalQueryData::m_Options, CObjMgr_LocalQueryData::m_Queries, CObjMgr_LocalQueryData::m_QuerySource, CObjMgr_LocalQueryData::m_QueryVector, ILocalQueryData::m_SeqBlk, CRef< C, Locker >::NotEmpty(), NULL, CBLAST_SequenceBlk::Reset(), and SafeSetupQueries().
◆ GetSequenceBlk() [2/3]
|
virtual |
Accessor for the BLAST_SequenceBlk structure.
Implements ILocalQueryData.
Definition at line 102 of file objmgrfree_query_data.cpp.
References CBLAST_SequenceBlk::Get(), CObjMgrFree_LocalQueryData::GetQueryInfo(), CObjMgrFree_LocalQueryData::m_BioseqSet, ILocalQueryData::m_Messages, CObjMgrFree_LocalQueryData::m_Options, CObjMgrFree_LocalQueryData::m_QuerySource, ILocalQueryData::m_SeqBlk, NCBI_CURRENT_FUNCTION, NCBI_THROW, CConstRef< C, Locker >::NotEmpty(), NULL, CBLAST_SequenceBlk::Reset(), and SafeSetupQueries().
◆ GetSequenceBlk() [3/3]
|
pure virtual |
Accessor for the BLAST_SequenceBlk structure.
Implemented in CObjMgrFree_LocalQueryData, and CObjMgr_LocalQueryData.
Referenced by BlastSetupPreliminarySearchEx(), CSetupFactory::CreateLookupTable(), CSetupFactory::CreateScoreBlock(), PsiBlastComputePssmScores(), CPsiBlastValidate::QueryFactory(), CDeltaBlast::Run(), CBlastPrelimSearch::Run(), CBlastSetupTestFixture::s_ValidateProtein130912(), CQuerySplitter::x_ComputeContextOffsets_NonTranslatedQueries(), CQuerySplitter::x_ComputeContextOffsets_TranslatedQueries(), CBlastTracebackSearch::x_Init(), CLocalVDBBlast::x_PrepareQuery(), CSplitQueryTestFixture::x_TestCContextTranslator(), and CSequenceDataTester::x_TestSingleSequence_Local().
◆ GetSequenceCompressedNucleotide()
|
static |
Auxiliary function to retrieve plus strand in compressed (ncbi4na) format.
- Parameters
-
sv abstraction to get sequence data [in]
- Returns
- requested data in compressed format
Definition at line 946 of file blast_setup_cxx.cpp.
References CompressNcbi2na(), CSeq_data_Base::e_Ncbi4na, IBlastSeqVector::GetCompressedPlusStrand(), and IBlastSeqVector::SetCoding().
Referenced by GetSequence_OMF().
◆ GetSequenceLengthAndId() [1/4]
| void GetSequenceLengthAndId | ( | const blast::IBlastSeqInfoSrc * | seqinfo_src, |
| int | oid, | ||
| CRef< CSeq_id > & | seqid, | ||
| TSeqPos * | length | ||
| ) |
Definition at line 51 of file blast_seqinfosrc_aux.cpp.
References _ASSERT, CSeq_id::BestRank(), FindBestChoice(), CSeq_id_Base::IsGi(), and SerialAssign().
◆ GetSequenceLengthAndId() [2/4]
| void GetSequenceLengthAndId | ( | const blast::IBlastSeqInfoSrc * | seqinfo_src, |
| int | oid, | ||
| int(*)(const CRef< CSeq_id > &) | rank_func, | ||
| CRef< CSeq_id > & | seqid, | ||
| TSeqPos * | length | ||
| ) |
Definition at line 72 of file blast_seqinfosrc_aux.cpp.
References _ASSERT, FindBestChoice(), CRef< C, Locker >::Reset(), and SerialAssign().
◆ GetSequenceLengthAndId() [3/4]
| void GetSequenceLengthAndId | ( | const IBlastSeqInfoSrc * | seqinfo_src, |
| int | oid, | ||
| CRef< objects::CSeq_id > & | seqid, | ||
| TSeqPos * | length | ||
| ) |
Retrieves subject sequence Seq-id and length.
- Parameters
-
seqinfo_src Source of subject sequences information [in] oid Ordinal id (index) of the subject sequence [in] seqid Subject sequence identifier to fill [out] length Subject sequence length [out]
Referenced by BlastHitList2SeqAlign_OMF(), BLASTPrelminSearchHitListToStdSeg(), PrintSAMHeader(), CSeedTop::Run(), s_BLAST_OneSubjectResults2CSeqAlign(), and s_CreateSeqAlign().
◆ GetSequenceLengthAndId() [4/4]
| void GetSequenceLengthAndId | ( | const IBlastSeqInfoSrc * | seqinfo_src, |
| int | oid, | ||
| int(*)(const CRef< objects::CSeq_id > &) | rank_func, | ||
| CRef< objects::CSeq_id > & | seqid, | ||
| TSeqPos * | length | ||
| ) |
Retrieves subject sequence Seq-id and length, using the provided sequence id ranking function.
- Parameters
-
seqinfo_src Source of subject sequences information [in] oid Ordinal id (index) of the subject sequence [in] rank_func Sequence id ranking function [in] seqid Subject sequence identifier to fill [out] length Subject sequence length [out]
◆ GetSequenceNucleotideBothStrands()
|
static |
Auxiliary function to retrieve both strands of a nucleotide sequence.
- Parameters
-
sv abstraction to get sequence data [in] encoding desired encoding for the data above [in] sentinel use or do not use sentinel bytes [in]
- Returns
- concatenated strands in requested encoding with sentinels as requested
Definition at line 1015 of file blast_setup_cxx.cpp.
References CalculateSeqBufferLength(), eNa_strand_both, eNa_strand_minus, eNa_strand_plus, eNoSentinels, eSentinels, GetSentinelByte(), GetSequenceSingleNucleotideStrand(), NStr::IntToString(), malloc(), minus(), NCBI_THROW, plus(), and IBlastSeqVector::size().
Referenced by GetSequence_OMF().
◆ GetSequenceParts()
|
static |
This retrieves (partial) sequence data from the remote BLAST server.
- Parameters
-
seqid A vector of Seq-ids for which sequence data are requested. [in] database A list of databases from which to get the sequences. [in] seqtype The residue type, 'p' from protein, 'n' for nucleotide. [in] ids The sequence IDs for those sequences which the seq data was seq_data Sequence data in CSeq_data format. [out] errors An error message (if any). [out] warnings A warning (if any). [out] verbose Produce verbose output. [in]
Definition at line 616 of file blast_services.cpp.
References CBlast4Client_Base::Ask(), database, CRef< C, Locker >::Empty(), MSerial_AsnText, NCBI_THROW, NcbiCout, s_BuildGetSeqPartsRequest(), and s_GetPartsFromReply().
Referenced by BOOST_AUTO_TEST_CASE(), CRemoteBlastDbAdapter::x_FetchData(), and CRemoteBlastDbAdapter::x_FetchDataByBatch().
◆ GetSequenceProtein()
|
static |
Protein sequences are always encoded in eBlastEncodingProtein and always have sentinel bytes around sequence data.
Definition at line 872 of file blast_setup_cxx.cpp.
References _ASSERT, AMINOACID_TO_NCBISTDAA, buf, CalculateSeqBufferLength(), CSeq_data_Base::e_Ncbistdaa, eBlastEncodingProtein, GetSentinelByte(), i, int, NStr::IntToString(), malloc(), min(), NCBI_THROW, NULL, AutoPtr< X, Del >::release(), AutoPtr< X, Del >::reset(), s_IsValidResidue(), IBlastSeqVector::SetCoding(), IBlastSeqVector::size(), and NStr::SizetToString().
Referenced by GetSequence_OMF().
◆ GetSequences()
|
static |
Get a set of Bioseqs given an input set of Seq-ids.
This retrieves the Bioseqs corresponding to the given Seq-ids from the blast4 server. Normally this will be much faster than consulting ID1 seperately for each sequence. Sometimes there are multiple sequences for a given Seq-id. In such cases, there are always 'non-ambiguous' ids available. This interface does not currently address this issue, and will simply return the Bioseqs corresponding to one of the sequences. Errors will be returned if the operation cannot be completed (or started). In the case of a sequence that cannot be found, the error will indicate the index of (and Seq-id of) the missing sequence; processing will continue, and the sequences that can be found will be returned along with the error.
- Parameters
-
seqids A vector of Seq-ids for which Bioseqs are requested. database A list of databases from which to get the sequences. seqtype The residue type, 'p' from protein, 'n' for nucleotide. bioseqs The vector used to return the requested Bioseqs. errors A null-separated list of errors. warnings A null-separated list of warnings. verbose Produce verbose output. [in] target_only Filter the defline to include only the requested id. [in]
Definition at line 571 of file blast_services.cpp.
References database, and s_GetSequences().
Referenced by BOOST_AUTO_TEST_CASE(), and CDUpdater::retrieveAllSequences().
◆ GetSequencesInfo()
|
static |
Get a set of Bioseqs without their sequence data given an input set of.
Seq-ids.
- Parameters
-
seqids A vector of Seq-ids for which Bioseqs are requested. database A list of databases from which to get the sequences. seqtype The residue type, 'p' from protein, 'n' for nucleotide. bioseqs The vector used to return the requested Bioseqs. errors A null-separated list of errors. warnings A null-separated list of warnings. verbose Produce verbose output. [in] target_only Filter the defline to include only the requested id. [in]
Definition at line 557 of file blast_services.cpp.
References database, and s_GetSequences().
Referenced by BOOST_AUTO_TEST_CASE(), CRemoteBlastDbAdapter::SeqidToOid(), and CRemoteBlastDbAdapter::SeqidToOidBatch().
◆ GetSequenceSingleNucleotideStrand()
|
static |
Auxiliary function to retrieve a single strand of a nucleotide sequence.
- Parameters
-
sv abstraction to get sequence data [in] encoding desired encoding for the data above [in] strand desired strand [in] sentinel use or do not use sentinel bytes [in]
- Returns
- Requested strand in desired encoding with/without sentinels
Definition at line 964 of file blast_setup_cxx.cpp.
References _ASSERT, BLASTNA_SIZE, buffer, CalculateSeqBufferLength(), CSeq_data_Base::e_Ncbi4na, eBlastEncodingNucleotide, eNa_strand_minus, eNa_strand_plus, eSentinels, GetSentinelByte(), IBlastSeqVector::GetStrandData(), i, NStr::IntToString(), malloc(), NCBI4NA_TO_BLASTNA, NCBI_THROW, NULL, AutoPtr< X, Del >::release(), AutoPtr< X, Del >::reset(), IBlastSeqVector::SetCoding(), ncbi::grid::netcache::search::fields::size, and IBlastSeqVector::size().
Referenced by GetSequence_OMF(), and GetSequenceNucleotideBothStrands().
◆ GetService() [1/2]
| string CRemoteBlast::GetService | ( | ) |
Get the service used for this search.
- Returns
- The value of the service parameter.
Definition at line 1897 of file remote_blast.cpp.
References CRemoteBlast::m_Service, and CRemoteBlast::x_GetRequestInfo().
Referenced by BOOST_AUTO_TEST_CASE(), and CRemoteBlast::GetSearchOptions().
◆ GetService() [2/2]
| string CImportStrategy::GetService | ( | ) | const |
Fetches service, such as psiblast, plain, megablast.
Definition at line 209 of file search_strategy.cpp.
References CImportStrategy::m_Request.
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetSigma()
|
static |
Data used in sequence weights computation.
- Parameters
-
pssm PSSM to extract data from [in] retval vector containing the sigma values or an empty vector if this data is not available [in|out]
Definition at line 374 of file psiblast_aux_priv.cpp.
References copy(), CPssm_Base::GetIntermediateData(), and CPssmIntermediateData_Base::GetSigma().
◆ GetSmithWatermanMode() [1/4]
|
inline |
Returns this mode, specifying that smith waterman rather than the normal blast heuristic should be used for final extensions.
into account when calculating expect values.
Definition at line 84 of file blast_advprot_options.hpp.
Referenced by BOOST_FIXTURE_TEST_CASE().
◆ GetSmithWatermanMode() [2/4]
| bool CBlastOptions::GetSmithWatermanMode | ( | ) | const |
Definition at line 1665 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetSmithWatermanMode(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
◆ GetSmithWatermanMode() [3/4]
|
inline |
Returns this mode, specifying that smith waterman rather than the normal blast heuristic should be used for final extensions.
into account when calculating expect values.
Definition at line 118 of file blastx_options.hpp.
◆ GetSmithWatermanMode() [4/4]
|
inline |
Definition at line 1202 of file blast_options_local_priv.hpp.
References eSmithWatermanTbck, BlastExtensionOptions::eTbackExt, and CBlastOptionsLocal::m_ExtnOpts.
Referenced by CBlastOptions::GetSmithWatermanMode().
◆ GetSplice()
|
inline |
Splice HSPs for each query.
Definition at line 1594 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_HitSaveOpts, and BlastHitSavingOptions::splice.
Referenced by CBlastOptions::GetSpliceAlignments().
◆ GetSpliceAlignments() [1/2]
| bool CBlastOptions::GetSpliceAlignments | ( | ) | const |
Splice HSPs for each query (for mappring RNA-Seq reads to a genome)
Definition at line 2176 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetSplice(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
◆ GetSpliceAlignments() [2/2]
|
inline |
Return the splice/unsplice alignments switch value.
- Returns
- True if alignments are spliced, false otherwise
Definition at line 207 of file magicblast_options.hpp.
Referenced by CMagicBlastThread::Main().
◆ GetStartingChunk()
Get the chunk number where context_in_chunk starts (i.e.
: location of its first chunk).
- Parameters
-
curr_chunk Chunk where the context_in_chunk is found [in] context_in_chunk Context in the split query [in]
- Returns
- the appropriate chunk number or kInvalidContext if the context is not valid in the query chunk (i.e.: strand not searched)
Definition at line 266 of file split_query_aux_priv.cpp.
References CContextTranslator::GetAbsoluteContext(), CContextTranslator::GetContextInChunk(), and kInvalidContext.
Referenced by CContextTranslator::CContextTranslator(), CQuerySplitter::x_ComputeContextOffsets_NonTranslatedQueries(), CQuerySplitter::x_ComputeContextOffsets_TranslatedQueries(), and CSplitQueryTestFixture::x_TestCContextTranslator().
◆ GetStrand() [1/4]
|
inline |
Accessor for the strand currently set.
Definition at line 233 of file blast_setup.hpp.
References IBlastSeqVector::m_Strand.
Referenced by CBlastSeqVectorFromCSeq_data::x_SetMinusStrand(), and CBlastSeqVectorFromCSeq_data::x_SetPlusStrand().
◆ GetStrand() [2/4]
|
virtual |
Return strand for a sequence.
- Parameters
-
i index of the sequence in the sequence container [in]
Implements IBlastQuerySource.
Definition at line 239 of file blast_objmgr_tools.cpp.
References CBlastQueryVector::GetQuerySeqLoc(), CBlastQueryVector::GetScope(), GetStrand(), i, CBlastQuerySourceOM::m_QueryVector, CBlastQuerySourceOM::m_TSeqLocVector, and CRef< C, Locker >::NotEmpty().
◆ GetStrand() [3/4]
|
virtual |
Return strand for a sequence.
- Parameters
-
index of the sequence in the sequence container [in]
Implements IBlastQuerySource.
Definition at line 251 of file bioseq_extract_data_priv.cpp.
References eNa_strand_both, eNa_strand_unknown, and CBlastQuerySourceBioseqSet::m_IsProt.
◆ GetStrand() [4/4]
|
pure virtual |
Return strand for a sequence.
- Parameters
-
index index of the sequence in the sequence container [in]
Implemented in CBlastQuerySourceBioseqSet, and CBlastQuerySourceOM.
Referenced by s_AdjustFirstContext(), SetupQueries_OMF(), and SetupQueryInfo_OMF().
◆ GetStrandData() [1/2]
|
inlinevirtual |
@inheritDoc
Reimplemented from IBlastSeqVector.
Definition at line 502 of file blast_objmgr_tools.cpp.
References buf, CBlastSeqVectorOM::m_SeqVector, and CBlastSeqVectorOM::x_FixStrand().
◆ GetStrandData() [2/2]
|
inlinevirtual |
Retrieve strand data in one chunk.
- Parameters
-
strand strand to retrieve [in] buf buffer in which to return the data, should be allocated by caller with enough capacity to copy the entire sequence data
- Note
- default implementation still gets it one character at a time
Reimplemented in CBlastSeqVectorOM.
Definition at line 208 of file blast_setup.hpp.
References buf, IsForward(), IBlastSeqVector::operator[](), IBlastSeqVector::size(), IBlastSeqVector::x_SetMinusStrand(), IBlastSeqVector::x_SetPlusStrand(), and IBlastSeqVector::x_Size().
Referenced by GetSequenceSingleNucleotideStrand().
◆ GetStrandOption() [1/5]
|
inline |
Returns StrandOption.
Definition at line 93 of file blast_nucl_options.hpp.
◆ GetStrandOption() [2/5]
| objects::ENa_strand CBlastOptions::GetStrandOption | ( | ) | const |
Definition at line 1451 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetStrandOption(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by BOOST_AUTO_TEST_CASE(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), SafeSetupQueries(), SafeSetupQueryInfo(), LinkHspTestFixture::setupCutoffScores(), LinkHspTestFixture::setupLinkHspInputTblastn(), setupQueryInfoForOffsetTranslation(), setupQueryStructures(), CQuerySplitter::x_ComputeQueryContextsForChunks(), CQuerySplitter::x_ComputeQueryIndicesForChunks(), CSequenceDataTester::x_Init(), and CSplitQueryTestFixture::x_PrepareBlastQueryStructures().
◆ GetStrandOption() [3/5]
|
inline |
Returns StrandOption.
Definition at line 64 of file blastx_options.hpp.
◆ GetStrandOption() [4/5]
|
inline |
Returns StrandOption.
Definition at line 66 of file tblastx_options.hpp.
◆ GetStrandOption() [5/5]
|
inline |
Definition at line 1001 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_QueryOpts, and QuerySetUpOptions::strand_option.
Referenced by CBlastOptions::GetStrandOption().
◆ GetString()
|
static |
Reference for requested publication.
Definition at line 112 of file version.cpp.
References int, and kReferences.
Referenced by BlastXML_FormatReport(), BOOST_AUTO_TEST_CASE(), CReference::GetHTMLFreeString(), s_DoTestReference(), and s_FillBlastOutput().
◆ GetSubject() [1/2]
| CRef< objects::CBlast4_subject > CImportStrategy::GetSubject | ( | ) |
Returns the target sequences.
This is then a choice of a database (for searches over a blast database) or as a list of Bioseqs (for bl2seq type searches).
Definition at line 223 of file search_strategy.cpp.
References CImportStrategy::m_Request, and CBlast4_queue_search_request_Base::SetSubject().
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetSubject() [2/2]
Retrieve the subject sequence.
Definition at line 258 of file bl2seq.hpp.
References CBl2Seq::m_tSubjects.
◆ GetSubjectBestHit() [1/2]
| bool CBlastOptions::GetSubjectBestHit | ( | ) | const |
Definition at line 1848 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetSubjectBestHit(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
◆ GetSubjectBestHit() [2/2]
|
inline |
Definition at line 1420 of file blast_options_local_priv.hpp.
References BlastHitSavingOptions::hsp_filt_opt, CBlastOptionsLocal::m_HitSaveOpts, NULL, and BlastHSPFilteringOptions::subject_besthit_opts.
Referenced by CBlastOptions::GetSubjectBestHit().
◆ GetSubjectEncoding()
| EBlastEncoding GetSubjectEncoding | ( | EBlastProgramType | program | ) |
Returns the encoding for the sequence data used in BLAST2Sequences for the subject.
- Parameters
-
program program type [in]
- Exceptions
-
CBlastException in case of unsupported program
Definition at line 1124 of file blast_setup_cxx.cpp.
References abort(), eBlastEncodingError, eBlastEncodingNcbi4na, eBlastEncodingNucleotide, eBlastEncodingProtein, eBlastTypeBlastn, eBlastTypeBlastp, eBlastTypeBlastx, eBlastTypeMapping, eBlastTypePhiBlastp, eBlastTypePsiBlast, eBlastTypePsiTblastn, eBlastTypeTblastn, and eBlastTypeTblastx.
Referenced by SetupSubjects_OMF().
◆ GetSubjectMaskingType() [1/3]
| ESubjectMaskingType CBlastOptionsBuilder::GetSubjectMaskingType | ( | ) |
Definition at line 762 of file blast_options_builder.cpp.
References CBlastOptionsBuilder::SOptional< T >::Get(), and CBlastOptionsBuilder::m_SubjectMaskingType.
Referenced by s_ImportDatabase().
◆ GetSubjectMaskingType() [2/3]
| ESubjectMaskingType CImportStrategy::GetSubjectMaskingType | ( | ) |
Get Subject Masking Type.
Definition at line 200 of file search_strategy.cpp.
References CImportStrategy::FetchData(), and CImportStrategy::m_Data.
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetSubjectMaskingType() [3/3]
| ESubjectMaskingType CRemoteBlast::GetSubjectMaskingType | ( | ) | const |
Definition at line 1508 of file remote_blast.cpp.
References CRemoteBlast::m_SubjectMaskingType.
◆ GetSubjectMasks()
| void CSearchResults::GetSubjectMasks | ( | TSeqLocInfoVector & | subj_masks | ) | const |
Retrieve the masked locations for the subject sequences in the contained alignment.
- Parameters
-
subj_masks masked locations [out]
Definition at line 335 of file blast_results.cpp.
References CSearchResults::m_SubjectMasks.
◆ GetSubjects()
|
inline |
Retrieve a vector of subject sequences.
Definition at line 272 of file bl2seq.hpp.
References CBl2Seq::m_tSubjects.
Referenced by BOOST_AUTO_TEST_CASE(), and CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest().
◆ GetSubjectSeqLocs()
| CBlast4_subject::TSeq_loc_list CRemoteBlast::GetSubjectSeqLocs | ( | ) |
Definition at line 1873 of file remote_blast.cpp.
References CRemoteBlast::m_SubjectSeqLocs, CRemoteBlast::x_GetRequestInfo(), and CRemoteBlast::x_HasRetrievedSubjects().
Referenced by s_ConvertSubjects2TSeqLocVector().
◆ GetSubjectSequences()
| list< CRef< objects::CBioseq > > CRemoteBlast::GetSubjectSequences | ( | ) |
Returns subject sequences if "bl2seq" mode used.
- Returns
- a list of bioseqs
Definition at line 1861 of file remote_blast.cpp.
References CRemoteBlast::m_SubjectSequences, CRemoteBlast::x_GetRequestInfo(), and CRemoteBlast::x_HasRetrievedSubjects().
Referenced by s_ConvertSubjects2TSeqLocVector().
◆ GetSumOfSequenceLengths()
| size_t ILocalQueryData::GetSumOfSequenceLengths | ( | ) |
Compute the sum of all the sequence's lengths.
Definition at line 107 of file query_data.cpp.
References ILocalQueryData::GetNumQueries(), ILocalQueryData::GetSeqLength(), i, and ILocalQueryData::m_SumOfSequenceLengths.
Referenced by BOOST_AUTO_TEST_CASE(), CSplitQueryTestFixture::QuerySplitter_BlastnMultiQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastnSingleQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastxMultiQueryMultiChunk(), and CSplitQueryTestFixture::QuerySplitter_BlastxSingleQueryMultiChunk().
◆ GetSumStatisticsMode() [1/2]
| bool CBlastOptions::GetSumStatisticsMode | ( | ) | const |
Sum statistics options.
Definition at line 2036 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetSumStatisticsMode(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CBlastnNode::Main(), CBlastpNode::Main(), CBlastxNode::Main(), CRPSBlastNode::Main(), CRPSTBlastnNode::Main(), CTblastnNode::Main(), CIgBlastnApp::CIgFormatter::Main(), CBlastFormatterApp::PrintFormattedOutput(), CDeltaBlastApp::Run(), CPsiBlastApp::Run(), CTblastxApp::Run(), CIgBlastnApp::Run(), CIgBlastpApp::Run(), CRMBlastnApp::Run(), CBlastnApp::x_RunMTBySplitDB(), CBlastpApp::x_RunMTBySplitDB(), CBlastxApp::x_RunMTBySplitDB(), CRPSBlastApp::x_RunMTBySplitDB(), CRPSTBlastnApp::x_RunMTBySplitDB(), and CTblastnApp::x_RunMTBySplitDB().
◆ GetSumStatisticsMode() [2/2]
|
inline |
Sum statistics options.
Definition at line 1520 of file blast_options_local_priv.hpp.
References BlastHitSavingOptions::do_sum_stats, CBlastOptionsLocal::m_HitSaveOpts, and true.
Referenced by CBlastOptions::GetSumStatisticsMode().
◆ GetTask() [1/2]
| string CImportStrategy::GetTask | ( | ) |
Fetches task, such as "megablast", "blastn", etc.
Definition at line 150 of file search_strategy.cpp.
References CImportStrategy::FetchData(), and CImportStrategy::m_Data.
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetTask() [2/2]
|
inline |
Returns the task used to create the remote search (if any)
Definition at line 456 of file remote_blast.hpp.
References CRemoteBlast::m_Task.
Referenced by CBlastFormatterApp::PrintFormattedOutput().
◆ GetTasks()
Retrieve the set of supported tasks.
Definition at line 212 of file blast_options_handle.cpp.
References CBlastOptionsFactory::eAll, CBlastOptionsFactory::eMapping, CBlastOptionsFactory::eNuclNucl, CBlastOptionsFactory::eProtProt, and set< Key, Compare >::insert().
Referenced by BOOST_AUTO_TEST_CASE(), CBlastnAppArgs::CBlastnAppArgs(), CBlastnVdbAppArgs::CBlastnVdbAppArgs(), CBlastpAppArgs::CBlastpAppArgs(), CRMBlastnAppArgs::CRMBlastnAppArgs(), and ThrowIfInvalidTask().
◆ GetTaxidList() [1/3]
| list< TTaxId > CBlastOptionsBuilder::GetTaxidList | ( | ) |
Get the Tax list.
Definition at line 799 of file blast_options_builder.cpp.
References CBlastOptionsBuilder::SOptional< T >::Get(), and CBlastOptionsBuilder::m_TaxidList.
Referenced by CRemoteBlast::GetSearchOptions(), and s_ImportDatabase().
◆ GetTaxidList() [2/3]
Definition at line 490 of file remote_blast.hpp.
References CRemoteBlast::m_TaxidList.
Referenced by CBlastFormatterApp::PrintFormattedOutput().
◆ GetTaxidList() [3/3]
Definition at line 277 of file search_strategy.cpp.
References eBlastOpt_TaxidList, set< Key, Compare >::insert(), and CImportStrategy::x_GetProgramOptionIntegerList().
◆ GetTaxIdWithWindowMaskerSupport() [1/2]
| objects::CBlast4_get_windowmasked_taxids_reply::Tdata CBlastServices::GetTaxIdWithWindowMaskerSupport | ( | ) |
Retrieve a list of NCBI taxonomy IDs for which there exists windowmasker masking data to support an alternative organism specific filtering.
Definition at line 656 of file blast_services.cpp.
References client, CBlastServices::m_Verbose, CBlastServices::m_WindowMaskedTaxIds, MSerial_AsnText, NCBI_THROW, and NcbiCout.
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetTaxIdWithWindowMaskerSupport() [2/2]
This function returns a list of NCBI taxonomy IDs for which there exists windowmasker masking data to support organism specific filtering.
Definition at line 454 of file winmask_filter.cpp.
References set< Key, Compare >::clear(), set< Key, Compare >::empty(), NStr::fConvErr_NoThrow, fFF_File, FindFiles(), CDirEntry::GetPathSeparator(), set< Key, Compare >::insert(), NON_CONST_ITERATE, s_FindPathToWM(), s_OldGetTaxIdWithWindowMaskerSupport(), s_WINDOW_MASKER_STAT_FILE_NAME(), and NStr::StringToInt().
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetTemplateLength()
|
inline |
Returns TemplateLength.
Definition at line 64 of file disc_nucl_options.hpp.
Referenced by BOOST_AUTO_TEST_CASE(), and BOOST_FIXTURE_TEST_CASE().
◆ GetTemplateType()
|
inline |
Returns TemplateType.
Definition at line 75 of file disc_nucl_options.hpp.
Referenced by BOOST_FIXTURE_TEST_CASE().
◆ GetThresh()
|
inline |
Returns threshold for Jaccard distance (range: 0-1)
Definition at line 64 of file blastp_kmer_options.hpp.
Referenced by CBlastKmerThread::Main(), and CBlastKmerSearch::Run().
◆ GetTitle() [1/4]
Return the title of a sequence.
- Parameters
-
index index of the sequence in the sequence container [in]
Implements IBlastQuerySource.
Definition at line 345 of file bioseq_extract_data_priv.cpp.
References CBioseq_Base::CanGetDescr(), CSeqdesc_Base::e_Molinfo, CSeqdesc_Base::e_Title, NStr::EndsWith(), CSeq_descr_Base::Get(), CBioseq_Base::GetDescr(), ITERATE, kEmptyStr, and CBlastQuerySourceBioseqSet::m_Bioseqs.
◆ GetTitle() [2/4]
Return the title of a sequence.
- Parameters
-
index index of the sequence in the sequence container [in]
Implements IBlastQuerySource.
Definition at line 347 of file blast_objmgr_tools.cpp.
References _ASSERT, CBioseq_Handle::CanGetDescr(), CSeqdesc_Base::e_Title, CScope::GetBioseqHandle(), CBioseq_Handle::GetDescr(), CSeq_loc::GetId(), CBlastQueryVector::GetScope(), CBlastQuerySourceOM::GetSeqLoc(), i, ITERATE, kEmptyStr, CBlastQuerySourceOM::m_QueryVector, CBlastQuerySourceOM::m_TSeqLocVector, CRef< C, Locker >::NotEmpty(), and CConstRef< C, Locker >::NotEmpty().
◆ GetTitle() [3/4]
Return the title of a sequence.
- Parameters
-
index index of the sequence in the sequence container [in]
- Returns
- the sequence title or kEmptyStr if not available
Implemented in CBlastQuerySourceOM, and CBlastQuerySourceBioseqSet.
Referenced by SetupQueries_OMF(), and SetupSubjects_OMF().
◆ GetTitle() [4/4]
| string CRemoteBlast::GetTitle | ( | void | ) |
Get the title assigned for this search.
Definition at line 2377 of file remote_blast.cpp.
References kBlast4SearchInfoReqName_Search, kBlast4SearchInfoReqValue_Title, CRemoteBlast::m_RID, s_BuildSearchInfoRequest(), CRemoteBlast::x_GetStringFromSearchInfoReply(), and CRemoteBlast::x_SendRequest().
◆ GetTotLength()
|
inline |
Returns total length.
Definition at line 103 of file seqsrc_multiseq.cpp.
References CMultiSeqInfo::m_iTotalLength.
◆ GetTSeqLocVector()
| TSeqLocVector CObjMgr_QueryFactory::GetTSeqLocVector | ( | ) |
Retrieves the TSeqLocVector used to construct this object or a conversion of the CBlastQueryVector provided.
Definition at line 400 of file objmgr_query_data.cpp.
References abort(), TMaskedQueryRegions::ConvertToCPacked_seqint(), CBlastQueryVector::GetMaskedRegions(), CBlastQueryVector::GetQuerySeqLoc(), CBlastQueryVector::GetScope(), i, CObjMgr_QueryFactory::m_QueryVector, CObjMgr_QueryFactory::m_SSeqLocVector, CRef< C, Locker >::NotEmpty(), CRef< C, Locker >::Reset(), CSeq_loc::SetPacked_int(), and CBlastQueryVector::Size().
Referenced by CLocalDbAdapter::CLocalDbAdapter(), and CBlastKmerSearch::Run().
◆ GetUngappedKarlinBlk()
|
inline |
Retrieve ungapped Karlin parameters.
Definition at line 97 of file blast_results.hpp.
Referenced by s_BuildArchiveAll().
◆ GetUnifiedP() [1/2]
| int CBlastOptions::GetUnifiedP | ( | ) | const |
Definition at line 1685 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetUnifiedP(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetUnifiedP() [2/2]
|
inline |
Definition at line 1220 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_ExtnOpts, and BlastExtensionOptions::unifiedP.
Referenced by CBlastOptions::GetUnifiedP().
◆ GetUseIndex() [1/2]
| bool CBlastOptions::GetUseIndex | ( | ) | const |
Definition at line 2574 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetUseIndex(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by BlastSetupPreliminarySearchEx(), CSetupFactory::InitializeMegablastDbIndex(), CBlastnNode::Main(), CRMBlastnApp::Run(), and CBlastnApp::x_RunMTBySplitDB().
◆ GetUseIndex() [2/2]
|
inline |
Definition at line 1829 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_UseMBIndex.
Referenced by CBlastOptions::GetUseIndex().
◆ GetWarnings()
| string CRemoteBlast::GetWarnings | ( | void | ) |
This returns any warnings encountered.
These do not necessarily indicate an error or even a potential error; some warnings are always returned from certain types of searches. (This is a debugging feature and warnings should probably not be returned to the end-user).
- Returns
- Empty string or newline seperated list of warnings.
Definition at line 1224 of file remote_blast.cpp.
References i, CRemoteBlast::m_Warn, and string.
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetWarningStrings()
| string CSearchResults::GetWarningStrings | ( | ) | const |
Retrieve a string with the query identifier followed by the warnings produced, returns a empty string if HasWarnings() returns false.
Definition at line 277 of file blast_results.cpp.
References eBlastSevWarning, TQueryMessages::GetQueryId(), ITERATE, CSearchResults::m_Errors, and string.
Referenced by CBlastAligner::GenerateAlignments().
◆ GetWarningVector()
This returns any warnings encountered as a vector of strings.
- See also
- CRemoteBlast::GetWarnings
- Returns
- Reference to a vector of warnings.
Definition at line 1240 of file remote_blast.cpp.
References CRemoteBlast::m_Warn.
Referenced by CRemoteBlast::GetResultSet(), CRemoteSeqSearch::Run(), CRemotePssmSearch::Run(), and s_BuildResultsRemote().
◆ GetWebFormatOptions()
| objects::CBlast4_parameters * CImportStrategy::GetWebFormatOptions | ( | ) |
Options for controlling formatting (psi blast iteration number also).
- Returns
- the web formatting options or NULL if unavailable
Definition at line 253 of file search_strategy.cpp.
References CBlast4_queue_search_request_Base::CanGetFormat_options(), CImportStrategy::m_Request, NULL, and CBlast4_queue_search_request_Base::SetFormat_options().
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetWeightedResidueFrequencies()
|
static |
Returns matrix of BLASTAA_SIZE by query size (dimensions are opposite of what is stored in the BlastScoreBlk) containing the weighted residue frequencies per position of the PSSM.
- Parameters
-
pssm PSSM to extract data from [in]
- Returns
- NULL if weighted residue frequencies are not available
Definition at line 311 of file psiblast_aux_priv.cpp.
References _ASSERT, BLASTAA_SIZE, Convert2Matrix(), ctll::empty(), CPssm_Base::GetByRow(), CPssm_Base::GetIntermediateData(), CPssm_Base::GetNumColumns(), CPssm_Base::GetNumRows(), CPssmIntermediateData_Base::GetWeightedResFreqsPerPos(), NULL, and ncbi::grid::netcache::search::fields::size.
◆ GetWindowMaskerDatabase() [1/3]
|
inline |
Get the window masker database name (or NULL if not set).
Definition at line 146 of file blast_nucl_options.hpp.
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetWindowMaskerDatabase() [2/3]
| const char * CBlastOptions::GetWindowMaskerDatabase | ( | ) | const |
Return the name of the windowmasker database to use.
Definition at line 1367 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetWindowMaskerDatabase(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by Blast_FindWindowMaskerLoc_Fwd(), and CBlastQuerySourceOM::x_CalculateMasks().
◆ GetWindowMaskerDatabase() [3/3]
|
inline |
Definition at line 981 of file blast_options_local_priv.hpp.
References SWindowMaskerOptions::database, QuerySetUpOptions::filtering_options, CBlastOptionsLocal::m_QueryOpts, NULL, and SBlastFilterOptions::windowMaskerOptions.
Referenced by CBlastOptions::GetWindowMaskerDatabase().
◆ GetWindowMaskerTaxId() [1/3]
|
inline |
Get the window masker taxid (or 0 if not set).
Definition at line 139 of file blast_nucl_options.hpp.
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetWindowMaskerTaxId() [2/3]
| int CBlastOptions::GetWindowMaskerTaxId | ( | ) | const |
Returns the tax id used for the windowmasker database to use, if set via SetWindowMaskerTaxId (otherwise, returns 0)
Definition at line 1343 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetWindowMaskerTaxId(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by Blast_FindWindowMaskerLoc_Fwd(), and CBlastQuerySourceOM::x_CalculateMasks().
◆ GetWindowMaskerTaxId() [3/3]
|
inline |
Definition at line 962 of file blast_options_local_priv.hpp.
References QuerySetUpOptions::filtering_options, CBlastOptionsLocal::m_QueryOpts, NULL, SWindowMaskerOptions::taxid, and SBlastFilterOptions::windowMaskerOptions.
Referenced by CBlastOptions::GetWindowMaskerTaxId().
◆ GetWindowSize() [1/3]
| int CBlastOptions::GetWindowSize | ( | ) | const |
Definition at line 1491 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetWindowSize(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by CBlastOptionsHandle::GetWindowSize().
◆ GetWindowSize() [2/3]
|
inline |
Returns WindowSize.
Definition at line 181 of file blast_options_handle.hpp.
References CBlastOptions::GetWindowSize(), and CBlastOptionsHandle::m_Opts.
Referenced by BOOST_AUTO_TEST_CASE(), and BOOST_FIXTURE_TEST_CASE().
◆ GetWindowSize() [3/3]
|
inline |
Definition at line 1093 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_InitWordOpts, and BlastInitialWordOptions::window_size.
Referenced by CBlastOptions::GetWindowSize().
◆ GetWordSize() [1/6]
|
inline |
Returns WordSize.
Definition at line 83 of file blast_nucl_options.hpp.
Referenced by BOOST_AUTO_TEST_CASE(), and BOOST_FIXTURE_TEST_CASE().
◆ GetWordSize() [2/6]
| int CBlastOptions::GetWordSize | ( | ) | const |
Definition at line 914 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetWordSize(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by BOOST_AUTO_TEST_CASE(), CSetupFactory::InitializeMegablastDbIndex(), CBlastnApp::Run(), CBlastpApp::Run(), CBlastxApp::Run(), CTblastnApp::Run(), and CIgBlast::x_SetupVSearch().
◆ GetWordSize() [3/6]
|
inline |
Returns WordSize.
Definition at line 72 of file blast_prot_options.hpp.
Referenced by BOOST_AUTO_TEST_CASE(), and BOOST_FIXTURE_TEST_CASE().
◆ GetWordSize() [4/6]
|
inline |
Returns WordSize.
Definition at line 67 of file blast_rps_options.hpp.
◆ GetWordSize() [5/6]
|
inline |
Return word size.
Definition at line 135 of file magicblast_options.hpp.
◆ GetWordSize() [6/6]
|
inline |
Definition at line 606 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_LutOpts, and LookupTableOptions::word_size.
Referenced by CBlastOptions::GetWordSize().
◆ GetWordThreshold() [1/4]
| double CBlastOptions::GetWordThreshold | ( | ) | const |
Returns WordThreshold.
Definition at line 875 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetWordThreshold(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
Referenced by BOOST_AUTO_TEST_CASE(), and CWordThresholdArg::ExtractAlgorithmOptions().
◆ GetWordThreshold() [2/4]
|
inline |
Returns WordThreshold.
Definition at line 66 of file blast_prot_options.hpp.
Referenced by BOOST_FIXTURE_TEST_CASE().
◆ GetWordThreshold() [3/4]
|
inline |
Returns WordThreshold.
Definition at line 65 of file blast_rps_options.hpp.
◆ GetWordThreshold() [4/4]
|
inline |
Definition at line 579 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_LutOpts, and LookupTableOptions::threshold.
Referenced by CBlastOptions::GetWordThreshold().
◆ GetXDropoff() [1/5]
|
inline |
Returns XDropoff.
Definition at line 161 of file blast_nucl_options.hpp.
Referenced by BOOST_FIXTURE_TEST_CASE().
◆ GetXDropoff() [2/5]
| double CBlastOptions::GetXDropoff | ( | ) | const |
Definition at line 1529 of file blast_options_cxx.cpp.
References CBlastOptionsLocal::GetXDropoff(), CBlastOptions::m_Local, and CBlastOptions::x_Throwx().
◆ GetXDropoff() [3/5]
|
inline |
Returns XDropoff.
Definition at line 79 of file blast_prot_options.hpp.
Referenced by BOOST_FIXTURE_TEST_CASE().
◆ GetXDropoff() [4/5]
|
inline |
Returns XDropoff.
Definition at line 72 of file blast_rps_options.hpp.
◆ GetXDropoff() [5/5]
|
inline |
Definition at line 1117 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_InitWordOpts, and BlastInitialWordOptions::x_dropoff.
Referenced by CBlastOptions::GetXDropoff().
◆ HasAlignments()
| bool CSearchResults::HasAlignments | ( | ) | const |
Return true if there are any alignments for this query.
Definition at line 318 of file blast_results.cpp.
References CRef< C, Locker >::Empty(), and CSearchResults::m_Alignment.
Referenced by BOOST_AUTO_TEST_CASE(), CBlastFormat::PrintPhiResult(), CSearchResults::TrimSeqAlign(), CIgBlast::x_FindDJ(), CIgBlast::x_ProcessCResult(), CIgBlast::x_ProcessDGeneResult(), and CPsiBlastApp::x_RunLocalPsiBlastIterations().
◆ HasConverged()
| bool CPsiBlastIterationState::HasConverged | ( | ) |
Determines if the PSI-BLAST search has converged (i.e.
: no more new sequences have been found since the last iteration)
- Returns
- true if search has converged, otherwise false.
Definition at line 68 of file psiblast_iteration.cpp.
References set< Key, Compare >::empty(), set< Key, Compare >::end(), set< Key, Compare >::find(), ITERATE, CPsiBlastIterationState::m_CurrentData, CPsiBlastIterationState::m_IterationsDone, and CPsiBlastIterationState::m_PreviousData.
Referenced by BOOST_AUTO_TEST_CASE(), CDeltaBlastApp::DoPsiBlastIterations(), and CPsiBlastApp::x_RunLocalPsiBlastIterations().
◆ HasDbFilteringAlgorithmId()
| bool CBlastOptionsBuilder::HasDbFilteringAlgorithmId | ( | ) |
Check whether a database filtering algorithm ID is specified.
Definition at line 737 of file blast_options_builder.cpp.
References CBlastOptionsBuilder::SOptional< T >::Have(), and CBlastOptionsBuilder::m_DbFilteringAlgorithmId.
Referenced by CRemoteBlast::GetSearchOptions(), and s_ImportDatabase().
◆ HasDbFilteringAlgorithmKey()
| bool CBlastOptionsBuilder::HasDbFilteringAlgorithmKey | ( | ) |
Check whether a database filtering algorithm key is specified.
Definition at line 747 of file blast_options_builder.cpp.
References CBlastOptionsBuilder::SOptional< T >::Have(), and CBlastOptionsBuilder::m_DbFilteringAlgorithmKey.
Referenced by CRemoteBlast::GetSearchOptions(), and s_ImportDatabase().
◆ HasErrors()
| bool CSearchResults::HasErrors | ( | ) | const |
Returns true if there are errors among the results for this object.
Definition at line 296 of file blast_results.cpp.
References eBlastSevError, ITERATE, and CSearchResults::m_Errors.
Referenced by CBlastAligner::GenerateAlignments(), and CRemoteBlastAligner::GenerateAlignments().
◆ HasGiList() [1/4]
|
virtual |
Returns true if the subject is restricted by a GI list.
Implements IBlastSeqInfoSrc.
Definition at line 87 of file seqinfosrc_seqdb.cpp.
References CSeqDB::GetGiList(), and CSeqDbSeqInfoSrc::m_iSeqDb.
◆ HasGiList() [2/4]
|
virtual |
Is the subject restricted by a GI list? (Always returns false).
Implements IBlastSeqInfoSrc.
Definition at line 104 of file seqinfosrc_seqvec.cpp.
◆ HasGiList() [3/4]
|
virtual |
Is the subject restricted by a GI list? (Always returns false).
Implements IBlastSeqInfoSrc.
Definition at line 89 of file seqinfosrc_bioseq.cpp.
◆ HasGiList() [4/4]
|
pure virtual |
Returns true if the subject is restricted by a GI list.
Implemented in CBioseqSeqInfoSrc, CSeqVecSeqInfoSrc, and CSeqDbSeqInfoSrc.
Referenced by GetFilteredRedundantGis(), and GetFilteredRedundantSeqids().
◆ HasMessages()
| bool TSearchMessages::HasMessages | ( | ) | const |
- Returns
- true if messages exist.
Definition at line 1002 of file blast_aux.cpp.
References ITERATE.
Referenced by BOOST_AUTO_TEST_CASE(), CEffectiveSearchSpaceCalculator::CEffectiveSearchSpaceCalculator(), CSetupFactory::CreateLookupTable(), CSetupFactory::CreateScoreBlock(), SetupQueries_OMF(), and CSplitQueryTestFixture::x_PrepareBlastQueryStructures().
◆ HasMoreIterations()
| bool CPsiBlastIterationState::HasMoreIterations | ( | ) | const |
Determines if more iterations are still needed.
- Returns
- true if there are more iterations to do, otherwise false.
Definition at line 58 of file psiblast_iteration.cpp.
References CPsiBlastIterationState::m_IterationsDone, and CPsiBlastIterationState::m_TotalNumIterationsToDo.
Referenced by BOOST_AUTO_TEST_CASE().
◆ HasSubjectMaskingType()
| bool CBlastOptionsBuilder::HasSubjectMaskingType | ( | ) |
Get Subject Maksing Type (soft/hard)
Definition at line 757 of file blast_options_builder.cpp.
References CBlastOptionsBuilder::SOptional< T >::Have(), and CBlastOptionsBuilder::m_SubjectMaskingType.
Referenced by s_ImportDatabase().
◆ HasWarnings()
| bool CSearchResults::HasWarnings | ( | ) | const |
Returns true if there are warnings among the results for this object.
Definition at line 307 of file blast_results.cpp.
References eBlastSevWarning, ITERATE, and CSearchResults::m_Errors.
Referenced by CBlastAligner::GenerateAlignments(), and CRemoteBlastAligner::GenerateAlignments().
◆ Have()
|
inline |
Check whether the value has been set.
Definition at line 219 of file blast_options_builder.hpp.
Referenced by CBlastOptionsBuilder::GetSearchOptions(), CBlastOptionsBuilder::HasDbFilteringAlgorithmId(), CBlastOptionsBuilder::HasDbFilteringAlgorithmKey(), CBlastOptionsBuilder::HasSubjectMaskingType(), CBlastOptionsBuilder::HaveEntrezQuery(), CBlastOptionsBuilder::HaveFinalDbSeq(), CBlastOptionsBuilder::HaveFirstDbSeq(), CBlastOptionsBuilder::HaveNegativeTaxidList(), CBlastOptionsBuilder::HaveQueryMasks(), CBlastOptionsBuilder::HaveTaxidList(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ HaveEntrezQuery()
| bool CBlastOptionsBuilder::HaveEntrezQuery | ( | ) |
Check whether an Entrez query is specified.
Definition at line 697 of file blast_options_builder.cpp.
References CBlastOptionsBuilder::SOptional< T >::Have(), and CBlastOptionsBuilder::m_EntrezQuery.
Referenced by CRemoteBlast::GetSearchOptions(), and s_ImportDatabase().
◆ HaveFinalDbSeq()
| bool CBlastOptionsBuilder::HaveFinalDbSeq | ( | ) |
Check whether an OID range end point is specified.
Definition at line 717 of file blast_options_builder.cpp.
References CBlastOptionsBuilder::SOptional< T >::Have(), and CBlastOptionsBuilder::m_FinalDbSeq.
Referenced by CRemoteBlast::GetSearchOptions().
◆ HaveFirstDbSeq()
| bool CBlastOptionsBuilder::HaveFirstDbSeq | ( | ) |
Check whether an OID range start point is specified.
Definition at line 707 of file blast_options_builder.cpp.
References CBlastOptionsBuilder::SOptional< T >::Have(), and CBlastOptionsBuilder::m_FirstDbSeq.
Referenced by CRemoteBlast::GetSearchOptions().
◆ HaveGiList()
| bool CBlastOptionsBuilder::HaveGiList | ( | ) |
Check whether a GI list is specified.
Definition at line 727 of file blast_options_builder.cpp.
References CBlastOptionsBuilder::m_GiList.
Referenced by CRemoteBlast::GetSearchOptions(), and s_ImportDatabase().
◆ HaveNegativeGiList()
| bool CBlastOptionsBuilder::HaveNegativeGiList | ( | ) |
Check whether a negative GI list is specified.
Definition at line 768 of file blast_options_builder.cpp.
References CBlastOptionsBuilder::m_NegativeGiList.
Referenced by CRemoteBlast::GetSearchOptions(), and s_ImportDatabase().
◆ HaveNegativeTaxidList()
| bool CBlastOptionsBuilder::HaveNegativeTaxidList | ( | ) |
Check whether a negative tax id list is specified.
Definition at line 804 of file blast_options_builder.cpp.
References CBlastOptionsBuilder::SOptional< T >::Have(), and CBlastOptionsBuilder::m_NegativeTaxidList.
Referenced by CRemoteBlast::GetSearchOptions(), and s_ImportDatabase().
◆ HaveQueryMasks()
| bool CBlastOptionsBuilder::HaveQueryMasks | ( | ) |
Check whether query masks are specified.
Definition at line 778 of file blast_options_builder.cpp.
References CBlastOptionsBuilder::SOptional< T >::Have(), and CBlastOptionsBuilder::m_QueryMasks.
◆ HaveTaxidList()
| bool CBlastOptionsBuilder::HaveTaxidList | ( | ) |
Definition at line 794 of file blast_options_builder.cpp.
References CBlastOptionsBuilder::SOptional< T >::Have(), and CBlastOptionsBuilder::m_TaxidList.
Referenced by CRemoteBlast::GetSearchOptions(), and s_ImportDatabase().
◆ ILocalQueryData()
|
inline |
Default constructor.
Definition at line 58 of file query_data.hpp.
◆ IndexedDbRunSearch()
|
static |
Run indexed search.
- Parameters
-
queries query data lut_options lookup table parameters word_options word parameters
Definition at line 577 of file blast_dbindex.cpp.
References CIndexedDb::DoPreSearch(), and CIndexedDb::Index_Set_Instance.
Referenced by SetUpDbIndexCallbacks().
◆ IndexedDbSetNumThreads()
|
static |
Set the number of concurrent search threads in the index structure.
- Parameters
-
n_threads number of concurrent search threads.
Definition at line 604 of file blast_dbindex.cpp.
References ASSERT, CIndexedDb::Index_Set_Instance, and CIndexedDb_New::SetNumThreads().
Referenced by SetUpDbIndexCallbacks().
◆ IndexedDbSetQueryInfo()
|
static |
Set information about unmasked query segments.
- Parameters
-
lt_wrap lookup table information to update locs_wrap set of unmasked query segments
Definition at line 618 of file blast_dbindex.cpp.
References LookupTableWrap::check_index_oid, LookupTableWrap::end_search_indication, CIndexedDb::Index_Set_Instance, LookupTableWrap::read_indexed_db, s_MB_IdbCheckOid(), s_MB_IdbGetResults(), s_MB_IdxEndSearchIndication(), and CIndexedDb::SetQueryInfo().
Referenced by SetUpDbIndexCallbacks().
◆ IndexedDbSetUsingThreads()
Set state of concurrency in the index structure.
- Parameters
-
multiple_threads 'true' if multiple search threads are used; 'false' otherwise
Definition at line 591 of file blast_dbindex.cpp.
References ASSERT, CIndexedDb::Index_Set_Instance, and CIndexedDb_New::SetMultipleThreads().
Referenced by SetUpDbIndexCallbacks().
◆ InitializeMegablastDbIndex()
|
static |
Initialize a megablast BLAST database index.
- Parameters
-
options BLAST options (will be modified to record the fact that the database index has been initialized [in|out]
Definition at line 429 of file setup_factory.cpp.
References _ASSERT, DbIndexInit(), eBlastTypeBlastn, eBlastTypeMapping, eIndexedMBLookupTable, eMixedMBLookupTable, ERR_POST_EX, CBlastOptions::GetIndexName(), CBlastOptions::GetIsOldStyleMBIndex(), CBlastOptions::GetMBIndexLoaded(), CBlastOptions::GetMBTemplateLength(), CBlastOptions::GetProgramType(), CBlastOptions::GetUseIndex(), CBlastOptions::GetWordSize(), CBlastOptions::SetLookupTableType(), CBlastOptions::SetMBIndexLoaded(), CBlastOptions::SetUseIndex(), and Warning().
Referenced by BlastSetupPreliminarySearchEx(), CBlastnNode::Main(), CRMBlastnApp::Run(), and CBlastnApp::x_RunMTBySplitDB().
◆ IntersectWith() [1/2]
Intersect hit with another hit and store result.
- Parameters
-
hit Hit [in] app Specifies whether intersection is to be perfromed on query or subject ranges [in]
Definition at line 598 of file cdd_pssm_input.cpp.
References CCddInputData::CHit::GetSegments(), ITERATE, and ct::sort().
◆ IntersectWith() [2/2]
Intersect hit segments with list of ranges and store result in hit segments.
- Parameters
-
segments List of ranges [in] app Specifies whether input ranges are to be intersected with query or subject ranges [in]
Definition at line 509 of file cdd_pssm_input.cpp.
References _ASSERT, CCddInputData::CHitSegment::AdjustRanges(), COpenRange< Position >::Empty(), CRange_Base::GetFrom(), CRange_Base::GetTo(), COpenRange< Position >::IntersectionWith(), CCddInputData::CHitSegment::IsEmpty(), ITERATE, max(), min(), NULL, and ct::sort().
Referenced by CCddInputData::x_RemoveMultipleCdHits().
◆ IsAtLeastOneQueryValid()
| bool ILocalQueryData::IsAtLeastOneQueryValid | ( | ) |
Determine if at least one query sequence is valid or not.
Definition at line 121 of file query_data.cpp.
References ILocalQueryData::GetNumQueries(), i, and ILocalQueryData::IsValidQuery().
◆ IsBlastDb()
|
inline |
Returns true if this object represents a BLAST database.
Definition at line 124 of file local_db_adapter.hpp.
References kEmptyStr, and CLocalDbAdapter::m_DbName.
Referenced by PrintSAMHeader(), CDeltaBlast::Run(), CLocalBlast::Run(), s_MakeEmptyResults(), CIgBlast::x_AnnotateDomain(), CMagicBlastApp::x_LogBlastSearchInfo(), and CMagicBlast::x_Run().
◆ IsConcordant()
|
inline |
Are an aligned pair concordant?
Definition at line 183 of file magicblast.hpp.
References CMagicBlastResults::m_Concordant.
◆ IsDbScanMode()
|
inline |
Returns true if this is not a database but is database scanning mode.
Definition at line 127 of file local_db_adapter.hpp.
References CLocalDbAdapter::m_DbScanMode.
Referenced by BOOST_AUTO_TEST_CASE(), CLocalBlast::Run(), s_MakeEmptyResults(), and CMagicBlast::x_Run().
◆ IsDbSearch()
| bool CRemoteBlast::IsDbSearch | ( | ) |
Return values states whether GetDatabases or GetSubjectSequences call should be used.
- Returns
- true indicates that GetDatabases should be used.
Definition at line 1849 of file remote_blast.cpp.
References CRef< C, Locker >::Empty(), CRemoteBlast::m_Dbs, CRemoteBlast::m_SubjectSeqLocs, CRemoteBlast::m_SubjectSequences, and CRemoteBlast::x_GetRequestInfo().
Referenced by CBlastFormatterApp::PrintFormattedOutput().
◆ IsDiskCacheActive()
|
inline |
Definition at line 474 of file remote_blast.hpp.
References CRemoteBlast::m_use_disk_cache.
◆ IsDiskCacheError()
|
inline |
disk cache error handling
Definition at line 477 of file remote_blast.hpp.
References CRemoteBlast::m_disk_cache_error_flag.
◆ IsEmpty() [1/2]
| bool CCddInputData::CHitSegment::IsEmpty | ( | void | ) | const |
Does the hit segment represent an empty range.
- Returns
- True if hit segment empty, false otherwise
Definition at line 798 of file cdd_pssm_input.cpp.
Referenced by CCddInputData::CHit::IntersectWith().
◆ IsEmpty() [2/2]
| bool CCddInputData::CHit::IsEmpty | ( | void | ) | const |
Is hit empty.
- Returns
- True if the hit is empty, false otherwise
The hit is considered non-empty if it contains at least one non-empty range
Definition at line 493 of file cdd_pssm_input.cpp.
References ITERATE.
Referenced by CCddInputData::CHit::Subtract().
◆ IsErrMsgArchive()
| bool CRemoteBlast::IsErrMsgArchive | ( | void | ) |
Definition at line 2683 of file remote_blast.cpp.
References CRemoteBlast::m_Archive, and NULL.
Referenced by CRemoteBlast::LoadFromArchive(), and CBlastFormatterApp::Run().
◆ IsFirstOfAPair() [1/3]
Is this sequence followed by a mate (for mapping short reads)
Implements IBlastQuerySource.
Definition at line 375 of file bioseq_extract_data_priv.cpp.
References eFirstSegment, and CBlastQuerySourceBioseqSet::GetSegmentInfo().
◆ IsFirstOfAPair() [2/3]
Is this sequence followed by a mate (for mapping short reads)
Implements IBlastQuerySource.
Definition at line 154 of file blast_objmgr_priv.hpp.
References NCBI_THROW.
◆ IsFirstOfAPair() [3/3]
Is this sequence followed by a mate (for mapping short reads)
Implemented in CBlastQuerySourceOM, and CBlastQuerySourceBioseqSet.
◆ IsIterativeSearch()
| bool CBlastOptions::IsIterativeSearch | ( | ) | const |
Definition at line 862 of file blast_options_cxx.cpp.
References eDeltaBlast, ePSIBlast, ePSITblastn, and CBlastOptions::GetProgram().
Referenced by CCmdLineBlastXML2ReportData::x_InitCommon().
◆ IsLocalId()
Returns true if the CSeq_id is a local id.
- Parameters
-
seqid Sequence identifier to examine [in]
- Returns
- if seqid is NULL or if it is NOT a local id, it returns false
Definition at line 1094 of file blast_aux.cpp.
References CSeq_id::eAcc_general, and CSeq_id::eAcc_local.
Referenced by BOOST_AUTO_TEST_CASE(), s_HasLocalIDs(), CRemoteBlast::x_InitQueries(), and CExportStrategy::x_Process_Query().
◆ IsMultiThreaded()
|
inline |
Returns true if more than 1 thread is specified.
Definition at line 380 of file setup_factory.hpp.
References CThreadable::kMinNumThreads, and CThreadable::m_NumThreads.
Referenced by BOOST_AUTO_TEST_CASE(), CBlastPrelimSearch::Run(), and CBlastPrelimSearch::SetNumberOfThreads().
◆ IsPaired()
|
inline |
Are alignments computed for paired reads.
Definition at line 180 of file magicblast.hpp.
References CMagicBlastResults::m_Paired.
◆ IsProtein() [1/2]
| bool CLocalDbAdapter::IsProtein | ( | ) | const |
Returns true if this object represents protein or nucleotide sequences.
Definition at line 178 of file local_db_adapter.cpp.
References abort(), Blast_SubjectIsProtein(), BlastSeqSrcGetIsProt(), CBlastOptionsHandle::GetOptions(), CBlastOptions::GetProgramType(), CSearchDatabase::IsProtein(), CLocalDbAdapter::m_DbInfo, CLocalDbAdapter::m_OptsHandle, CLocalDbAdapter::m_SeqSrc, and true.
◆ IsProtein() [2/2]
|
inline |
Determine whether this database contains protein sequences or not.
Definition at line 144 of file uniform_search.hpp.
References CSearchDatabase::eBlastDbIsProtein, and CSearchDatabase::GetMoleculeType().
Referenced by CLocalDbAdapter::IsProtein(), s_InitializeSubject(), CBlastDatabaseArgs::SetSearchDatabase(), CSearchDatabase::x_InitializeDb(), and CSearchDatabase::x_ValidateMaskingAlgorithm().
◆ IsQuerySplit()
|
inline |
Determines whether the query sequence(s) are split or not.
Definition at line 88 of file split_query.hpp.
References CQuerySplitter::GetNumberOfChunks().
Referenced by BOOST_AUTO_TEST_CASE(), and CBlastPrelimSearch::Run().
◆ IsValidBlastDb()
Returns true if the BLAST database specified exists in the NCBI servers.
- Parameters
-
dbname BLAST database name [in] is_protein is this a protein database? [in]
Definition at line 355 of file blast_services.cpp.
References dbname(), CBlastServices::GetDatabaseInfo(), and result.
Referenced by BOOST_AUTO_TEST_CASE(), and CRemoteBlastDbAdapter::CRemoteBlastDbAdapter().
◆ IsValidQuery()
| bool ILocalQueryData::IsValidQuery | ( | size_t | index | ) |
Determine if a given query sequence is valid or not.
Definition at line 85 of file query_data.cpp.
References _ASSERT, BlastQueryInfo::contexts, BlastQueryInfo::first_context, ILocalQueryData::GetQueryInfo(), i, BlastContextInfo::is_valid, BlastContextInfo::query_index, and ILocalQueryData::x_ValidateIndex().
Referenced by ILocalQueryData::IsAtLeastOneQueryValid().
◆ kGapChar()
The representation of a gap in ASCII format.
Referenced by CGapAnalysis::x_AddGapsFromBases(), CPsiBlastInputClustalW::x_CopyQueryToMsa(), CPsiBlastInputClustalW::x_ExtractAlignmentData(), CPsiBlastInputClustalW::x_ExtractQueryFromMsa(), CCddInputData::x_ValidateMsa(), and CPsiBlastInputClustalW::x_ValidateQueryInMsa().
◆ kNoArchiveFile()
Referenced by CRemoteBlast::x_GetRequestInfoFromFile().
◆ kNoRIDSpecified()
Referenced by CRemoteBlast::GetResultSet(), and CRemoteBlast::x_GetRequestInfoFromRID().
◆ LastAligned()
|
inline |
Is the mate aligned.
Definition at line 204 of file magicblast.hpp.
References CMagicBlastResults::fUnaligned, and CMagicBlastResults::m_LastInfo.
◆ ListFrames()
| const set< CBlastQueryFilteredFrames::ETranslationFrame > & CBlastQueryFilteredFrames::ListFrames | ( | ) |
Returns the list of frame values for which this object contains masking information.
Definition at line 1637 of file blast_setup_cxx.cpp.
References set< Key, Compare >::empty(), set< Key, Compare >::insert(), ITERATE, CBlastQueryFilteredFrames::m_Frames, and CBlastQueryFilteredFrames::m_Seqlocs.
Referenced by BOOST_AUTO_TEST_CASE(), CBlastQueryFilteredFrames::Empty(), and s_RestrictSeqLocs_Multiframe().
◆ LoadFromArchive()
| bool CRemoteBlast::LoadFromArchive | ( | ) |
Loads next chunk of archive from file.
Definition at line 1658 of file remote_blast.cpp.
References Critical(), eDiag_Critical, eDiag_Error, eDiag_Fatal, eDiag_Info, eDiag_Trace, eDiag_Warning, Error(), Fatal(), Info(), CRemoteBlast::IsErrMsgArchive(), ITERATE, LOG_POST, CRemoteBlast::m_Archive, CRemoteBlast::m_Errs, CRemoteBlast::m_ObjectStream, msg(), CRef< C, Locker >::Reset(), Trace(), Warning(), and CRemoteBlast::x_GetRequestInfoFromFile().
Referenced by BOOST_AUTO_TEST_CASE(), CBlastFormatterApp::PrintFormattedOutput(), CBlastFormatterVdbApp::PrintFormattedOutput(), CBlastFormatterApp::Run(), and CBlastFormatterVdbApp::Run().
◆ LoadSequencesToScope() [1/2]
| void LoadSequencesToScope | ( | CScope::TIds & | ids, |
| vector< TSeqRange > & | ranges, | ||
| CRef< CScope > & | scope | ||
| ) |
Definition at line 1111 of file blast_aux.cpp.
References _TRACE, CScope::AddBioseq(), CSeqMap::CanResolveRange(), delta(), CSeq_inst_Base::eMol_not_set, CSeq_inst_Base::eRepr_virtual, CSeqMap::fFindAnyLeaf, CScope::GetBioseqHandles(), CBioseq_Handle::GetSeqMap(), CBioseq_Handle::GetTSE_Handle(), i, ITERATE, kInvalidSeqPos, SerialClone(), CSeq_inst_Base::SetExt(), CSeq_interval_Base::SetFrom(), CSeq_interval_Base::SetId(), CBioseq_Base::SetInst(), SSeqMapSelector::SetLinkUsedTSE(), CSeq_inst_Base::SetMol(), CSeq_inst_Base::SetRepr(), and CSeq_interval_Base::SetTo().
◆ LoadSequencesToScope() [2/2]
| void LoadSequencesToScope | ( | objects::CScope::TIds & | ids, |
| vector< TSeqRange > & | ranges, | ||
| CRef< objects::CScope > & | scope | ||
| ) |
This method retrieve sequence data in bulk to scope @ids seq id list [in] @ranges seq range list [in] @scope sconfigured with data loader for retrieving seqs [in] | retrieved bioseqs [out].
Referenced by BlastFormatter_PreFetchSequenceData().
◆ LocalBlastResults2SeqAlign()
| TSeqAlignVector LocalBlastResults2SeqAlign | ( | BlastHSPResults * | hsp_results, |
| ILocalQueryData & | local_data, | ||
| const IBlastSeqInfoSrc & | seqinfo_src, | ||
| EBlastProgramType | program, | ||
| bool | gapped, | ||
| bool | oof_mode, | ||
| vector< TSeqLocInfoVector > & | subj_masks, | ||
| EResultType | result_type = eDatabaseSearch |
||
| ) |
Convert traceback output into Seq-align format.
This converts the traceback stage output into a standard Seq-align. The result_type argument indicates whether the seqalign is for a database search or a sequence comparison (eDatabaseSearch or eSequenceComparison). The seqinfo_src argument is used to translate oids into Seq-ids.
- Parameters
-
hsp_results Results of a traceback search. [in] local_data The queries used to perform the search. [in] seqinfo_src Provides sequence identifiers and meta-data. [in] program The type of search done. [in] gapped True if this was a gapped search. [in] oof_mode True if out-of-frame matches are allowed. [in] subj_masks If applicable, it'll be populated with subject masks that intersect the HSPs (each element corresponds to a query) [in|out] result_type Specify how to arrange the results in the return value. [in]
Definition at line 1983 of file blast_seqalign.cpp.
References Blast_ProgramIsPhiBlast(), eSequenceComparison, ILocalQueryData::GetQueryInfo(), BlastQueryInfo::pattern_info, PhiBlastResults2SeqAlign_OMF(), s_BlastResults2SeqAlignDatabaseSearch_OMF(), and s_BlastResults2SeqAlignSequenceCmp_OMF().
Referenced by CBlastTracebackSearch::Run().
◆ LocateIndex()
|
inlineprivate |
Find an index corresponding to the given subject id.
- Parameters
-
oid The subject sequence id.
- Returns
- Index of the corresponding index data in this->indices_.
Definition at line 225 of file blast_dbindex.cpp.
References assert, i, and CIndexedDb_Old::seqmap_.
Referenced by CIndexedDb_Old::CheckOid(), and CIndexedDb_Old::GetResults().
◆ Main()
|
inlineprotectedvirtual |
Derived (user-created) class must provide a real thread function.
Implements CThread.
Definition at line 138 of file prelim_search_runner.hpp.
References BLASTERR_DB_MEMORY_MAP, BLASTERR_DB_OPEN_FILES, CSeqDBException::eOpenFileErr, CException::GetErrCode(), CPrelimSearchThread::m_InternalData, and CPrelimSearchThread::m_OptsMemento.
◆ MakeLocalQueryData()
| CRef< ILocalQueryData > IQueryFactory::MakeLocalQueryData | ( | const CBlastOptions * | opts | ) |
Creates and caches an ILocalQueryData.
Definition at line 52 of file query_data.cpp.
References CRef< C, Locker >::Empty(), IQueryFactory::m_LocalQueryData, CRef< C, Locker >::Reset(), and IQueryFactory::x_MakeLocalQueryData().
Referenced by BlastSetupPreliminarySearchEx(), BOOST_AUTO_TEST_CASE(), CContextTranslator::CContextTranslator(), CEffectiveSearchSpaceCalculator::CEffectiveSearchSpaceCalculator(), CMagicBlastThread::Main(), PsiBlastComputePssmScores(), CPsiBlastValidate::QueryFactory(), CSplitQueryTestFixture::QuerySplitter_BlastnMultiQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastnSingleQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastxMultiQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastxSingleQueryMultiChunk(), CDeltaBlast::Run(), CLocalBlast::Run(), CBlastPrelimSearch::Run(), CBlastTracebackSearch::Run(), s_MakeEmptyResults(), CBlastSetupTestFixture::s_ValidateProtein130912(), CBlastPrelimSearch::SetNumberOfThreads(), CMagicBlast::x_BuildResultSet(), CMagicBlast::x_BuildSeqAlignSet(), CBlastPrelimSearch::x_BuildStdSegList(), CQuerySplitter::x_ComputeContextOffsets_NonTranslatedQueries(), CQuerySplitter::x_ComputeContextOffsets_TranslatedQueries(), CBlastTracebackSearch::x_Init(), CLocalVDBBlast::x_PrepareQuery(), CMagicBlast::x_Run(), CSplitQueryTestFixture::x_TestCContextTranslator(), CSequenceDataTester::x_TestSingleSequence_Local(), and CSplitQueryTestFixture::x_ValidateLocalQueryData().
◆ MakeRemoteQueryData()
| CRef< IRemoteQueryData > IQueryFactory::MakeRemoteQueryData | ( | ) |
Creates and caches an IRemoteQueryData.
Definition at line 61 of file query_data.cpp.
References CRef< C, Locker >::Empty(), IQueryFactory::m_RemoteQueryData, CRef< C, Locker >::Reset(), and IQueryFactory::x_MakeRemoteQueryData().
Referenced by CQueryFactoryInfo::CQueryFactoryInfo(), CLocalDbAdapter::MakeSeqInfoSrc(), CRemoteSeqSearch::SetQueryFactory(), CRemoteBlast::SetSubjectSequences(), CRemoteBlast::x_InitQueries(), and CSequenceDataTester::x_TestSingleSequence_Remote().
◆ MakeSeqInfoSrc()
| IBlastSeqInfoSrc * CLocalDbAdapter::MakeSeqInfoSrc | ( | ) |
Retrieves or constructs the IBlastSeqInfoSrc.
- Note
- ownership of the constructed object is handled by this class
Definition at line 151 of file local_db_adapter.cpp.
References _ASSERT, abort(), Blast_SubjectIsProtein(), IRemoteQueryData::GetBioseqSet(), CSearchDatabase::GetFilteringAlgorithm(), CBlastOptionsHandle::GetOptions(), CBlastOptions::GetProgramType(), CSearchDatabase::GetSeqDb(), CLocalDbAdapter::m_DbInfo, CLocalDbAdapter::m_OptsHandle, CLocalDbAdapter::m_SeqInfoSrc, CLocalDbAdapter::m_SubjectFactory, CLocalDbAdapter::m_Subjects, IQueryFactory::MakeRemoteQueryData(), CRef< C, Locker >::NotEmpty(), CConstRef< C, Locker >::NotEmpty(), and true.
Referenced by PrintSAMHeader(), CLocalBlast::Run(), CPsiBlastImpl::Run(), CSeedTop::Run(), s_MakeEmptyResults(), CMagicBlast::x_BuildResultSet(), CMagicBlast::x_BuildSeqAlignSet(), CBlastPrelimSearch::x_BuildStdSegList(), and CMagicBlast::x_Run().
◆ MakeSeqSrc()
| BlastSeqSrc * CLocalDbAdapter::MakeSeqSrc | ( | ) |
Retrieves or constructs the BlastSeqSrc.
- Note
- ownership of the constructed object is handled by this class
Definition at line 125 of file local_db_adapter.cpp.
References _ASSERT, abort(), CSetupFactory::CreateBlastSeqSrc(), CBlastOptionsHandle::GetOptions(), CBlastOptions::GetProgramType(), CLocalDbAdapter::m_DbInfo, CLocalDbAdapter::m_DbScanMode, CLocalDbAdapter::m_OptsHandle, CLocalDbAdapter::m_SeqSrc, CLocalDbAdapter::m_SubjectFactory, CLocalDbAdapter::m_Subjects, MultiSeqBlastSeqSrcInit(), CRef< C, Locker >::NotEmpty(), CConstRef< C, Locker >::NotEmpty(), QueryFactoryBlastSeqSrcInit(), and s_CheckForBlastSeqSrcErrors().
Referenced by BOOST_AUTO_TEST_CASE(), CBlastPrelimSearch::CBlastPrelimSearch(), PrintSAMHeader(), CPsiBlastImpl::Run(), and CSeedTop::Run().
◆ MakeSplicedSeg()
| void MakeSplicedSeg | ( | CSpliced_seg & | spliced_seg, |
| CRef< CSeq_id > | product_id, | ||
| CRef< CSeq_id > | genomic_id, | ||
| int | product_length, | ||
| const HSPChain * | chain | ||
| ) |
Convert a spliced alignmeny in BlastHSPChain into Spliced_seg.
- Parameters
-
spliced_seg Spliced_seg object [in] [out] product_id Sequence id of a read/query [in] genomic_id Sequence id a genome/subject [in] chain Alignment to be converted [in]
Definition at line 453 of file blast_seqalign.cpp.
References _ASSERT, BLASTNA_TO_IUPACNA, JumperEditsBlock::edits, BlastSeg::end, CSpliced_seg_Base::eProduct_type_transcript, BlastSeg::frame, BlastHSP::gap_info, HSPContainer::hsp, HSPChain::hsps, i, int, BlastHSPMappingInfo::left_edge, BlastHSP::map_info, MAPPER_SPLICE_SIGNAL, MAX, HSPContainer::next, NULL, JumperEditsBlock::num_edits, BlastSeg::offset, prev(), BlastHSP::query, JumperEdit::query_base, JumperEdit::query_pos, BlastHSPMappingInfo::right_edge, s_Frame2Strand(), s_ValidateExon(), CSpliced_seg_Base::SetExons(), CSpliced_seg_Base::SetGenomic_id(), CSpliced_seg_Base::SetProduct_id(), CSpliced_seg_Base::SetProduct_length(), CSpliced_seg_Base::SetProduct_type(), GapEditScript::size, BlastHSP::subject, JumperEdit::subject_base, and CSpliced_seg::Validate().
Referenced by s_CreateSeqAlign().
◆ Map()
| CRange<Position> Map | ( | const CRange< Position > & | target, |
| const CRange< Position > & | range | ||
| ) |
Definition at line 826 of file blast_aux.cpp.
References COpenRange< Position >::Empty(), CRange_Base::GetFrom(), CRange_Base::GetTo(), max(), min(), compile_time_bits::range(), CRange_Base::SetFrom(), and CRange_Base::SetTo().
Referenced by Blast_GetSeqLocInfoVector(), CSeqportUtil_implementation::GetMapToIndex(), CDiscrepancyPanel::OnAutofix(), s_ConvertBlastnMasks(), CProjectFileWriter::x_FindParent(), CReportEntry::x_MapPos(), and CBioseqContext::x_SetOpticalMapPoints().
◆ MaskedQueryRegionsToPackedSeqLoc()
| CRef< objects::CSeq_loc > MaskedQueryRegionsToPackedSeqLoc | ( | const TMaskedQueryRegions & | sloc | ) |
Interface to build a CSeq-loc from a TMaskedQueryRegion; note that conversion conversion in this direction can be lossy.
It might be better to convert the calling code to use a CBlastQueryVector.
Definition at line 462 of file blast_aux_priv.cpp.
References TMaskedQueryRegions::ConvertToCPacked_seqint(), CRef< C, Locker >::NotEmpty(), and CRef< C, Locker >::Reset().
Referenced by CBlastQuerySourceOM::GetMask(), and CBlastQueryVector::GetMasks().
◆ MinIndexWordSize() [1/3]
|
virtual |
Get the minimum acceptable word size to use with indexed search.
- Returns
- the minimum acceptable word size
Implements CIndexedDb.
Definition at line 1088 of file blast_dbindex.cpp.
References CIndexedDb_Old::index_names_, and s_GetMinimumSupportedWordSizeByIndex().
◆ MinIndexWordSize() [2/3]
|
privatevirtual |
Implements CIndexedDb.
Definition at line 935 of file blast_dbindex.cpp.
References s_GetMinimumSupportedWordSizeByIndex(), and CIndexedDb_New::volumes_.
◆ MinIndexWordSize() [3/3]
|
pure virtual |
Implemented in CIndexedDb_New, and CIndexedDb_Old.
Referenced by s_CheckMinWordSize().
◆ MultiSeqBlastSeqSrcInit()
| BlastSeqSrc* MultiSeqBlastSeqSrcInit | ( | TSeqLocVector & | seq_vector, |
| EBlastProgramType | program, | ||
| bool | dbscan_mode = false |
||
| ) |
Initialize the sequence source structure.
- Parameters
-
seq_vector Vector of sequence locations [in] program Type of BLAST to be performed [in] dbscanmode Database search mode (not pairwise) [in]
Definition at line 555 of file seqsrc_multiseq.cpp.
References BlastSeqSrcNew(), BlastSeqSrcNewInfo::constructor, BlastSeqSrcNewInfo::ctor_argument, NULL, and s_MultiSeqSrcNew().
Referenced by BOOST_AUTO_TEST_CASE(), CLocalDbAdapter::MakeSeqSrc(), CBlastKmerSearch::Run(), and CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest().
◆ NCBI_EXCEPTION_DEFAULT() [1/6]
| CBlastException::NCBI_EXCEPTION_DEFAULT | ( | CBlastException | , |
| CException | |||
| ) |
◆ NCBI_EXCEPTION_DEFAULT() [2/6]
| CBlastServicesException::NCBI_EXCEPTION_DEFAULT | ( | CBlastServicesException | , |
| CException | |||
| ) |
Include standard NCBI exception behavior.
◆ NCBI_EXCEPTION_DEFAULT() [3/6]
| CBlastSystemException::NCBI_EXCEPTION_DEFAULT | ( | CBlastSystemException | , |
| CException | |||
| ) |
◆ NCBI_EXCEPTION_DEFAULT() [4/6]
| CPssmEngineException::NCBI_EXCEPTION_DEFAULT | ( | CPssmEngineException | , |
| CBlastException | |||
| ) |
◆ NCBI_EXCEPTION_DEFAULT() [5/6]
| CRemoteBlastException::NCBI_EXCEPTION_DEFAULT | ( | CRemoteBlastException | , |
| CBlastException | |||
| ) |
◆ NCBI_EXCEPTION_DEFAULT() [6/6]
| CSearchException::NCBI_EXCEPTION_DEFAULT | ( | CSearchException | , |
| CException | |||
| ) |
Include standard NCBI exception behavior.
◆ NeedWait()
◆ NetworkFrame2FrameNumber()
| CSeqLocInfo::ETranslationFrame NetworkFrame2FrameNumber | ( | objects::EBlast4_frame_type | frame, |
| EBlastProgramType | program | ||
| ) |
Converts Blast4-frame-type into CSeqLocInfo::ETranslationFrame.
- Parameters
-
frame frame as specified by objects::EBlast4_frame_type program CORE BLAST program type
Definition at line 1991 of file remote_blast.cpp.
References _TROUBLE, abort(), Blast_QueryIsTranslated(), eBlast4_frame_type_minus1, eBlast4_frame_type_minus2, eBlast4_frame_type_minus3, eBlast4_frame_type_plus1, eBlast4_frame_type_plus2, eBlast4_frame_type_plus3, CSeqLocInfo::eFrameMinus1, CSeqLocInfo::eFrameMinus2, CSeqLocInfo::eFrameMinus3, CSeqLocInfo::eFrameNotSet, CSeqLocInfo::eFramePlus1, CSeqLocInfo::eFramePlus2, and CSeqLocInfo::eFramePlus3.
Referenced by CRemoteBlast::GetMasks().
◆ NetworkProgram2BlastProgramType()
| EBlastProgramType NetworkProgram2BlastProgramType | ( | const string & | program, |
| const string & | service | ||
| ) |
Function to convert from program and service name into the CORE BLAST program type This is based on the values set in the various CBlastOptionsHandle subclasses (look for SetRemoteProgramAndService_Blast3 in include tree)
- Note
- This function needs to be updated if the program/service name combinations change
Definition at line 1933 of file remote_blast.cpp.
References _ASSERT, abort(), BlastProgram2Number(), eBlastTypePsiBlast, eBlastTypeRpsBlast, eBlastTypeRpsTblastn, and eBlastTypeUndefined.
Referenced by BOOST_AUTO_TEST_CASE(), CRemoteBlast::GetMasks(), CExportStrategy::x_Process_Query(), and CRemoteBlast::x_QueryMaskingLocationsToNetwork().
◆ NewScope()
Definition at line 126 of file blast_input_unit_test_aux.hpp.
References CBlastScopeSourceWrapper::m_ScopeSrc.
Referenced by BOOST_AUTO_TEST_CASE(), and s_RetrieveSequenceLength().
◆ NullRunSearch()
|
static |
No-op callback to run indexed search.
Used when index search is not enabled.
- See also
- DbIndexRunSearchFnType()
Definition at line 115 of file blast_dbindex.cpp.
Referenced by ClearDbIndexCallbacks().
◆ NullSetNumThreads()
|
static |
No-op callback for setting the number of threads.
- See also
- DbIndexSetNumThreadsFnType()
Definition at line 103 of file blast_dbindex.cpp.
Referenced by ClearDbIndexCallbacks().
◆ NullSetQueryInfo()
|
static |
No-op callback for setting query info.
Used when index search is not enabled.
- See also
- DbIndexSetQueryInfoFnType()
Definition at line 108 of file blast_dbindex.cpp.
Referenced by ClearDbIndexCallbacks().
◆ NullSetUsingThreads()
No-op callback for setting concurrency state.
- See also
- DbIndexSetUsingThreadsFnType()
Definition at line 98 of file blast_dbindex.cpp.
Referenced by ClearDbIndexCallbacks().
◆ operator Blast_ExtendWord *() [1/2]
|
inline |
Definition at line 322 of file blast_aux.hpp.
◆ operator Blast_ExtendWord *() [2/2]
|
inline |
Definition at line 322 of file blast_aux.hpp.
◆ operator Blast_Message *() [1/2]
|
inline |
Definition at line 352 of file blast_aux.hpp.
◆ operator Blast_Message *() [2/2]
|
inline |
Definition at line 352 of file blast_aux.hpp.
◆ operator BLAST_SequenceBlk *() [1/2]
|
inline |
Definition at line 309 of file blast_aux.hpp.
◆ operator BLAST_SequenceBlk *() [2/2]
|
inline |
Definition at line 309 of file blast_aux.hpp.
◆ operator BlastDatabaseOptions *() [1/2]
|
inline |
Definition at line 331 of file blast_aux.hpp.
◆ operator BlastDatabaseOptions *() [2/2]
|
inline |
Definition at line 331 of file blast_aux.hpp.
◆ operator BlastEffectiveLengthsOptions *() [1/2]
|
inline |
Definition at line 338 of file blast_aux.hpp.
◆ operator BlastEffectiveLengthsOptions *() [2/2]
|
inline |
Definition at line 338 of file blast_aux.hpp.
◆ operator BlastEffectiveLengthsParameters *() [1/2]
|
inline |
Definition at line 340 of file blast_aux.hpp.
◆ operator BlastEffectiveLengthsParameters *() [2/2]
|
inline |
Definition at line 340 of file blast_aux.hpp.
◆ operator BlastExtensionOptions *() [1/2]
|
inline |
Definition at line 323 of file blast_aux.hpp.
◆ operator BlastExtensionOptions *() [2/2]
|
inline |
Definition at line 323 of file blast_aux.hpp.
◆ operator BlastExtensionParameters *() [1/2]
|
inline |
Definition at line 324 of file blast_aux.hpp.
◆ operator BlastExtensionParameters *() [2/2]
|
inline |
Definition at line 324 of file blast_aux.hpp.
◆ operator BlastGapAlignStruct *() [1/2]
|
inline |
Definition at line 342 of file blast_aux.hpp.
◆ operator BlastGapAlignStruct *() [2/2]
|
inline |
Definition at line 342 of file blast_aux.hpp.
◆ operator BlastHitSavingOptions *() [1/2]
|
inline |
Definition at line 326 of file blast_aux.hpp.
◆ operator BlastHitSavingOptions *() [2/2]
|
inline |
Definition at line 326 of file blast_aux.hpp.
◆ operator BlastHitSavingParameters *() [1/2]
|
inline |
Definition at line 328 of file blast_aux.hpp.
◆ operator BlastHitSavingParameters *() [2/2]
|
inline |
Definition at line 328 of file blast_aux.hpp.
◆ operator BlastHSPResults *() [1/2]
|
inline |
Definition at line 343 of file blast_aux.hpp.
◆ operator BlastHSPResults *() [2/2]
|
inline |
Definition at line 343 of file blast_aux.hpp.
◆ operator BlastInitialWordOptions *() [1/2]
|
inline |
Definition at line 318 of file blast_aux.hpp.
◆ operator BlastInitialWordOptions *() [2/2]
|
inline |
Definition at line 318 of file blast_aux.hpp.
◆ operator BlastInitialWordParameters *() [1/2]
|
inline |
Definition at line 320 of file blast_aux.hpp.
◆ operator BlastInitialWordParameters *() [2/2]
|
inline |
Definition at line 320 of file blast_aux.hpp.
◆ operator BlastMaskLoc *() [1/2]
|
inline |
Definition at line 354 of file blast_aux.hpp.
◆ operator BlastMaskLoc *() [2/2]
|
inline |
Definition at line 354 of file blast_aux.hpp.
◆ operator BlastQueryInfo *() [1/2]
|
inline |
Definition at line 311 of file blast_aux.hpp.
◆ operator BlastQueryInfo *() [2/2]
|
inline |
Definition at line 311 of file blast_aux.hpp.
◆ operator BlastScoreBlk *() [1/2]
|
inline |
Definition at line 333 of file blast_aux.hpp.
◆ operator BlastScoreBlk *() [2/2]
|
inline |
Definition at line 333 of file blast_aux.hpp.
◆ operator BlastScoringOptions *() [1/2]
|
inline |
Definition at line 334 of file blast_aux.hpp.
◆ operator BlastScoringOptions *() [2/2]
|
inline |
Definition at line 334 of file blast_aux.hpp.
◆ operator BlastScoringParameters *() [1/2]
|
inline |
Definition at line 335 of file blast_aux.hpp.
◆ operator BlastScoringParameters *() [2/2]
|
inline |
Definition at line 335 of file blast_aux.hpp.
◆ operator BlastSeqLoc *() [1/2]
|
inline |
Definition at line 355 of file blast_aux.hpp.
◆ operator BlastSeqLoc *() [2/2]
|
inline |
Definition at line 355 of file blast_aux.hpp.
◆ operator BlastSeqSrc *() [1/2]
|
inline |
Definition at line 350 of file blast_aux.hpp.
◆ operator BlastSeqSrc *() [2/2]
|
inline |
Definition at line 350 of file blast_aux.hpp.
◆ operator BlastSeqSrcIterator *() [1/2]
|
inline |
Definition at line 351 of file blast_aux.hpp.
◆ operator BlastSeqSrcIterator *() [2/2]
|
inline |
Definition at line 351 of file blast_aux.hpp.
◆ operator bool()
| CPsiBlastIterationState::operator bool | ( | ) |
Allow implicit conversion to a boolean value, returning true if there are more iterations to perform or false if iterations are done.
- See also
- HasConverged, HasMoreIterations
Definition at line 94 of file psiblast_iteration.cpp.
◆ operator double **()
|
inline |
Retrieves data in the format expected by the C CORE APIs.
Definition at line 330 of file pssm_engine.cpp.
References SNcbiMatrix2DoubleMatrix::m_Data.
◆ operator LookupTableOptions *() [1/2]
|
inline |
Definition at line 314 of file blast_aux.hpp.
◆ operator LookupTableOptions *() [2/2]
|
inline |
Definition at line 314 of file blast_aux.hpp.
◆ operator LookupTableWrap *() [1/2]
|
inline |
Definition at line 315 of file blast_aux.hpp.
◆ operator LookupTableWrap *() [2/2]
|
inline |
Definition at line 315 of file blast_aux.hpp.
◆ operator PSIBlastOptions *() [1/2]
|
inline |
Definition at line 330 of file blast_aux.hpp.
◆ operator PSIBlastOptions *() [2/2]
|
inline |
Definition at line 330 of file blast_aux.hpp.
◆ operator PSIDiagnosticsRequest *() [1/2]
|
inline |
Definition at line 347 of file blast_aux.hpp.
◆ operator PSIDiagnosticsRequest *() [2/2]
|
inline |
Definition at line 347 of file blast_aux.hpp.
◆ operator PSIDiagnosticsResponse *() [1/2]
|
inline |
Definition at line 348 of file blast_aux.hpp.
◆ operator PSIDiagnosticsResponse *() [2/2]
|
inline |
Definition at line 348 of file blast_aux.hpp.
◆ operator PSIMatrix *() [1/2]
|
inline |
Definition at line 346 of file blast_aux.hpp.
◆ operator PSIMatrix *() [2/2]
|
inline |
Definition at line 346 of file blast_aux.hpp.
◆ operator PSIMsa *() [1/2]
|
inline |
Definition at line 345 of file blast_aux.hpp.
◆ operator PSIMsa *() [2/2]
|
inline |
Definition at line 345 of file blast_aux.hpp.
◆ operator QuerySetUpOptions *() [1/2]
|
inline |
Definition at line 312 of file blast_aux.hpp.
◆ operator QuerySetUpOptions *() [2/2]
|
inline |
Definition at line 312 of file blast_aux.hpp.
◆ operator SBlastProgress *() [1/2]
|
inline |
Definition at line 357 of file blast_aux.hpp.
◆ operator SBlastProgress *() [2/2]
|
inline |
Definition at line 357 of file blast_aux.hpp.
◆ operator!=() [1/2]
| bool CBlastOptions::operator!= | ( | const CBlastOptions & | rhs | ) | const |
Definition at line 819 of file blast_options_cxx.cpp.
◆ operator!=() [2/2]
| bool CBlastOptionsLocal::operator!= | ( | const CBlastOptionsLocal & | rhs | ) | const |
Definition at line 561 of file blast_options_local_priv.cpp.
◆ operator&() [1/31]
|
inline |
Definition at line 309 of file blast_aux.hpp.
◆ operator&() [2/31]
|
inline |
Definition at line 311 of file blast_aux.hpp.
◆ operator&() [3/31]
|
inline |
Definition at line 312 of file blast_aux.hpp.
◆ operator&() [4/31]
|
inline |
Definition at line 314 of file blast_aux.hpp.
◆ operator&() [5/31]
|
inline |
Definition at line 315 of file blast_aux.hpp.
◆ operator&() [6/31]
|
inline |
Definition at line 318 of file blast_aux.hpp.
◆ operator&() [7/31]
|
inline |
Definition at line 320 of file blast_aux.hpp.
◆ operator&() [8/31]
|
inline |
Definition at line 322 of file blast_aux.hpp.
◆ operator&() [9/31]
|
inline |
Definition at line 323 of file blast_aux.hpp.
◆ operator&() [10/31]
|
inline |
Definition at line 324 of file blast_aux.hpp.
◆ operator&() [11/31]
|
inline |
Definition at line 326 of file blast_aux.hpp.
◆ operator&() [12/31]
|
inline |
Definition at line 328 of file blast_aux.hpp.
◆ operator&() [13/31]
|
inline |
Definition at line 330 of file blast_aux.hpp.
◆ operator&() [14/31]
|
inline |
Definition at line 331 of file blast_aux.hpp.
◆ operator&() [15/31]
|
inline |
Definition at line 333 of file blast_aux.hpp.
◆ operator&() [16/31]
|
inline |
Definition at line 334 of file blast_aux.hpp.
◆ operator&() [17/31]
|
inline |
Definition at line 335 of file blast_aux.hpp.
◆ operator&() [18/31]
|
inline |
Definition at line 338 of file blast_aux.hpp.
◆ operator&() [19/31]
|
inline |
Definition at line 340 of file blast_aux.hpp.
◆ operator&() [20/31]
|
inline |
Definition at line 342 of file blast_aux.hpp.
◆ operator&() [21/31]
|
inline |
Definition at line 343 of file blast_aux.hpp.
◆ operator&() [22/31]
|
inline |
Definition at line 345 of file blast_aux.hpp.
◆ operator&() [23/31]
|
inline |
Definition at line 346 of file blast_aux.hpp.
◆ operator&() [24/31]
|
inline |
Definition at line 347 of file blast_aux.hpp.
◆ operator&() [25/31]
|
inline |
Definition at line 348 of file blast_aux.hpp.
◆ operator&() [26/31]
|
inline |
Definition at line 350 of file blast_aux.hpp.
◆ operator&() [27/31]
|
inline |
Definition at line 351 of file blast_aux.hpp.
◆ operator&() [28/31]
|
inline |
Definition at line 352 of file blast_aux.hpp.
◆ operator&() [29/31]
|
inline |
Definition at line 354 of file blast_aux.hpp.
◆ operator&() [30/31]
|
inline |
Definition at line 355 of file blast_aux.hpp.
◆ operator&() [31/31]
|
inline |
Definition at line 357 of file blast_aux.hpp.
◆ operator()() [1/22]
|
inline |
Definition at line 62 of file prelim_search_runner.hpp.
References _ASSERT, Blast_RunPreliminarySearchWithInterrupt(), and SBlastProgressReset().
◆ operator()() [2/22]
| const BlastRPSInfo * CBlastRPSInfo::operator() | ( | ) | const |
Accessor for the underlying C structure (managed by this class)
Definition at line 615 of file rps_aux.cpp.
References CBlastRPSInfo::m_RpsInfo.
◆ operator()() [3/22]
| const BlastRPSAuxInfo * CBlastRPSAuxInfo::operator() | ( | void | ) | const |
Lend the caller the pointer to the data structure this object manages.
Caller MUST NOT deallocate the return value.
Definition at line 127 of file rps_aux.cpp.
References CBlastRPSAuxInfo::m_Data.
◆ operator()() [4/22]
| const BlastRPSAuxInfo * CRpsAuxFile::operator() | ( | void | ) | const |
Lend the caller the pointer to the data structure this object manages.
Caller MUST NOT deallocate the return value.
Definition at line 232 of file rps_aux.cpp.
References CRpsAuxFile::m_Data.
◆ operator()() [5/22]
| const BlastRPSLookupFileHeader * CRpsLookupTblFile::operator() | ( | void | ) | const |
Lend the caller the pointer to the data structure this object manages.
Caller MUST NOT deallocate the return value.
Definition at line 306 of file rps_aux.cpp.
References CRpsLookupTblFile::m_Data.
◆ operator()() [6/22]
| const BlastRPSProfileHeader * CRpsPssmFile::operator() | ( | void | ) | const |
Lend the caller the pointer to the data structure this object manages.
Caller MUST NOT deallocate the return value.
Definition at line 353 of file rps_aux.cpp.
References CRpsPssmFile::m_Data.
◆ operator()() [7/22]
| const BlastRPSProfileHeader * CRpsFreqsFile::operator() | ( | void | ) | const |
Lend the caller the pointer to the data structure this object manages.
Caller MUST NOT deallocate the return value.
Definition at line 403 of file rps_aux.cpp.
References CRpsFreqsFile::m_Data.
◆ operator()() [8/22]
| const BlastRPSProfileHeader * CRpsObsrFile::operator() | ( | void | ) | const |
Lend the caller the pointer to the data structure this object manages.
Caller MUST NOT deallocate the return value.
Definition at line 452 of file rps_aux.cpp.
References CRpsObsrFile::m_Data.
◆ operator()() [9/22]
| const BlastRPSFreqRatiosHeader * CRpsFreqRatiosFile::operator() | ( | void | ) | const |
Lend the caller the pointer to the data structure this object manages.
Caller MUST NOT deallocate the return value.
Definition at line 502 of file rps_aux.cpp.
References CRpsFreqRatiosFile::m_Data.
◆ operator()() [10/22]
|
inline |
Returns true if its argument's frame corresponds to the one used to create this object.
- Parameters
-
seqlocinfo the object to examine [in]
Definition at line 147 of file blast_aux.hpp.
References CRef< C, Locker >::Empty(), CSeqLocInfo::GetFrame(), CFrameFinder::m_Frame, NCBI_THROW, and true.
◆ operator()() [11/22]
|
inline |
Definition at line 395 of file cdd_pssm_input.hpp.
◆ operator()() [12/22]
|
inline |
Definition at line 188 of file blast_aux.hpp.
◆ operator()() [13/22]
|
inline |
Definition at line 372 of file cdd_pssm_input.hpp.
◆ operator()() [14/22]
|
inline |
Definition at line 578 of file blast_options_builder.cpp.
References SBlast4ParamFinder::m_Target2Find, CBlast4Field::Match(), and CRef< C, Locker >::NotEmpty().
◆ operator()() [15/22]
|
inline |
Operator to determine if *a is less than *b.
Definition at line 75 of file blast_aux_priv.hpp.
◆ operator()() [16/22]
|
inline |
Operator to determine if *a is equal to *b.
Definition at line 84 of file blast_aux_priv.hpp.
◆ operator()() [17/22]
|
inline |
Definition at line 475 of file magicblast.cpp.
◆ operator()() [18/22]
|
inline |
Definition at line 586 of file magicblast.cpp.
References a, b, eNa_strand_minus, eNa_strand_plus, CSeq_align::GetSeqStart(), and CSeq_align::GetSeqStrand().
◆ operator()() [19/22]
|
inline |
Definition at line 615 of file magicblast.cpp.
References a, b, eNa_strand_minus, eNa_strand_plus, CSeq_align::GetSeqStart(), and CSeq_align::GetSeqStrand().
◆ operator()() [20/22]
| void CPsiBlastAlignmentProcessor::operator() | ( | const objects::CSeq_align_set & | alignments, |
| double | evalue_inclusion_threshold, | ||
| THitIdentifiers & | output | ||
| ) |
Extract all the THitId which have evalues below the inclusion threshold.
- Parameters
-
alignments alignments corresponding to one query sequence [in] evalue_inclusion_threshold All hits in the above alignment which have evalues below this parameter will be included in the return value [in] output Return value of this method [out]
Definition at line 550 of file psiblast_aux_priv.cpp.
References CSeq_id_Handle::GetHandle(), GetLowestEvalue(), ITERATE, and output.
◆ operator()() [21/22]
Definition at line 382 of file cdd_pssm_input.hpp.
◆ operator()() [22/22]
|
inline |
Definition at line 429 of file igblast.hpp.
References ScorePositionSort::m_scope, and ScorePositionSort::s_CompareSeqAlignByScoreAndPosition().
◆ operator*() [1/2]
|
inline |
The a reference to the wrapped object.
Definition at line 126 of file setup_factory.hpp.
References CStructWrapper< TData >::m_Data.
◆ operator*() [2/2]
|
inline |
Convenience to allow datap->method to use SeqDB methods.
Definition at line 84 of file seqsrc_seqdb.cpp.
References _ASSERT, CRef< C, Locker >::Empty(), and SSeqDB_SeqSrc_Data::seqdb.
◆ operator->() [1/64]
|
inline |
Definition at line 309 of file blast_aux.hpp.
◆ operator->() [2/64]
|
inline |
Definition at line 311 of file blast_aux.hpp.
◆ operator->() [3/64]
|
inline |
Definition at line 312 of file blast_aux.hpp.
◆ operator->() [4/64]
|
inline |
Definition at line 314 of file blast_aux.hpp.
◆ operator->() [5/64]
|
inline |
Definition at line 315 of file blast_aux.hpp.
◆ operator->() [6/64]
|
inline |
Definition at line 318 of file blast_aux.hpp.
◆ operator->() [7/64]
|
inline |
Definition at line 320 of file blast_aux.hpp.
◆ operator->() [8/64]
|
inline |
Definition at line 322 of file blast_aux.hpp.
◆ operator->() [9/64]
|
inline |
Definition at line 323 of file blast_aux.hpp.
◆ operator->() [10/64]
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Definition at line 324 of file blast_aux.hpp.
◆ operator->() [11/64]
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Definition at line 326 of file blast_aux.hpp.
◆ operator->() [12/64]
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Definition at line 328 of file blast_aux.hpp.
◆ operator->() [13/64]
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Definition at line 330 of file blast_aux.hpp.
◆ operator->() [14/64]
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Definition at line 331 of file blast_aux.hpp.
◆ operator->() [15/64]
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Definition at line 333 of file blast_aux.hpp.
◆ operator->() [16/64]
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Definition at line 334 of file blast_aux.hpp.
◆ operator->() [17/64]
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Definition at line 335 of file blast_aux.hpp.
◆ operator->() [18/64]
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Definition at line 338 of file blast_aux.hpp.
◆ operator->() [19/64]
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Definition at line 340 of file blast_aux.hpp.
◆ operator->() [20/64]
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Definition at line 342 of file blast_aux.hpp.
◆ operator->() [21/64]
|
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Definition at line 343 of file blast_aux.hpp.
◆ operator->() [22/64]
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Definition at line 345 of file blast_aux.hpp.
◆ operator->() [23/64]
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Definition at line 346 of file blast_aux.hpp.
◆ operator->() [24/64]
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Definition at line 347 of file blast_aux.hpp.
◆ operator->() [25/64]
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Definition at line 348 of file blast_aux.hpp.
◆ operator->() [26/64]
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Definition at line 350 of file blast_aux.hpp.
◆ operator->() [27/64]
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Definition at line 351 of file blast_aux.hpp.
◆ operator->() [28/64]
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Definition at line 352 of file blast_aux.hpp.
◆ operator->() [29/64]
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Definition at line 354 of file blast_aux.hpp.
◆ operator->() [30/64]
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Definition at line 355 of file blast_aux.hpp.
◆ operator->() [31/64]
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Definition at line 357 of file blast_aux.hpp.
◆ operator->() [32/64]
|
inline |
The a pointer to the wrapped object.
Definition at line 132 of file setup_factory.hpp.
References CStructWrapper< TData >::m_Data.
◆ operator->() [33/64]
|
inline |
Convenience to allow datap->method to use SeqDB methods.
Definition at line 77 of file seqsrc_seqdb.cpp.
References _ASSERT, CRef< C, Locker >::Empty(), and SSeqDB_SeqSrc_Data::seqdb.
◆ operator->() [34/64]
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inline |
Definition at line 309 of file blast_aux.hpp.
◆ operator->() [35/64]
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Definition at line 311 of file blast_aux.hpp.
◆ operator->() [36/64]
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Definition at line 312 of file blast_aux.hpp.
◆ operator->() [37/64]
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Definition at line 314 of file blast_aux.hpp.
◆ operator->() [38/64]
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Definition at line 315 of file blast_aux.hpp.
◆ operator->() [39/64]
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Definition at line 318 of file blast_aux.hpp.
◆ operator->() [40/64]
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Definition at line 320 of file blast_aux.hpp.
◆ operator->() [41/64]
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Definition at line 322 of file blast_aux.hpp.
◆ operator->() [42/64]
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Definition at line 323 of file blast_aux.hpp.
◆ operator->() [43/64]
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Definition at line 324 of file blast_aux.hpp.
◆ operator->() [44/64]
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Definition at line 326 of file blast_aux.hpp.
◆ operator->() [45/64]
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Definition at line 328 of file blast_aux.hpp.
◆ operator->() [46/64]
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Definition at line 330 of file blast_aux.hpp.
◆ operator->() [47/64]
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Definition at line 331 of file blast_aux.hpp.
◆ operator->() [48/64]
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Definition at line 333 of file blast_aux.hpp.
◆ operator->() [49/64]
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Definition at line 334 of file blast_aux.hpp.
◆ operator->() [50/64]
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Definition at line 335 of file blast_aux.hpp.
◆ operator->() [51/64]
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Definition at line 338 of file blast_aux.hpp.
◆ operator->() [52/64]
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Definition at line 340 of file blast_aux.hpp.
◆ operator->() [53/64]
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Definition at line 342 of file blast_aux.hpp.
◆ operator->() [54/64]
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Definition at line 343 of file blast_aux.hpp.
◆ operator->() [55/64]
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Definition at line 345 of file blast_aux.hpp.
◆ operator->() [56/64]
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Definition at line 346 of file blast_aux.hpp.
◆ operator->() [57/64]
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Definition at line 347 of file blast_aux.hpp.
◆ operator->() [58/64]
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Definition at line 348 of file blast_aux.hpp.
◆ operator->() [59/64]
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Definition at line 350 of file blast_aux.hpp.
◆ operator->() [60/64]
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Definition at line 351 of file blast_aux.hpp.
◆ operator->() [61/64]
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Definition at line 352 of file blast_aux.hpp.
◆ operator->() [62/64]
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Definition at line 354 of file blast_aux.hpp.
◆ operator->() [63/64]
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Definition at line 355 of file blast_aux.hpp.
◆ operator->() [64/64]
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Definition at line 357 of file blast_aux.hpp.
◆ operator<<() [1/2]
| ostream& operator<< | ( | ostream & | out, |
| const CContextTranslator & | rhs | ||
| ) |
- Parameters
-
out stream to print this object [in|out] rhs object to print [in]
Definition at line 286 of file split_query_aux_priv.cpp.
References i, CContextTranslator::m_AbsoluteContexts, CContextTranslator::m_ContextsPerChunk, CContextTranslator::m_StartingChunks, out(), and s_PrintVector().
◆ operator<<() [2/2]
| ostream& operator<< | ( | ostream & | out, |
| const CSplitQueryBlk & | rhs | ||
| ) |
- Parameters
-
out stream to print this object [in|out] rhs object to print [in]
Definition at line 219 of file split_query_blk.cpp.
References CSplitQueryBlk::GetContextOffsets(), CSplitQueryBlk::GetNumChunks(), CSplitQueryBlk::GetQueryContexts(), CSplitQueryBlk::GetQueryIndices(), out(), and s_PrintVector().
◆ operator=() [1/49]
|
private |
Prevent assignment.
◆ operator=() [2/49]
|
private |
Prohibit assignment operator.
◆ operator=() [3/49]
|
privatedelete |
◆ operator=() [4/49]
◆ operator=() [5/49]
|
private |
Disallow assignment operator.
◆ operator=() [6/49]
| CBlastAncillaryData & CBlastAncillaryData::operator= | ( | const CBlastAncillaryData & | rhs | ) |
Assignment operator.
Definition at line 156 of file blast_results.cpp.
References CBlastAncillaryData::do_copy().
◆ operator=() [7/49]
|
private |
Disallow assignment operator.
◆ operator=() [8/49]
| CBlastOptionsLocal & CBlastOptionsLocal::operator= | ( | const CBlastOptionsLocal & | optsLocal | ) |
Assignment operator.
Definition at line 79 of file blast_options_local_priv.cpp.
References CBlastOptionsLocal::x_DoDeepCopy().
◆ operator=() [9/49]
|
inline |
Assignment operator.
Definition at line 81 of file blast_options_cxx.cpp.
References CBlastOptionsRemote::x_DoDeepCopy().
◆ operator=() [10/49]
|
private |
Disallow assignment operator.
◆ operator=() [11/49]
|
private |
Prohibit assignment operator.
◆ operator=() [12/49]
|
private |
Disallow assignment operator.
◆ operator=() [13/49]
|
private |
Prohibit assignment operator.
◆ operator=() [14/49]
|
private |
Prohibit assignment operator.
◆ operator=() [15/49]
|
private |
Disallow assignment operator.
◆ operator=() [16/49]
|
private |
Prohibit assignment.
◆ operator=() [17/49]
|
private |
Disallow assignment operator.
◆ operator=() [18/49]
|
protected |
Prohibit assignment operator.
◆ operator=() [19/49]
|
private |
Disallow assignment operator.
◆ operator=() [20/49]
|
private |
Disallow assignment operator.
◆ operator=() [21/49]
|
private |
◆ operator=() [22/49]
|
private |
Fobidding assignment operator.
◆ operator=() [23/49]
◆ operator=() [24/49]
|
private |
Prohibit assignment operator.
◆ operator=() [25/49]
|
private |
Prohibit assignment operator.
◆ operator=() [26/49]
|
protected |
Prohibit assignment operator.
◆ operator=() [27/49]
|
private |
Disallow assignment operator.
◆ operator=() [28/49]
|
private |
◆ operator=() [29/49]
|
private |
Disallow assignment operator.
◆ operator=() [30/49]
|
private |
Disallow assignment operator.
◆ operator=() [31/49]
|
private |
Prohibit assignment operator.
◆ operator=() [32/49]
|
private |
Prohibit assignment operator.
◆ operator=() [33/49]
◆ operator=() [34/49]
|
private |
Prohibit assignment operator.
◆ operator=() [35/49]
|
private |
prohibit assignment operator
◆ operator=() [36/49]
|
private |
prohibit assignment operator
◆ operator=() [37/49]
|
private |
Prohibit assignment operator.
◆ operator=() [38/49]
|
private |
Disallow assignment operator.
◆ operator=() [39/49]
|
private |
Prohibit assignment operator.
◆ operator=() [40/49]
|
private |
Prohibit assignment operator.
◆ operator=() [41/49]
|
private |
Prohibit assignment operator.
◆ operator=() [42/49]
|
private |
Prohibit assignment.
◆ operator=() [43/49]
|
private |
Disallow assignment operator.
◆ operator=() [44/49]
|
private |
Prohibit assignment operator.
◆ operator=() [45/49]
|
private |
Do not allow assignment operator.
◆ operator=() [46/49]
|
private |
Disallow assignment operator.
◆ operator=() [47/49]
|
private |
Disallow assignment operator.
◆ operator=() [48/49]
|
inline |
Assign the field from another optional field.
Definition at line 237 of file blast_options_builder.hpp.
◆ operator=() [49/49]
|
private |
Prohibit assignment operator.
◆ operator==() [1/2]
| bool CBlastOptions::operator== | ( | const CBlastOptions & | rhs | ) | const |
Definition at line 808 of file blast_options_cxx.cpp.
References CBlastOptions::m_Local, and NCBI_THROW.
◆ operator==() [2/2]
| bool CBlastOptionsLocal::operator== | ( | const CBlastOptionsLocal & | rhs | ) | const |
Definition at line 507 of file blast_options_local_priv.cpp.
References a, b, CBlastOptionsLocal::m_DbOpts, CBlastOptionsLocal::m_DeltaBlastOpts, CBlastOptionsLocal::m_EffLenOpts, CBlastOptionsLocal::m_ExtnOpts, CBlastOptionsLocal::m_HitSaveOpts, CBlastOptionsLocal::m_InitWordOpts, CBlastOptionsLocal::m_LutOpts, CBlastOptionsLocal::m_Program, CBlastOptionsLocal::m_PSIBlastOpts, CBlastOptionsLocal::m_QueryOpts, CBlastOptionsLocal::m_ScoringOpts, x_BlastDatabaseOptions_cmp(), x_BlastEffectiveLengthsOptions_cmp(), x_BlastScoringOptions_cmp(), x_LookupTableOptions_cmp(), x_QuerySetupOptions_cmp(), and x_safe_memcmp().
◆ operator[]() [1/8]
| CRef< CSearchResults > CSearchResultSet::operator[] | ( | const objects::CSeq_id & | ident | ) |
Allow array-like access with CSeq_id indices to CSearchResults contained by this object.
- Parameters
-
ident query sequence identifier [in]
- Note
- it only works for results of type eDatabaseSearch
Definition at line 431 of file blast_results.cpp.
References CSeq_id::e_YES, eDatabaseSearch, i, CSearchResultSet::m_Results, CSearchResultSet::m_ResultType, and NCBI_THROW.
◆ operator[]() [2/8]
| CConstRef< CSearchResults > CSearchResultSet::operator[] | ( | const objects::CSeq_id & | ident | ) | const |
Allow array-like access with CSeq_id indices to const CSearchResults contained by this object.
- Parameters
-
ident query sequence identifier [in]
- Note
- it only works for results of type eDatabaseSearch
Definition at line 416 of file blast_results.cpp.
References CSeq_id::e_YES, eDatabaseSearch, i, CSearchResultSet::m_Results, CSearchResultSet::m_ResultType, and NCBI_THROW.
◆ operator[]() [3/8]
| BlastSeqLoc ** CBlastQueryFilteredFrames::operator[] | ( | int | frame | ) |
Access the BlastSeqLocs for a given frame.
A pointer is returned to the list of BlastSeqLocs associated with a given frame.
- Parameters
-
frame The specific frame, expressed as a value from ETranslationFrame, on which this interval falls.
Definition at line 1762 of file blast_setup_cxx.cpp.
References CBlastQueryFilteredFrames::m_Seqlocs, and CBlastQueryFilteredFrames::x_VerifyFrame().
◆ operator[]() [4/8]
|
inline |
Allow array-like access with integer indices to CSearchResults contained by this object.
- Parameters
-
i query sequence index if result type is eDatabaseSearch, otherwise it's the query-subject index [in]
Definition at line 363 of file blast_results.hpp.
References i, and CSearchResultSet::m_Results.
◆ operator[]() [5/8]
|
inline |
Allow array-like access with integer indices to const CSearchResults contained by this object.
- Parameters
-
i query sequence index if result type is eDatabaseSearch, otherwise it's the query-subject index [in]
Definition at line 371 of file blast_results.hpp.
References i, and CSearchResultSet::m_Results.
◆ operator[]() [6/8]
@inheritDoc
Implements IBlastSeqVector.
Definition at line 162 of file bioseq_extract_data_priv.cpp.
References CBlastSeqVectorFromCSeq_data::m_SequenceData, NCBI_THROW, and CBlastSeqVectorFromCSeq_data::x_Size().
◆ operator[]() [7/8]
@inheritDoc
Implements IBlastSeqVector.
Definition at line 499 of file blast_objmgr_tools.cpp.
References CBlastSeqVectorOM::m_SeqVector.
◆ operator[]() [8/8]
Allows index-based access to the sequence data.
Implemented in CBlastSeqVectorOM, and CBlastSeqVectorFromCSeq_data.
Referenced by IBlastSeqVector::GetStrandData().
◆ PackedSeqLocToMaskedQueryRegions()
| TMaskedQueryRegions PackedSeqLocToMaskedQueryRegions | ( | CConstRef< objects::CSeq_loc > | sloc, |
| EBlastProgramType | program, | ||
| bool | assume_both_strands = false |
||
| ) |
Auxiliary function to convert a Seq-loc describing masked query regions to a TMaskedQueryRegions object.
- Parameters
-
sloc Seq-loc to use as source (must be Packed-int or Seq-int) [in] program BLAST program type [in] assume_both_strands ignores the strand of sloc_in and adds masking locations to both strands in return value. This is irrelevant for protein queries
- Returns
- List of masked query regions.
- Exceptions
-
CBlastException if Seq-loc type cannot be converted to Packed-int
Definition at line 369 of file blast_aux_priv.cpp.
References Blast_QueryIsProtein(), CSeq_loc_Base::e_not_set, CSeqLocInfo::eFrameMinus1, CSeqLocInfo::eFrameNotSet, CSeqLocInfo::eFramePlus1, CConstRef< C, Locker >::Empty(), eNa_strand_both, eNa_strand_minus, eNa_strand_plus, CSeq_loc_Base::GetPacked_int(), int, CConstRef< C, Locker >::IsNull(), CSeq_loc_Base::IsPacked_int(), ITERATE, NCBI_THROW, prog, CConstRef< C, Locker >::Reset(), and CSeq_loc::SetPacked_int().
Referenced by Blast_FindDustFilterLoc(), CObjMgr_QueryFactory::ExtractUserSpecifiedMasks(), CBlastQuerySourceOM::GetMaskedRegions(), CBlastFastaInputSource::GetNextSequence(), and s_BlastSeqLoc2MaskedRegions().
◆ ParseDBNames()
|
staticprivate |
Generate a list of BLAST database names from a single string.
- Parameters
-
db_spec string containing space separated list of names db_names [out] resulting list of database names
Definition at line 631 of file blast_dbindex.cpp.
References SEP.
Referenced by CIndexedDb_New::CIndexedDb_New().
◆ PhiBlastResults2SeqAlign_OMF()
| TSeqAlignVector PhiBlastResults2SeqAlign_OMF | ( | const BlastHSPResults * | results, |
| EBlastProgramType | prog, | ||
| class ILocalQueryData & | query, | ||
| const IBlastSeqInfoSrc * | seqinfo_src, | ||
| const SPHIQueryInfo * | pattern_info, | ||
| vector< TSeqLocInfoVector > & | subj_masks | ||
| ) |
Definition at line 1647 of file blast_seqalign.cpp.
References BlastHitList2SeqAlign_OMF(), BlastHSPResults::hitlist_array, NULL, pattern_info(), PHIBlast_HSPResultsSplit(), prog, query, results, and sfree.
Referenced by LocalBlastResults2SeqAlign().
◆ Post()
|
virtual |
Save and post diag message.
Implements CDiagHandler.
Definition at line 1155 of file blast_aux.cpp.
References DEFINE_STATIC_MUTEX, CBlastAppDiagHandler::m_handler, CBlastAppDiagHandler::m_messages, CBlastAppDiagHandler::m_save, SDiagMessage::m_Severity, NULL, CDiagHandler::Post(), NStr::Sanitize(), and SDiagMessage::Write().
◆ PreSearch()
|
private |
Invoke the seed search procedure on each of the loaded indices.
Each search is run in a separate thread. The function waits until all threads are complete before it returns.
- Parameters
-
queries Queries descriptor. locs Unmasked intervals of queries. lut_options Lookup table parameters, like target word size. word_options Contains window size of two-hits based search.
Definition at line 1036 of file blast_dbindex.cpp.
References CIndexedDb_Old::index_, CIndexedDb_Old::index_names_, CDbIndex::Load(), NCBI_THROW, result, results, CIndexedDb_Old::results_, CDbIndex::Search(), CIndexedDb_Old::seqmap_, CDbIndex::StartSeq(), CDbIndex::StopSeq(), CDbIndex::SSearchOptions::two_hits, CException::what(), BlastInitialWordOptions::window_size, LookupTableOptions::word_size, and CDbIndex::SSearchOptions::word_size.
Referenced by CIndexedDb_Old::DoPreSearch().
◆ Print()
|
inlinevirtual |
Print version information.
- Returns
- String representation of the version, Version information is printed in the following forms:
- <ver_major>.<ver_minor>.<patch_level>
- <ver_major>.<ver_minor>.<patch_level> (<name>) Return empty string if major version is undefined (< 0).
Reimplemented from CVersionInfo.
Reimplemented in ncbi::blast::CBlastVdbVersion.
Definition at line 59 of file version.hpp.
References CVersionInfo::Print().
Referenced by CBlastnAppArgs::CBlastnAppArgs(), CBlastnVdbAppArgs::CBlastnVdbAppArgs(), CBlastpAppArgs::CBlastpAppArgs(), CBlastxAppArgs::CBlastxAppArgs(), CDeltaBlastAppArgs::CDeltaBlastAppArgs(), CIgBlastpAppArgs::CIgBlastpAppArgs(), CKBlastpAppArgs::CKBlastpAppArgs(), CPsiBlastAppArgs::CPsiBlastAppArgs(), CRPSBlastAppArgs::CRPSBlastAppArgs(), CRPSTBlastnAppArgs::CRPSTBlastnAppArgs(), CTblastnAppArgs::CTblastnAppArgs(), CTblastnVdbAppArgs::CTblastnVdbAppArgs(), CTblastxAppArgs::CTblastxAppArgs(), ncbi::blast::CBlastVdbVersion::Print(), and s_BuildArchiveAll().
◆ Process() [1/7]
|
virtual |
The work to process the alignment is done here.
Implements IPssmInputData.
Definition at line 210 of file msa_pssm_input.cpp.
References CPsiBlastInputClustalW::m_Msa, CPsiBlastInputClustalW::m_MsaDimensions, NCBI_THROW, PSIMsaNew(), CPsiBlastInputClustalW::x_CopyQueryToMsa(), CPsiBlastInputClustalW::x_ExtractAlignmentData(), and CPsiBlastInputClustalW::x_ExtractQueryForPssm().
Referenced by BOOST_AUTO_TEST_CASE().
◆ Process() [2/7]
|
inlinevirtual |
No-op as we assume the data is passed in to the constructor.
Implements IPssmInputFreqRatios.
Definition at line 95 of file psi_pssm_input.hpp.
◆ Process() [3/7]
|
virtual |
The work to process the alignment is done here.
Implements IPssmInputData.
Definition at line 122 of file psi_pssm_input.cpp.
References _ASSERT, CPsiBlastInputData::m_Msa, CPsiBlastInputData::m_MsaDimensions, CPsiBlastInputData::m_Query, NCBI_THROW, NULL, PSIMsaDimensions::num_seqs, PSIMsaNew(), CPsiBlastInputData::x_CopyQueryToMsa(), CPsiBlastInputData::x_CountAndSelectQualifyingAlignments(), CPsiBlastInputData::x_ExtractAlignmentData(), and CPsiBlastInputData::x_ExtractQueryForPssm().
◆ Process() [4/7]
|
pure virtual |
Algorithm to produce multiple sequence alignment structure should be implemented in this method.
This will be invoked by the CPssmEngine object before calling GetData()
Implemented in SU_PSSMInput, CNullPssmInput, CPssmInputFlankingGaps, CdPssmInput, CPsiBlastInputData, and CPsiBlastInputClustalW.
Referenced by CPssmEngine::x_CreatePssmFromMsa().
◆ Process() [5/7]
|
pure virtual |
Algorithm to produce the PSSM's frequecy ratios should be implemented in this method.
This will be invoked by the CPssmEngine object before calling GetData()
Implemented in CPsiBlastInputFreqRatios.
Referenced by CPssmEngine::x_CreatePssmFromFreqRatios().
◆ Process() [6/7]
|
virtual |
Pre-process CD matches to query.
Make multiple alignment of CDs matching the query. Get the weghted counts and effective numbers of observations for each match.
Implements IPssmInputCdd.
Definition at line 113 of file cdd_pssm_input.cpp.
References _ASSERT, PSICdMsa::dimensions, PSIBlastOptions::inclusion_ethresh, CCddInputData::m_CddData, CCddInputData::m_Hits, CCddInputData::m_MinEvalue, CCddInputData::m_MsaDimensions, CCddInputData::m_Opts, CCddInputData::m_QueryData, NCBI_THROW, PSIMsaDimensions::num_seqs, PSICdMsa::query, PSIMsaDimensions::query_length, CCddInputData::x_CreateMsa(), CCddInputData::x_ExtractQueryForPssm(), CCddInputData::x_FillHitsData(), CCddInputData::x_ProcessAlignments(), CCddInputData::x_RemoveMultipleCdHits(), CCddInputData::x_ValidateHits(), and CCddInputData::x_ValidateMsa().
◆ Process() [7/7]
|
pure virtual |
Pre-process CDs used for PSSM computation.
Implemented in CPssmInputWithNoCDs, and CCddInputData.
Referenced by CPssmEngine::x_CreatePssmFromCDD().
◆ ProgramNameToEnum()
| EProgram ProgramNameToEnum | ( | const std::string & | program_name | ) |
Map a string into an element of the ncbi::blast::EProgram enumeration (except eBlastProgramMax).
- Parameters
-
program_name [in]
- Returns
- an element of the ncbi::blast::EProgram enumeration, except eBlastProgramMax
- Exceptions
-
CBlastException if the string does not map into any of the EProgram elements
Definition at line 757 of file blast_aux.cpp.
References _ASSERT, eBlastn, eBlastp, eBlastx, eDeltaBlast, eDiscMegablast, eMapper, eMegablast, ePSIBlast, ePSITblastn, eRPSBlast, eRPSTblastn, eTblastn, eTblastx, eVecScreen, NCBI_THROW, NStr::StartsWith(), ThrowIfInvalidTask(), and NStr::ToLower().
Referenced by BOOST_AUTO_TEST_CASE(), CBlastOptionsBuilder::ComputeProgram(), CBlastnAppArgs::GetQueryBatchSize(), CBlastnNodeArgs::GetQueryBatchSize(), CIgBlastnAppArgs::GetQueryBatchSize(), CIgBlastpAppArgs::GetQueryBatchSize(), CRMBlastnAppArgs::GetQueryBatchSize(), CBlastnVdbAppArgs::GetQueryBatchSize(), CBlastDemoApplication::Run(), CBlastSampleApplication::Run(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), and CBlastFormat::x_WrapAlignmentInSeqAnnot().
◆ PsiBlastAddAncillaryPssmData()
| void PsiBlastAddAncillaryPssmData | ( | objects::CPssmWithParameters & | pssm, |
| int | gap_open, | ||
| int | gap_extend | ||
| ) |
Even though the query sequence and the matrix gap costs are not a product of the PSSM engine, set them as they are required for the PSI-BLAST (query sequence) and RPS-BLAST/formatrpsdb (gap costs)
- Parameters
-
pssm PSSM to modify [in|out] gap_open Gap opening cost associated with the matrix used to build the PSSM [in] gap_extend Gap extension cost associated with the matrix used to build the PSSM [in]
Definition at line 426 of file psiblast_aux_priv.cpp.
References _ASSERT.
Referenced by PsiBlastComputePssmFromAlignment(), and PsiBlastComputePssmScores().
◆ PsiBlastComputePssmFromAlignment()
| CRef< objects::CPssmWithParameters > PsiBlastComputePssmFromAlignment | ( | const objects::CBioseq & | query, |
| CConstRef< objects::CSeq_align_set > | alignment, | ||
| CRef< objects::CScope > | database_scope, | ||
| const CPSIBlastOptionsHandle & | opts_handle, | ||
| CConstRef< CBlastAncillaryData > | ancillary_data, | ||
| PSIDiagnosticsRequest * | diagnostics_req = 0 |
||
| ) |
Computes a PSSM from the result of a PSI-BLAST iteration.
- Parameters
-
query Query sequence [in] alignment BLAST pairwise alignment obtained from the PSI-BLAST iteration [in] database_scope Scope from which the database sequences will be retrieved [in] opts_handle PSI-BLAST options [in] diagnostics_req Optional requests for diagnostics data from the PSSM engine [in]
Definition at line 102 of file psiblast.cpp.
References _ASSERT, SBlastSequence::data, data, eBlastEncodingProtein, eNa_strand_unknown, eSentinels, CPSIBlastOptions::Get(), AutoPtr< X, Del >::get(), CBlastQuerySourceBioseqSet::GetBlastSequence(), CBlastProteinOptionsHandle::GetGapExtensionCost(), CBlastProteinOptionsHandle::GetGapOpeningCost(), CPSIBlastOptionsHandle::GetInclusionThreshold(), CBlastProteinOptionsHandle::GetMatrixName(), CPSIBlastOptionsHandle::GetPseudoCount(), PSIBlastOptions::inclusion_ethresh, input(), ITERATE, SBlastSequence::length, NcbiEmptyString, PSIBlastOptions::pseudo_count, PsiBlastAddAncillaryPssmData(), PSIBlastOptionsNew(), query, CPssmEngine::Run(), and CPssmEngine::SetUngappedStatisticalParams().
Referenced by CPsiBlastApp::ComputePssmForNextIteration(), CDeltaBlastApp::ComputePssmForNextPsiBlastIteration(), and CPsiBlastTestFixture::x_ComputePssmForNextIteration().
◆ PsiBlastComputePssmScores()
| void PsiBlastComputePssmScores | ( | CRef< objects::CPssmWithParameters > | pssm, |
| const CBlastOptions & | opts | ||
| ) |
Given a PSSM with frequency ratios and options, invoke the PSSM engine to compute the scores.
- Parameters
-
pssm object containing the PSSM's frequency ratios [in|out] opts PSSM engine options [in]
Definition at line 466 of file psiblast_aux_priv.cpp.
References _ASSERT, BLASTAA_SIZE, CPssm_Base::GetFinalData(), CScorematPssmConverter::GetFreqRatios(), CBlastOptions::GetGapExtensionCost(), CBlastOptions::GetGapOpeningCost(), CPssmFinalData_Base::GetH(), CPssmFinalData_Base::GetKappa(), CPssmFinalData_Base::GetLambda(), CBlastOptions::GetMatrixName(), CPssm_Base::GetNumRows(), CPssmWithParameters_Base::GetPssm(), CPssmFinalData_Base::GetScores(), ILocalQueryData::GetSeqLength(), ILocalQueryData::GetSequenceBlk(), BLAST_SequenceBlk::length, IQueryFactory::MakeLocalQueryData(), PsiBlastAddAncillaryPssmData(), query, CPssmEngine::Run(), s_AdjustFrequencyRatiosMatrixToMatchScoreMatrix(), and BLAST_SequenceBlk::sequence.
Referenced by CPsiBl2SeqTestFixture::CPsiBl2SeqTestFixture(), CPsiBlastTestFixture::CPsiBlastTestFixture(), and CPsiBlastImpl::x_CreatePssmScoresFromFrequencyRatios().
◆ PsiBlastSetupScoreBlock()
| void PsiBlastSetupScoreBlock | ( | BlastScoreBlk * | score_blk, |
| CConstRef< objects::CPssmWithParameters > | pssm, | ||
| TSearchMessages & | messages, | ||
| CConstRef< CBlastOptions > | options | ||
| ) |
Setup CORE BLAST score block structure with data from the scoremat PSSM.
- Note
- this function might modify the composition based statistics settings.
- Parameters
-
score_blk BlastScoreBlk structure to set up [in|out] pssm scoremat PSSM [in] messages Error/warning messages [in|out] options PSI-BLAST options [in|out]
Definition at line 76 of file psiblast_aux_priv.cpp.
References _ASSERT, eBlastSevWarning, eCompositionBasedStats, eDeltaBlast, eNoCompositionBasedStats, eNumCompoAdjustModes, CScorematPssmConverter::GetFreqRatios(), CScorematPssmConverter::GetScores(), kEpsilon, CPssm::kInvalidStat, log, NCBI_THROW, r(), and SPsiBlastScoreMatrixNew().
Referenced by BlastSetupPreliminarySearchEx(), and CBlastTracebackSearch::x_Init().
◆ Pssm()
|
static |
Perform validation on the PSSM.
- Parameters
-
pssm PSSM as specified in scoremat.asn [in] require_scores Set to true if scores MUST be present (otherwise, either scores or frequency ratios are acceptable) [in]
- Exceptions
-
CBlastException on failure when validating data
Definition at line 569 of file psiblast_aux_priv.cpp.
References NStr::IntToString(), msg(), and NCBI_THROW.
Referenced by CPsiBlastImpl::SetPssm(), CRemoteBlast::SetQueries(), CLocalPssmSearch::SetQuery(), CExportStrategy::x_Process_Pssm(), and CPsiBlastImpl::x_Validate().
◆ push_back() [1/2]
|
inline |
Add results to the end of the container.
Definition at line 289 of file magicblast.hpp.
References CMagicBlastResultSet::m_Results.
◆ push_back() [2/2]
| void CSearchResultSet::push_back | ( | CSearchResultSet::value_type & | element | ) |
Add a value to the back of this container.
- Parameters
-
element element to add [in]
Definition at line 609 of file blast_results.cpp.
References CSearchResultSet::m_NumQueries, and CSearchResultSet::m_Results.
Referenced by CDeltaBlast::Run(), s_AddNewResultSet(), CIgBlast::s_AppendResults(), s_CombineSearchSets(), and CIgBlast::x_ConvertResultType().
◆ QueryFactory()
|
static |
Function to perform sanity checks on the query factory.
Definition at line 628 of file psiblast_aux_priv.cpp.
References _ASSERT, abort(), CFormatGuess::eNucleotide, CPsiBlastValidate::eQFT_Query, CPsiBlastValidate::eQFT_Subject, CException::GetMsg(), ILocalQueryData::GetNumQueries(), CBlastOptionsHandle::GetOptions(), ILocalQueryData::GetSequenceBlk(), BLAST_SequenceBlk::length, IQueryFactory::MakeLocalQueryData(), NCBI_THROW, NPOS, NULL, BLAST_SequenceBlk::sequence_start, and CFormatGuess::SequenceType().
Referenced by CLocalDbAdapter::CLocalDbAdapter(), and CPsiBlastImpl::x_Validate().
◆ QueryFactoryBlastSeqSrcInit() [1/2]
| BlastSeqSrc* QueryFactoryBlastSeqSrcInit | ( | const TSeqLocVector & | subj_seqs, |
| EBlastProgramType | program | ||
| ) |
Initialize the sequence source structure from a TSeqLocVector.
- Parameters
-
subj_seqs TSeqLocVector object from which the queries will be manufactured [in] program Type of BLAST to be performed [in]
- Note
- this is deprecated, use MultiSeqBlastSeqSrcInit instead
Definition at line 570 of file seqsrc_query_factory.cpp.
References ctll::empty(), and s_QueryFactoryBlastSeqSrcInit().
◆ QueryFactoryBlastSeqSrcInit() [2/2]
| BlastSeqSrc * QueryFactoryBlastSeqSrcInit | ( | CRef< IQueryFactory > | query_factory, |
| EBlastProgramType | program | ||
| ) |
Initialize the sequence source structure from a query factory.
- Parameters
-
query_factory Factory from which the queries will be manufactured [in] program Type of BLAST to be performed [in]
Definition at line 562 of file seqsrc_query_factory.cpp.
References ctll::empty(), and s_QueryFactoryBlastSeqSrcInit().
Referenced by CLocalDbAdapter::MakeSeqSrc().
◆ QueryHasMultipleFrames()
| bool CBlastQueryFilteredFrames::QueryHasMultipleFrames | ( | ) | const |
Check whether the query is multiframe for this type of search.
Definition at line 1705 of file blast_setup_cxx.cpp.
References eBlastTypeBlastn, eBlastTypeBlastp, eBlastTypeBlastx, eBlastTypeMapping, eBlastTypePhiBlastp, eBlastTypePsiBlast, eBlastTypePsiTblastn, eBlastTypeRpsBlast, eBlastTypeRpsTblastn, eBlastTypeTblastn, eBlastTypeTblastx, CBlastQueryFilteredFrames::m_Program, and NCBI_THROW.
Referenced by BOOST_AUTO_TEST_CASE(), and s_AddMask().
◆ Read()
| int CBlastHSPListQueueData::Read | ( | BlastHSPList ** | hsp_list | ) |
Read from the queue.
◆ Release() [1/32]
|
inline |
Definition at line 309 of file blast_aux.hpp.
Referenced by SafeSetupQueries().
◆ Release() [2/32]
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Definition at line 311 of file blast_aux.hpp.
Referenced by SafeSetupQueryInfo(), SetupQueryInfo_OMF(), and setupQueryStructures().
◆ Release() [3/32]
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Definition at line 312 of file blast_aux.hpp.
◆ Release() [4/32]
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Definition at line 314 of file blast_aux.hpp.
◆ Release() [5/32]
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Definition at line 315 of file blast_aux.hpp.
◆ Release() [6/32]
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Definition at line 318 of file blast_aux.hpp.
◆ Release() [7/32]
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Definition at line 320 of file blast_aux.hpp.
◆ Release() [8/32]
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Definition at line 322 of file blast_aux.hpp.
◆ Release() [9/32]
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Definition at line 323 of file blast_aux.hpp.
◆ Release() [10/32]
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Definition at line 324 of file blast_aux.hpp.
◆ Release() [11/32]
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Definition at line 326 of file blast_aux.hpp.
◆ Release() [12/32]
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Definition at line 328 of file blast_aux.hpp.
◆ Release() [13/32]
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Definition at line 330 of file blast_aux.hpp.
◆ Release() [14/32]
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Definition at line 331 of file blast_aux.hpp.
◆ Release() [15/32]
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Definition at line 333 of file blast_aux.hpp.
◆ Release() [16/32]
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Definition at line 334 of file blast_aux.hpp.
◆ Release() [17/32]
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Definition at line 335 of file blast_aux.hpp.
◆ Release() [18/32]
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Definition at line 338 of file blast_aux.hpp.
Referenced by CEffectiveSearchSpacesMemento::CEffectiveSearchSpacesMemento().
◆ Release() [19/32]
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Definition at line 340 of file blast_aux.hpp.
◆ Release() [20/32]
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Definition at line 342 of file blast_aux.hpp.
◆ Release() [21/32]
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Definition at line 343 of file blast_aux.hpp.
◆ Release() [22/32]
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Definition at line 345 of file blast_aux.hpp.
◆ Release() [23/32]
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Definition at line 346 of file blast_aux.hpp.
◆ Release() [24/32]
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Definition at line 347 of file blast_aux.hpp.
◆ Release() [25/32]
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Definition at line 348 of file blast_aux.hpp.
◆ Release() [26/32]
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Definition at line 350 of file blast_aux.hpp.
◆ Release() [27/32]
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Definition at line 351 of file blast_aux.hpp.
◆ Release() [28/32]
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Definition at line 352 of file blast_aux.hpp.
◆ Release() [29/32]
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Definition at line 354 of file blast_aux.hpp.
◆ Release() [30/32]
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Definition at line 355 of file blast_aux.hpp.
Referenced by CSeqLoc2BlastSeqLoc().
◆ Release() [31/32]
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Definition at line 357 of file blast_aux.hpp.
◆ Release() [32/32]
| void CBlastQueryFilteredFrames::Release | ( | int | frame | ) |
Release the BlastSeqLocs for a given frame.
The given frame is cleared (the data removed) without freeing the associated objects. The calling code takes responsibility for freeing the associated list of objects.
- Parameters
-
frame The specific frame, expressed as a value from ETranslationFrame, on which this interval falls.
Definition at line 1579 of file blast_setup_cxx.cpp.
References map_checker< Container >::erase(), CBlastQueryFilteredFrames::m_Seqlocs, and CBlastQueryFilteredFrames::m_SeqlocTails.
Referenced by s_AddMask().
◆ RemapToQueryLoc()
| void RemapToQueryLoc | ( | CRef< CSeq_align > | sar, |
| const CSeq_loc & | query | ||
| ) |
Remaps Seq-align offsets relative to the query Seq-loc.
Since the query strands were already taken into account when CSeq_align was created, only start position shifts in the CSeq_loc's are relevant in this function.
- Parameters
-
sar Seq-align for a given query [in] [out] query The query Seq-loc [in]
Definition at line 1515 of file blast_seqalign.cpp.
References _ASSERT, CSeq_align::OffsetRow(), and query.
Referenced by BlastHitList2SeqAlign_OMF(), and s_BLAST_OneSubjectResults2CSeqAlign().
◆ RemoveBLASTDBEnvVar()
|
inline |
Definition at line 92 of file blast_input_unit_test_aux.hpp.
References IRegistry::Get(), CAutoNcbiConfigFile::kSection, CAutoNcbiConfigFile::m_BlastDb, CAutoNcbiConfigFile::m_Registry, and IRWRegistry::Set().
Referenced by BOOST_AUTO_TEST_CASE().
◆ RemoveDuplicates()
| void TSearchMessages::RemoveDuplicates | ( | ) |
Find and remove redundant messages.
Definition at line 1043 of file blast_aux.cpp.
References NON_CONST_ITERATE, and ct::sort().
Referenced by Blast_Message2TSearchMessages(), and TSearchMessages::Combine().
◆ reserve()
|
inline |
Reserve memory for a number of result elemetns.
Definition at line 286 of file magicblast.hpp.
References CMagicBlastResultSet::m_Results.
◆ Reset() [1/31]
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inline |
Definition at line 322 of file blast_aux.hpp.
◆ Reset() [2/31]
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Definition at line 352 of file blast_aux.hpp.
Referenced by BOOST_AUTO_TEST_CASE().
◆ Reset() [3/31]
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Definition at line 309 of file blast_aux.hpp.
Referenced by ILocalQueryData::FlushSequenceData(), CObjMgr_LocalQueryData::GetSequenceBlk(), and CObjMgrFree_LocalQueryData::GetSequenceBlk().
◆ Reset() [4/31]
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inline |
Definition at line 331 of file blast_aux.hpp.
Referenced by CBlastOptionsLocal::x_Copy_CBlastDatabaseOptions().
◆ Reset() [5/31]
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inline |
Definition at line 338 of file blast_aux.hpp.
Referenced by CEffectiveSearchSpacesMemento::CEffectiveSearchSpacesMemento(), CBlastOptionsLocal::x_Copy_CBlastEffectiveLengthsOptions(), and CEffectiveSearchSpacesMemento::~CEffectiveSearchSpacesMemento().
◆ Reset() [6/31]
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Definition at line 340 of file blast_aux.hpp.
◆ Reset() [7/31]
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Definition at line 323 of file blast_aux.hpp.
Referenced by CBlastOptionsLocal::CBlastOptionsLocal(), and CBlastOptionsLocal::x_Copy_CBlastExtensionOptions().
◆ Reset() [8/31]
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Definition at line 324 of file blast_aux.hpp.
◆ Reset() [9/31]
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Definition at line 342 of file blast_aux.hpp.
◆ Reset() [10/31]
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Definition at line 326 of file blast_aux.hpp.
Referenced by CBlastOptionsLocal::CBlastOptionsLocal(), and CBlastOptionsLocal::x_Copy_CBlastHitSavingOptions().
◆ Reset() [11/31]
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Definition at line 328 of file blast_aux.hpp.
◆ Reset() [12/31]
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Definition at line 343 of file blast_aux.hpp.
◆ Reset() [13/31]
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Definition at line 318 of file blast_aux.hpp.
Referenced by CBlastOptionsLocal::CBlastOptionsLocal(), and CBlastOptionsLocal::x_Copy_CBlastInitialWordOptions().
◆ Reset() [14/31]
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Definition at line 320 of file blast_aux.hpp.
◆ Reset() [15/31]
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Definition at line 354 of file blast_aux.hpp.
◆ Reset() [16/31]
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Definition at line 311 of file blast_aux.hpp.
Referenced by CPhiblastTestFixture::CPhiblastTestFixture(), CObjMgr_LocalQueryData::GetQueryInfo(), and CObjMgrFree_LocalQueryData::GetQueryInfo().
◆ Reset() [17/31]
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inline |
Definition at line 333 of file blast_aux.hpp.
Referenced by BOOST_AUTO_TEST_CASE(), CPssmEngine::x_InitializeScoreBlock(), and CPhiblastTestFixture::~CPhiblastTestFixture().
◆ Reset() [18/31]
|
inline |
Definition at line 334 of file blast_aux.hpp.
Referenced by CBlastOptionsLocal::CBlastOptionsLocal(), and CBlastOptionsLocal::x_Copy_CBlastScoringOptions().
◆ Reset() [19/31]
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inline |
Definition at line 335 of file blast_aux.hpp.
◆ Reset() [20/31]
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Definition at line 355 of file blast_aux.hpp.
◆ Reset() [21/31]
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Definition at line 350 of file blast_aux.hpp.
Referenced by RandomlyFailingMockSeqSrcTestFixture::RandomlyFailingMockSeqSrcTestFixture(), and RandomlyFailingMockSeqSrcTestFixture::~RandomlyFailingMockSeqSrcTestFixture().
◆ Reset() [22/31]
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inline |
Definition at line 351 of file blast_aux.hpp.
◆ Reset() [23/31]
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inline |
Definition at line 314 of file blast_aux.hpp.
Referenced by CBlastOptionsLocal::CBlastOptionsLocal(), and CBlastOptionsLocal::x_Copy_CLookupTableOptions().
◆ Reset() [24/31]
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inline |
Definition at line 315 of file blast_aux.hpp.
Referenced by CPhiblastTestFixture::~CPhiblastTestFixture().
◆ Reset() [25/31]
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Definition at line 330 of file blast_aux.hpp.
Referenced by CBlastOptionsLocal::x_Copy_CPSIBlastOptions().
◆ Reset() [26/31]
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Definition at line 347 of file blast_aux.hpp.
Referenced by CDeltaBlast::Run().
◆ Reset() [27/31]
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inline |
Definition at line 348 of file blast_aux.hpp.
◆ Reset() [28/31]
Definition at line 346 of file blast_aux.hpp.
◆ Reset() [29/31]
Definition at line 345 of file blast_aux.hpp.
◆ Reset() [30/31]
|
inline |
Definition at line 312 of file blast_aux.hpp.
Referenced by CBlastOptionsLocal::CBlastOptionsLocal(), and CBlastOptionsLocal::x_Copy_CQuerySetUpOptions().
◆ Reset() [31/31]
|
inline |
Definition at line 357 of file blast_aux.hpp.
◆ ResetBlastSeqSrcIteration()
| void CLocalDbAdapter::ResetBlastSeqSrcIteration | ( | ) |
This method should be called so that if the implementation has an internal "bookmark" of the chunks of the database it has assigned to different threads, this can be reset at the start of a PSI-BLAST iteration (or when reusing the same object to iterate over the database/subjects when the query is split).
This method should be called before calling MakeSeqSrc() to ensure proper action on retrieving the BlastSeqSrc (in some cases it might cause a re-construction of the underlying BlastSeqSrc implementation). Note that in some cases, this operation might not apply
Definition at line 100 of file local_db_adapter.cpp.
References BlastSeqSrcResetChunkIterator(), and CLocalDbAdapter::m_SeqSrc.
Referenced by CPsiBlastImpl::Run().
◆ ResetMessages()
| void CBlastAppDiagHandler::ResetMessages | ( | void | ) |
Reset messgae buffer, erase all saved message.
Definition at line 1174 of file blast_aux.cpp.
References DEFINE_STATIC_MUTEX, and CBlastAppDiagHandler::m_messages.
Referenced by CPsiBlastApp::DoIterations(), CBlastAppDiagHandler::DoNotSaveMessages(), CDeltaBlastApp::DoPsiBlastIterations(), CBlastnNode::Main(), CBlastpNode::Main(), CBlastxNode::Main(), CRPSBlastNode::Main(), CRPSTBlastnNode::Main(), CTblastnNode::Main(), CDeltaBlastApp::Run(), CTblastxApp::Run(), CPsiBlastApp::x_RunLocalPsiBlastIterations(), CBlastnApp::x_RunMTBySplitDB(), CBlastpApp::x_RunMTBySplitDB(), CBlastxApp::x_RunMTBySplitDB(), CRPSBlastApp::x_RunMTBySplitDB(), CRPSTBlastnApp::x_RunMTBySplitDB(), and CTblastnApp::x_RunMTBySplitDB().
◆ ResetValue()
|
inline |
Remove any objects matching this Blast4 field object.
The given field object represents a Blast4 field to remove from the list of remote options.
- Parameters
-
opt Field object representing option to remove.
Definition at line 133 of file blast_options_cxx.cpp.
References CBlastOptionsRemote::x_ResetValue().
Referenced by CBlastOptions::SetFilterString(), CBlastOptions::SetWindowMaskerDatabase(), and CBlastOptions::SetWindowMaskerTaxId().
◆ Run() [1/19]
|
virtual |
Perform BLAST search Assuming N queries and M subjects, the structure of the returned vector is as follows, with types indicated in parenthesis: TSeqAlignVector = [ {Results for query 1 and subject 1 (Seq-align-set)}, {Results for query 1 and subject 2 (Seq-align-set)}, ...
{Results for query 1 and subject M (Seq-align-set)}, {Results for query 2 and subject 1 (Seq-align-set)}, {Results for query 2 and subject 2 (Seq-align-set)}, ... {Results for query 2 and subject M (Seq-align-set)}, {Results for query 3 and subject 1 (Seq-align-set)}, ... {Results for query N and subject M (Seq-align-set)} ]
Definition at line 173 of file bl2seq.cpp.
References CBl2Seq::CSearchResultSet2TSeqAlignVector(), CBl2Seq::m_Results, CRef< C, Locker >::NotEmpty(), CBl2Seq::RunEx(), and CBl2Seq::x_BuildAncillaryData().
Referenced by BOOST_AUTO_TEST_CASE(), CMultiAligner::x_AlignFillerBlocks(), CBLASTSeqToolJob::x_CreateProjectItems(), CSplignJob::x_CreateProjectItems(), CSplignApp::x_GetBl2SeqHits(), and CProSplignJob::x_SetupAndRuntBlastn().
◆ Run() [2/19]
| CRef< CSearchResultSet > CDeltaBlast::Run | ( | void | ) |
Run the DELTA-BLAST engine with one iteration.
Definition at line 83 of file deltablast.cpp.
References _ASSERT, BlastQueryInfo::contexts, CRef< C, Locker >::Empty(), CPSIBlastOptions::Get(), CLocalDbAdapter::GetDatabaseName(), CDeltaBlastOptionsHandle::GetDomainInclusionThreshold(), CBlastProteinOptionsHandle::GetGapExtensionCost(), CBlastProteinOptionsHandle::GetGapOpeningCost(), CBlastProteinOptionsHandle::GetMatrixName(), CRef< C, Locker >::GetNonNullPointer(), CConstRef< C, Locker >::GetNonNullPointer(), CThreadable::GetNumberOfThreads(), ILocalQueryData::GetNumQueries(), CBlastOptionsHandle::GetOptions(), ILocalQueryData::GetQueryInfo(), ILocalQueryData::GetSeq_loc(), ILocalQueryData::GetSequenceBlk(), i, PSIBlastOptions::inclusion_ethresh, CLocalDbAdapter::IsBlastDb(), CDeltaBlast::m_DomainDb, CDeltaBlast::m_DomainResults, CDeltaBlast::m_Options, CDeltaBlast::m_Pssm, CDeltaBlast::m_Queries, CDeltaBlast::m_Results, CDeltaBlast::m_Subject, IQueryFactory::MakeLocalQueryData(), NON_CONST_ITERATE, NULL, PSIBlastOptionsNew(), PSIDiagnosticsRequestNewEx(), CSearchResultSet::push_back(), BlastContextInfo::query_length, BlastContextInfo::query_offset, CPSIDiagnosticsRequest::Reset(), CRef< C, Locker >::Reset(), results, CPsiBl2Seq::Run(), CPsiBlast::Run(), BLAST_SequenceBlk::sequence_start, CThreadable::SetNumberOfThreads(), CSearchResultSet::size(), and CDeltaBlast::x_FindDomainHits().
Referenced by BOOST_AUTO_TEST_CASE().
◆ Run() [3/19]
| CRef< CSearchResultSet > CLocalBlast::Run | ( | void | ) |
Executes the search.
Definition at line 167 of file local_blast.cpp.
References _ASSERT, BLAST_PROF_MARK2, BLASTERR_DB_MEMORY_MAP, BLASTERR_DB_OPEN_FILES, BlastErrorCode2String(), CBlastPrelimSearch::CheckInternalData(), TSearchMessages::Combine(), CBlastException::eCoreBlastError, eDatabaseSearch, CSeqDBException::eOpenFileErr, eSequenceComparison, CException::GetErrCode(), CBlastPrelimSearch::GetFilteredQueryRegions(), CThreadable::GetNumberOfThreads(), ILocalQueryData::GetNumQueries(), ILocalQueryData::GetQueryMessages(), CBlastPrelimSearch::GetSearchMessages(), CBlastTracebackSearch::GetSearchMessages(), ILocalQueryData::GetSeq_loc(), i, CLocalDbAdapter::IsBlastDb(), CLocalDbAdapter::IsDbScanMode(), CLocalBlast::m_batch_num_str, CLocalBlast::m_InternalData, CLocalBlast::m_LocalDbAdapter, CLocalBlast::m_Messages, CLocalBlast::m_Opts, CLocalBlast::m_PrelimSearch, CLocalBlast::m_QueryFactory, CLocalBlast::m_SeqInfoSrc, SInternalData::m_SeqSrc, CLocalBlast::m_TbackSearch, IQueryFactory::MakeLocalQueryData(), CLocalDbAdapter::MakeSeqInfoSrc(), msg(), NCBI_THROW, CRef< C, Locker >::NotEmpty(), NULL, CRef< C, Locker >::Reset(), CBlastPrelimSearch::Run(), CBlastTracebackSearch::Run(), s_InitSeqInfoSrc(), CSearchResultSet::SetFilteredQueryRegions(), CBlastPrelimSearch::SetNumberOfThreads(), CThreadable::SetNumberOfThreads(), CBlastTracebackSearch::SetResultType(), IBlastSeqInfoSrc::Size(), and CException::what().
Referenced by Blast_FindRepeatFilterLoc(), BOOST_AUTO_TEST_CASE(), CBlastAligner::GenerateAlignments(), CBlastnNode::Main(), CBlastpNode::Main(), CBlastxNode::Main(), CTblastnNode::Main(), RpsTestFixture::NuclSearch(), CLocalSeqSearch::Run(), CIgBlast::Run(), CTblastxApp::Run(), CRMBlastnApp::Run(), CVectorScreen::Run(), CBlastKmerSearch::Run(), CBlastDemoApplication::Run(), CBl2Seq::RunEx(), s_RunLocalVDBSearch(), CDeltaBlast::x_FindDomainHits(), CMultiAligner::x_FindRPSHits(), CVecscreenRun::x_RunBlast(), CPsiBlastApp::x_RunLocalPsiBlastIterations(), CBlastnApp::x_RunMTBySplitDB(), CBlastpApp::x_RunMTBySplitDB(), CBlastxApp::x_RunMTBySplitDB(), and CTblastnApp::x_RunMTBySplitDB().
◆ Run() [4/19]
|
virtual |
Run the search.
Implements ISearch.
Definition at line 94 of file local_search.cpp.
References CRef< C, Locker >::Empty(), CConstRef< C, Locker >::Empty(), CLocalSeqSearch::m_Database, CLocalSeqSearch::m_LocalBlast, CLocalSeqSearch::m_QueryFactory, CLocalSeqSearch::m_SearchOpts, NCBI_THROW, CRef< C, Locker >::Reset(), and CLocalBlast::Run().
◆ Run() [5/19]
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virtual |
Run a single iteration of the search.
Implements ISearch.
Definition at line 156 of file local_search.cpp.
References CConstRef< C, Locker >::Empty(), CLocalPssmSearch::m_Pssm, CLocalPssmSearch::m_SearchOpts, CLocalPssmSearch::m_Subject, NCBI_THROW, query, CConstRef< C, Locker >::Reset(), and CPsiBlast::Run().
◆ Run() [6/19]
| CRef< SInternalData > CBlastPrelimSearch::Run | ( | void | ) |
Borrow the internal data and results results.
Definition at line 206 of file prelim_stage.cpp.
References _ASSERT, _TRACE, TSearchMessages::AddMessageAllQueries(), BlastErrorCode2String(), BlastHSPStreamMerge(), BlastSeqSrcGetNumSeqs(), BlastSeqSrcResetChunkIterator(), CSetupFactory::CreateScoreBlock(), CBlastOptions::CreateSnapshot(), eBlastSevWarning, ILocalQueryData::FlushSequenceData(), CSplitQueryBlk::GetCStruct(), GetDbIndexRunSearchFn(), GetDbIndexSetUsingThreadsFn(), CException::GetMsg(), CQuerySplitter::GetNumberOfChunks(), CThreadable::GetNumberOfThreads(), CQuerySplitter::GetQueryFactoryForChunk(), ILocalQueryData::GetSequenceBlk(), i, CThreadable::IsMultiThreaded(), CQuerySplitter::IsQuerySplit(), kBlastErrMsg_CantCalculateUngappedKAParams, kBlastMessageNoContext, SInternalData::m_HspStream, CBlastPrelimSearch::m_InternalData, CBlastPrelimSearch::m_Messages, CBlastPrelimSearch::m_Options, SInternalData::m_Queries, CBlastPrelimSearch::m_QueryFactory, SInternalData::m_SeqSrc, IQueryFactory::MakeLocalQueryData(), msg(), NCBI_THROW, NPOS, NULL, CQuerySplitter::Split(), SplitQuery_CreateChunkData(), SplitQuery_SetEffectiveSearchSpace(), and CBlastPrelimSearch::x_LaunchMultiThreadedSearch().
Referenced by BOOST_AUTO_TEST_CASE(), CLocalBlast::Run(), CPsiBlastImpl::Run(), CBlastPrelimSearch::Run(), and CMagicBlast::x_Run().
◆ Run() [7/19]
| CRef< CSearchResultSet > CPsiBl2Seq::Run | ( | void | ) |
Run the PSI-BLAST 2 Sequences engine.
Definition at line 92 of file psibl2seq.cpp.
References eSequenceComparison, CPsiBl2Seq::m_Impl, CPsiBlastImpl::Run(), and CPsiBlastImpl::SetResultType().
Referenced by CdBlaster::blast(), BOOST_AUTO_TEST_CASE(), CSimpleB2SWrapper::DoBlast2Seqs(), CdBlaster::psiBlast(), and CDeltaBlast::Run().
◆ Run() [8/19]
| CRef< CSearchResultSet > CPsiBlast::Run | ( | void | ) |
Run the PSI-BLAST engine for one iteration.
Definition at line 95 of file psiblast.cpp.
References CThreadable::GetNumberOfThreads(), CPsiBlast::m_Impl, CPsiBlastImpl::Run(), and CThreadable::SetNumberOfThreads().
Referenced by BOOST_AUTO_TEST_CASE(), CDeltaBlastApp::DoPsiBlastIterations(), CTblastnNode::Main(), CDeltaBlast::Run(), CLocalPssmSearch::Run(), s_RunPsiVDBSearch(), CPsiBlastApp::x_RunLocalPsiBlastIterations(), and CTblastnApp::x_RunMTBySplitDB().
◆ Run() [9/19]
| CRef< CPssmWithParameters > CPssmEngine::Run | ( | void | ) |
Runs the PSSM engine to compute the PSSM.
Definition at line 285 of file pssm_engine.cpp.
References CPssmEngine::m_PssmInput, CPssmEngine::m_PssmInputCdd, CPssmEngine::m_PssmInputFreqRatios, NCBI_THROW, CPssmEngine::x_CreatePssmFromCDD(), CPssmEngine::x_CreatePssmFromFreqRatios(), and CPssmEngine::x_CreatePssmFromMsa().
Referenced by BOOST_AUTO_TEST_CASE(), CreateBlastMatrix(), PssmMaker::make(), PsiBlastComputePssmFromAlignment(), PsiBlastComputePssmScores(), CPsiBlastArgs::x_CreatePssmFromMsa(), and CMakeProfileDBApp::x_RPSUpdateStatistics().
◆ Run() [10/19]
|
virtual |
Run the search.
Implements ISearch.
Definition at line 146 of file remote_search.cpp.
References CRemoteBlast::GetWarningVector(), CRemoteSeqSearch::m_RemoteBlast, CRemoteSeqSearch::m_Warnings, CRef< C, Locker >::Reset(), s_BuildResultsRemote(), CRemoteBlast::SubmitSync(), and CRemoteSeqSearch::x_RemoteBlast().
◆ Run() [11/19]
|
virtual |
Run the search.
Implements ISearch.
Definition at line 341 of file remote_search.cpp.
References CRemoteBlast::GetWarningVector(), CRemotePssmSearch::m_RemoteBlast, CRemotePssmSearch::m_Warnings, CRef< C, Locker >::Reset(), s_BuildResultsRemote(), CRemoteBlast::SubmitSync(), and CRemotePssmSearch::x_RemoteBlast().
◆ Run() [12/19]
| CRef< CSearchResultSet > CBlastTracebackSearch::Run | ( | void | ) |
Run the traceback search.
Definition at line 191 of file traceback_stage.cpp.
References _ASSERT, Blast_HSPResultsFree(), Blast_ProgramIsPhiBlast(), Blast_RunTracebackSearchWithInterrupt(), BlastBuildSearchResultSet(), eBlastTypePsiBlast, CSBlastProgress::Get(), CBlastOptions::GetGappedMode(), ILocalQueryData::GetNumQueries(), CBlastOptions::GetOutOfFrameMode(), ILocalQueryData::GetSeq_loc(), BlastHitSavingOptions::hitlist_size, i, CThreadable::kMinNumThreads, SDatabaseScanData::kNoPhiBlastPattern, LocalBlastResults2SeqAlign(), CBlastOptionsMemento::m_DbOpts, CBlastTracebackSearch::m_DBscanInfo, CBlastOptionsMemento::m_EffLenOpts, CBlastOptionsMemento::m_ExtnOpts, SInternalData::m_FnInterrupt, CBlastOptionsMemento::m_HitSaveOpts, SInternalData::m_HspStream, CBlastTracebackSearch::m_InternalData, SInternalData::m_LookupTable, CBlastTracebackSearch::m_Messages, SDatabaseScanData::m_NumPatOccurInDB, CThreadable::m_NumThreads, CBlastTracebackSearch::m_Options, CBlastTracebackSearch::m_OptsMemento, CBlastOptionsMemento::m_ProgramType, SInternalData::m_ProgressMonitor, CBlastOptionsMemento::m_PSIBlastOpts, SInternalData::m_Queries, CBlastTracebackSearch::m_QueryFactory, SInternalData::m_QueryInfo, CBlastTracebackSearch::m_ResultType, SInternalData::m_RpsData, SInternalData::m_ScoreBlk, CBlastOptionsMemento::m_ScoringOpts, CBlastTracebackSearch::m_SeqInfoSrc, SInternalData::m_SeqSrc, IQueryFactory::MakeLocalQueryData(), NCBI_THROW, NULL, SPHIPatternSearchBlk::num_patterns_db, SBlastHitsParameters::prelim_hitlist_size, CRef< C, Locker >::Reset(), SBlastHitsParametersFree(), SBlastHitsParametersNew(), and WrapStruct().
Referenced by BOOST_AUTO_TEST_CASE(), CLocalBlast::Run(), CPsiBlastImpl::Run(), and CTracebackSearchTestFixture::x_Traceback().
◆ Run() [13/19]
| CRef< CSearchResultSet > CIgBlast::Run | ( | void | ) |
Run the Ig-BLAST engine.
Definition at line 356 of file igblast.cpp.
References _ASSERT, eBlastn, eBlastp, CRef< C, Locker >::Empty(), eNoCompositionBasedStats, CDiagContext::Extra(), GetDiagContext(), CRemoteBlast::GetResultSet(), CRemoteBlast::GetRID(), CIgBlastOptions::m_CustomInternalData, CIgBlastOptions::m_D_penalty, CIgBlastOptions::m_Db, CIgBlastOptions::m_DetectOverlap, CIgBlast::m_EntrezQuery, CIgBlastOptions::m_ExtendAlign3end, CIgBlastOptions::m_ExtendAlign5end, CIgBlast::m_IgOptions, CIgBlast::m_IsLocal, CIgBlastOptions::m_IsProtein, CIgBlastOptions::m_J_penalty, CIgBlast::m_LocalDb, CIgBlastOptions::m_MinJLength, CIgBlastOptions::m_MinVLength, CIgBlastOptions::m_NumAlign, CIgBlast::m_NumThreads, CIgBlast::m_Options, CIgBlast::m_RemoteDb, CIgBlast::m_RID, CIgBlast::m_Subject, NcbiEmptyString, CRef< C, Locker >::NotEmpty(), CDiagContext_Extra::Print(), CRef< C, Locker >::Reset(), result, results, CLocalBlast::Run(), CIgBlast::s_AppendResults(), CIgBlast::s_SortResultsByEvalue(), CBlastOptions::SetCompositionBasedStats(), CRemoteBlast::SetEntrezQuery(), CBlastOptionsHandle::SetEvalueThreshold(), CBlastOptions::SetGapExtensionCost(), CBlastOptions::SetGapOpeningCost(), CBlastOptionsHandle::SetHitlistSize(), CBlastOptions::SetMismatchPenalty(), CThreadable::SetNumberOfThreads(), CBlastOptionsHandle::SetOptions(), CBlastOptions::SetWordSize(), CRemoteBlast::Submit(), CIgBlast::x_AnnotateC(), CIgBlast::x_AnnotateD(), CIgBlast::x_AnnotateDJ(), CIgBlast::x_AnnotateDomain(), CIgBlast::x_AnnotateJ(), CIgBlast::x_AnnotateV(), CIgBlast::x_ConvertResultType(), CIgBlast::x_ExtendAlign3end(), CIgBlast::x_ExtendAlign5end(), CIgBlast::x_ProcessCResult(), CIgBlast::x_ProcessDGeneResult(), CIgBlast::x_ProcessDJResult(), CIgBlast::x_ScreenByAlignLength(), CIgBlast::x_SetAnnotation(), CIgBlast::x_SetChainType(), CIgBlast::x_SetupCRegionSearch(), CIgBlast::x_SetupDbSearch(), CIgBlast::x_SetupDJSearch(), CIgBlast::x_SetupNoOverlapDSearch(), and CIgBlast::x_SetupVSearch().
Referenced by CIgBlastnApp::CIgWorker::Main(), and CIgBlastpApp::Run().
◆ Run() [14/19]
| CRef< CSearchResultSet > CPsiBlastImpl::Run | ( | void | ) |
Run the PSI-BLAST engine for one iteration.
Definition at line 122 of file psiblast_impl.cpp.
References _ASSERT, CThreadable::GetNumberOfThreads(), CBlastOptionsHandle::GetOptions(), CBlastPrelimSearch::GetSearchMessages(), CPsiBlastImpl::m_OptsHandle, CPsiBlastImpl::m_Pssm, CPsiBlastImpl::m_Query, CPsiBlastImpl::m_Results, CPsiBlastImpl::m_ResultType, SInternalData::m_ScoreBlk, CPsiBlastImpl::m_Subject, CLocalDbAdapter::MakeSeqInfoSrc(), CLocalDbAdapter::MakeSeqSrc(), CRef< C, Locker >::NotEmpty(), CLocalDbAdapter::ResetBlastSeqSrcIteration(), CBlastPrelimSearch::Run(), CBlastTracebackSearch::Run(), CPssm::SetH(), CPssm::SetHUngapped(), CPssm::SetKappa(), CPssm::SetKappaUngapped(), CPssm::SetLambda(), CPssm::SetLambdaUngapped(), CBlastPrelimSearch::SetNumberOfThreads(), CThreadable::SetNumberOfThreads(), and CBlastTracebackSearch::SetResultType().
Referenced by CPsiBl2Seq::Run(), and CPsiBlast::Run().
◆ Run() [15/19]
|
pure virtual |
Run the search to completion.
Implemented in CRemotePssmSearch, CRemoteSeqSearch, CLocalPssmSearch, and CLocalSeqSearch.
◆ Run() [16/19]
| CSeedTop::TSeedTopResults CSeedTop::Run | ( | CBioseq_Handle & | b_hdl | ) |
Definition at line 182 of file seedtop.cpp.
References CBlastOptionsFactory::Create(), eBlastp, CBioseq_Handle::GetScope(), CBioseq_Handle::GetSeqId(), CSeedTop::Run(), CSeq_loc::SetId(), CSeq_loc::SetWhole(), and subject.
◆ Run() [17/19]
| CSeedTop::TSeedTopResults CSeedTop::Run | ( | CRef< CLocalDbAdapter > | db | ) |
Definition at line 102 of file seedtop.cpp.
References _ASSERT, BLAST_SEQSRC_EOF, BLAST_SEQSRC_ERROR, BlastSeqSrcGetNumSeqs(), BlastSeqSrcGetSequence(), BlastSeqSrcIteratorFree(), BlastSeqSrcIteratorNewEx(), BlastSeqSrcIteratorNext(), BlastSeqSrcReleaseSequence(), BlastSequenceBlkFree(), calloc(), eBlastEncodingProtein, BlastSeqSrcGetSeqArg::encoding, GetOffsetArraySize(), GetSequenceLengthAndId(), i, ITERATE, CSeedTop::m_Lookup, CSeedTop::m_Units, CLocalDbAdapter::MakeSeqInfoSrc(), CLocalDbAdapter::MakeSeqSrc(), MAX, NULL, BlastSeqSrcGetSeqArg::oid, BlastOffsetPair::phi_offsets, PHIBlastScanSubject(), BlastOffsetPair::s_end, BlastOffsetPair::s_start, BlastSeqSrcGetSeqArg::seq, BLAST_SequenceBlk::sequence, sfree, and CSeedTop::x_GetPatternRanges().
Referenced by CSeedTopApp::Run(), and CSeedTop::Run().
◆ Run() [18/19]
Definition at line 368 of file prelim_stage.cpp.
References l(), CBlastPrelimSearch::Run(), and CBlastPrelimSearch::x_BuildStdSegList().
◆ Run() [19/19]
| CRef< CSeq_align_set > CMagicBlast::Run | ( | void | ) |
Run the RNA-Seq mapping.
Definition at line 70 of file magicblast.cpp.
References Blast_MappingResultsFree(), Blast_MappingResultsNew(), BlastHSPStreamMappingClose(), SInternalData::m_HspStream, CMagicBlast::m_InternalData, CRef< C, Locker >::Reset(), results, WrapStruct(), CMagicBlast::x_BuildSeqAlignSet(), and CMagicBlast::x_Run().
Referenced by BOOST_AUTO_TEST_CASE().
◆ RunEx() [1/2]
| CRef< CSearchResultSet > CBl2Seq::RunEx | ( | void | ) |
Performs the same functionality as Run(), but it returns a different data type.
- Note
- the number of CSearchResultSet::value_type objects in this function's return value will be (number of queries * number of subjects)
Definition at line 196 of file bl2seq.cpp.
References _ASSERT, Blast_DiagnosticsCopy(), CLocalBlast::GetSearchMessages(), CBl2Seq::m_Blast, SInternalData::m_Diagnostics, CLocalBlast::m_InternalData, CBl2Seq::m_Messages, CBl2Seq::m_Results, CBl2Seq::mi_pDiagnostics, CRef< C, Locker >::NotEmpty(), CLocalBlast::Run(), and CBl2Seq::x_InitCLocalBlast().
Referenced by BOOST_AUTO_TEST_CASE(), CBl2Seq::Run(), CMultiAligner::x_AlignClusterQueries(), and CIgBlast::x_AnnotateDomain().
◆ RunEx() [2/2]
| CRef< CMagicBlastResultSet > CMagicBlast::RunEx | ( | void | ) |
Definition at line 87 of file magicblast.cpp.
References Blast_MappingResultsFree(), Blast_MappingResultsNew(), BlastHSPStreamMappingClose(), SInternalData::m_HspStream, CMagicBlast::m_InternalData, CRef< C, Locker >::Reset(), results, WrapStruct(), CMagicBlast::x_BuildResultSet(), and CMagicBlast::x_Run().
Referenced by BOOST_AUTO_TEST_CASE(), and CMagicBlastThread::Main().
◆ RunSimple()
| BlastHSPResults * CBlastTracebackSearch::RunSimple | ( | ) |
Runs the traceback but only returns the HSP's and not the Seq-Align.
Definition at line 295 of file traceback_stage.cpp.
References _ASSERT, Blast_ProgramIsPhiBlast(), Blast_RunTracebackSearchWithInterrupt(), eBlastTypePsiBlast, CSBlastProgress::Get(), BlastHitSavingOptions::hitlist_size, CThreadable::kMinNumThreads, SDatabaseScanData::kNoPhiBlastPattern, CBlastOptionsMemento::m_DbOpts, CBlastTracebackSearch::m_DBscanInfo, CBlastOptionsMemento::m_EffLenOpts, CBlastOptionsMemento::m_ExtnOpts, SInternalData::m_FnInterrupt, CBlastOptionsMemento::m_HitSaveOpts, SInternalData::m_HspStream, CBlastTracebackSearch::m_InternalData, SInternalData::m_LookupTable, SDatabaseScanData::m_NumPatOccurInDB, CThreadable::m_NumThreads, CBlastTracebackSearch::m_OptsMemento, CBlastOptionsMemento::m_ProgramType, SInternalData::m_ProgressMonitor, CBlastOptionsMemento::m_PSIBlastOpts, SInternalData::m_Queries, SInternalData::m_QueryInfo, SInternalData::m_RpsData, SInternalData::m_ScoreBlk, CBlastOptionsMemento::m_ScoringOpts, SInternalData::m_SeqSrc, NCBI_THROW, NULL, SPHIPatternSearchBlk::num_patterns_db, SBlastHitsParameters::prelim_hitlist_size, SBlastHitsParametersFree(), and SBlastHitsParametersNew().
Referenced by BOOST_AUTO_TEST_CASE().
◆ s_AddMask()
|
static |
Adds seqloc_frames to mask.
- Parameters
-
prog BLAST program [in] mask data structure to add the mask to [in|out] query_index index of the query for which to add the mask [in] seqloc_frames mask to add [in] strand strand on which the mask is being added [in] query_length length of the query [in]
Definition at line 320 of file blast_setup_cxx.cpp.
References _ASSERT, abort(), assert, BLAST_ContextToFrame(), Blast_ProgramIsPhiBlast(), Blast_QueryIsNucleotide(), Blast_QueryIsTranslated(), eBlastTypeBlastx, CSeqLocInfo::eFrameMinus1, CSeqLocInfo::eFramePlus1, eNa_strand_both, eNa_strand_minus, eNa_strand_plus, GetNumberOfContexts(), i, mask, prog, CBlastQueryFilteredFrames::QueryHasMultipleFrames(), CBlastQueryFilteredFrames::Release(), s_ComputeStartEndContexts(), total_size, and CBlastQueryFilteredFrames::UseProteinCoords().
Referenced by SetupQueries_OMF().
◆ s_AddScoresToSeqAlign()
|
static |
Given an HSP structure, creates a list of scores and inserts them into a Seq-align.
- Parameters
-
seqalign Seq-align object to fill [in] [out] hsp An HSP structure [in] gi_list List of GIs for the subject sequence.
Definition at line 1253 of file blast_seqalign.cpp.
References s_BuildScoreList(), and CSeq_align_Base::SetScore().
Referenced by BLASTHspListToSeqAlign().
◆ s_AddUserObjectToSeqAlign()
|
static |
Produce UserObject with Seq-ids to limit formatting to ("use_this_gi")
- Parameters
-
seqalign Seq-align object to fill in [in][out] seqid_list list of strings with seqids [in]
Definition at line 1234 of file blast_seqalign.cpp.
References CUser_object::AddField(), CSeq_align_Base::SetExt(), and CUser_object_Base::SetType().
Referenced by BLASTHspListToSeqAlign(), and BLASTUngappedHspListToSeqAlign().
◆ s_AdjustFirstContext()
|
static |
Adjust first context depending on the first query strand.
Definition at line 127 of file blast_setup_cxx.cpp.
References _ASSERT, Blast_QueryIsTranslated(), eBlastTypeBlastn, eBlastTypeMapping, eNa_strand_minus, eNa_strand_unknown, BlastQueryInfo::first_context, IBlastQuerySource::GetStrand(), prog, s_BlastSetup_GetStrand(), and true.
Referenced by SetupQueryInfo_OMF().
◆ s_AdjustFrequencyRatiosMatrixToMatchScoreMatrix()
|
static |
After creating the PSSM from frequency ratios, adjust the frequency ratios matrix to match the dimensions of the score matrix.
- Parameters
-
pssm matrix to adjust [in|out]
Definition at line 440 of file psiblast_aux_priv.cpp.
References _ASSERT, and BLASTAA_SIZE.
Referenced by PsiBlastComputePssmScores().
◆ s_AdjustNegativeSubjFrameInBlastn()
|
static |
This function changes the subject frame for HSPs if the program is blastn and the subject was specified with a negative strand.
This is necessary because the engine doesn't handle negative strands in subjects for blastn (it does for translated searches).
- Parameters
-
subj_strand Strand for the subject sequence [in] program BLAST program [in] hsp_list list of HSPs to possibly adjust [in]
Definition at line 1722 of file blast_seqalign.cpp.
References _ASSERT, eBlastTypeBlastn, eBlastTypeMapping, eNa_strand_minus, BlastSeg::frame, BlastHSPList::hsp_array, BlastHSPList::hspcnt, and BlastHSP::subject.
Referenced by s_BLAST_OneSubjectResults2CSeqAlign().
◆ s_AppendResults()
|
staticprivate |
Append blast results to the final results.
Definition at line 1992 of file igblast.cpp.
References TQueryMessages::Combine(), CRef< C, Locker >::Empty(), CSearchResults::GetErrors(), GetSeqId(), i, ITERATE, CIgBlastResults::m_NumActualC, CIgBlastResults::m_NumActualD, CIgBlastResults::m_NumActualJ, CIgBlastResults::m_NumActualV, CSearchResultSet::push_back(), query, r(), CRef< C, Locker >::Reset(), result, results, s_SeqAlignInSet(), CSeq_align_set_Base::Set(), and CIgBlastResults::SetSeqAlign().
Referenced by CIgBlast::Run().
◆ s_AreSequencesEqual()
|
static |
Returns true iff sequence is identical to query.
Definition at line 170 of file msa_pssm_input.cpp.
References CAliasBase< TPrim >::Get(), i, query, and ncbi::grid::netcache::search::fields::size.
Referenced by CPsiBlastInputClustalW::x_ExtractQueryForPssm().
◆ s_BLAST_OneSubjectResults2CSeqAlign()
|
static |
Extracts results from the BlastHSPResults structure for only one subject sequence, identified by its index, and converts them into a vector of CSeq_align_set objects.
Returns one vector element per query sequence; The CSeq_align_set consists of as many CSeq_align-s as there are HSPs in the BlastHSPList for each query-subject pair
- Parameters
-
results results from running the BLAST algorithm [in] query_data All query sequences [in] seqinfo_src Source of subject sequences information [in] prog type of BLAST program [in] subj_idx Index of this subject sequence in a set [in] is_gapped Is this a gapped search? [in] is_ooframe Is it a search with out-of-frame gapping? [in]
- Returns
- Vector of seqalign sets (one set per query sequence).
Definition at line 1752 of file blast_seqalign.cpp.
References _ASSERT, Blast_HSPListSortByEvalue(), BLASTHspListToSeqAlign(), BLASTUngappedHspListToSeqAlign(), CreateEmptySeq_align_set(), BlastSeg::end, GetFilteredRedundantSeqids(), CSeq_loc::GetId(), IBlastSeqInfoSrc::GetMasks(), ILocalQueryData::GetNumQueries(), ILocalQueryData::GetSeq_loc(), ILocalQueryData::GetSeqLength(), IBlastSeqInfoSrc::GetSeqLoc(), GetSequenceLengthAndId(), BlastHSPList::hsp_array, BlastHSPList::hspcnt, BlastHitList::hsplist_array, BlastHitList::hsplist_count, i, CSeq_id_Base::IsGi(), NON_CONST_ITERATE, NULL, BlastSeg::offset, BlastHSPList::oid, prog, RemapToQueryLoc(), CRef< C, Locker >::Reset(), results, s_AdjustNegativeSubjFrameInBlastn(), s_RemapToSubjectLoc(), SerialAssign(), CSeq_align_set_Base::Set(), CRange_Base::SetFrom(), CRange_Base::SetTo(), and BlastHSP::subject.
Referenced by s_BlastResults2SeqAlignSequenceCmp_OMF().
◆ s_BlastHSP2SeqAlign()
|
static |
Converts a traceback editing block to a Seq-align, provided the 2 sequence identifiers.
- Parameters
-
program Type of BLAST program [in] hsp Internal HSP structure [in] id1 Query sequence identifier [in] id2 Subject sequence identifier [in] query_length Length of query sequence [in] subject_length Length of subject sequence [in]
- Returns
- Resulting Seq-align object.
Definition at line 660 of file blast_seqalign.cpp.
References _ASSERT, eBlastTypeBlastx, eBlastTypePsiTblastn, eBlastTypeRpsTblastn, eBlastTypeTblastn, eBlastTypeTblastx, eGapAlignDecline, CSeq_align_Base::eType_partial, first(), BlastHSP::gap_info, i, kBlastAlignmentDim, NULL, GapEditScript::op_type, s_CollectSeqAlignData(), s_CorrectUASequence(), s_CreateSeqAlign(), BlastHSP::score, CSeq_align_Base::SetDim(), CSeq_align_Base::SetSegs(), CSeq_align_Base::SetType(), GapEditScript::size, ncbi::grid::netcache::search::fields::size, and t.
Referenced by BLASTHspListToSeqAlign().
◆ s_BlastMessageToException()
|
static |
Definition at line 359 of file blast_options_local_priv.cpp.
References Blast_MessageFree(), Blast_Message::message, msg(), NCBI_THROW, NcbiEmptyString, and NULL.
Referenced by CBlastOptionsLocal::Validate().
◆ s_BlastResults2SeqAlignDatabaseSearch_OMF()
|
static |
Definition at line 1942 of file blast_seqalign.cpp.
References _ASSERT, _TRACE, BlastHitList2SeqAlign_OMF(), CSeq_align_set_Base::Get(), prog, query, and results.
Referenced by LocalBlastResults2SeqAlign().
◆ s_BlastResults2SeqAlignSequenceCmp_OMF()
|
static |
Definition at line 1897 of file blast_seqalign.cpp.
References _ASSERT, ILocalQueryData::GetNumQueries(), i, prog, results, s_BLAST_OneSubjectResults2CSeqAlign(), s_TransposeSeqAlignVector(), and IBlastSeqInfoSrc::Size().
Referenced by LocalBlastResults2SeqAlign().
◆ s_BlastSeqLoc2CSeqloc() [1/2]
|
static |
Convert a list of mask locations to a CSeq_loc object.
- Parameters
-
query Query sequence location [in] scope Scope for use by object manager [in] loc_list List of mask locations [in]
- Returns
- List of mask locations in a CSeq_loc form or NULL if loc_list is NULL
Definition at line 78 of file repeats_filter_cxx.cpp.
References GetId(), SSeqRange::left, BlastSeqLoc::next, NULL, query, SSeqRange::right, CSeq_loc::SetNull(), CSeq_loc::SetPacked_int(), and BlastSeqLoc::ssr.
Referenced by s_BlastSeqLoc2CSeqloc(), s_BlastSeqLoc2MaskedRegions(), and s_FillMaskLocFromBlastResults().
◆ s_BlastSeqLoc2CSeqloc() [2/2]
|
static |
Convert a list of mask locations to a CSeq_loc object.
- Parameters
-
query Query sequence location [in] loc_list List of mask locations [in]
- Returns
- List of mask locations in a CSeq_loc form.
Definition at line 105 of file repeats_filter_cxx.cpp.
References query, and s_BlastSeqLoc2CSeqloc().
◆ s_BlastSeqLoc2MaskedRegions()
| TMaskedQueryRegions s_BlastSeqLoc2MaskedRegions | ( | const CSeq_loc & | query, |
| CScope * | scope, | ||
| BlastSeqLoc * | loc_list, | ||
| EBlastProgramType | program | ||
| ) |
Convert a list of mask locations to TMaskedQueryRegions.
- Parameters
-
query Query sequence location [in] scope Scope for use by object manager [in] loc_list List of mask locations [in] program type of blast search [in]
- Returns
- List of mask locations in TMaskedQueryRegions form.
Definition at line 118 of file repeats_filter_cxx.cpp.
References PackedSeqLocToMaskedQueryRegions(), query, and s_BlastSeqLoc2CSeqloc().
Referenced by s_FillMaskLocFromBlastResults().
◆ s_BlastSetup_GetStrand()
|
static |
Internal function to choose between the strand specified in a Seq-loc (which specified the query strand) and the strand obtained from the CBlastOptions.
- Parameters
-
seqloc_strand strand extracted from the query Seq-loc [in] program program type from the CORE's point of view [in] strand_opt strand as specified by the BLAST options [in]
Definition at line 97 of file blast_setup_cxx.cpp.
References Blast_QueryIsNucleotide(), Blast_QueryIsProtein(), eNa_strand_both, and eNa_strand_unknown.
Referenced by BlastSetup_GetStrand(), s_AdjustFirstContext(), SetupQueries_OMF(), and SetupQueryInfo_OMF().
◆ s_BuildArchiveAll()
|
static |
Definition at line 84 of file build_archive.cpp.
References _ASSERT, CBlast4_request_Base::CanGetBody(), CRemoteBlast::ConvertToRemoteMasks(), CSeq_align_set_Base::Get(), CBlast4_request_Base::GetBody(), CBlastAncillaryData::GetGappedKarlinBlk(), CBlastAncillaryData::GetLengthAdjustment(), CBlastAncillaryData::GetPsiGappedKarlinBlk(), CBlastAncillaryData::GetPsiUngappedKarlinBlk(), CBlast4_request_body_Base::GetQueue_search(), CBlastAncillaryData::GetSearchSpace(), CBlast4_queue_search_request_Base::GetService(), CBlastAncillaryData::GetUngappedKarlinBlk(), NStr::Int8ToString(), CSeq_align_set::IsEmpty(), CBlast4_request_body_Base::IsQueue_search(), ITERATE, CRef< C, Locker >::NotEmpty(), CConstRef< C, Locker >::NotEmpty(), CBlastVersion::Print(), result, results, s_Convert_to_CBlast_ka_block(), CSeq_align_set_Base::Set(), and CBlast4_request_Base::SetIdent().
Referenced by BlastBuildArchive().
◆ s_BuildGetSeqPartsRequest()
|
static |
Build Sequence Parts Fetching Request.
This method builds a blast4 request designed to fetch sequence data
- Parameters
-
seqids The seqids and ranges of the sequences to fetch. database The database or databases containing the desired sequences. seqtype Either 'p' or 'n' for protein or nucleotide. errors Returned string containing any errors encountered.
- Returns
- The blast4 sequence fetching request object.
Definition at line 307 of file blast_services.cpp.
References copy(), database, CRef< C, Locker >::Reset(), s_SeqTypeToResidue(), CBlast4_request_Base::SetBody(), CBlast4_get_seq_parts_request_Base::SetDatabase(), CBlast4_request_body_Base::SetGet_sequence_parts(), CBlast4_database_Base::SetName(), CBlast4_get_seq_parts_request_Base::SetSeq_locations(), and CBlast4_database_Base::SetType().
Referenced by CBlastServices::GetSequenceParts().
◆ s_BuildGetSeqRequest()
|
static |
Build Sequence Fetching Request.
This method builds a blast4 request designed to fetch a list of bioseqs from the blast4 server.
- Parameters
-
seqids The seqids of the sequences to fetch. database The database or databases containing the desired sequences. seqtype Either 'p' or 'n' for protein or nucleotide. errors Returned string containing any errors encountered. skip_seq_data If true, the sequence data will NOT be fetched target_only If true, only requested seq_id will be returned
- Returns
- The blast4 sequence fetching request object.
Definition at line 182 of file blast_services.cpp.
References database, ITERATE, CRef< C, Locker >::Reset(), s_SeqTypeToResidue(), CBlast4_request_Base::SetBody(), CBlast4_get_sequences_request_Base::SetDatabase(), CBlast4_request_body_Base::SetGet_sequences(), CBlast4_database_Base::SetName(), CBlast4_get_sequences_request_Base::SetSeq_ids(), CBlast4_get_sequences_request_Base::SetSkip_seq_data(), CBlast4_get_sequences_request_Base::SetTarget_only(), and CBlast4_database_Base::SetType().
Referenced by s_GetSequences().
◆ s_BuildMaskedRanges()
| void s_BuildMaskedRanges | ( | CSeqMasker::TMaskList & | masks, |
| const CSeq_loc & | seqloc, | ||
| CSeq_id & | query_id, | ||
| TMaskedQueryRegions * | mqr, | ||
| CRef< CSeq_loc > * | psl | ||
| ) |
Definition at line 156 of file winmask_filter.cpp.
References eExtreme_Positional, CSeqLocInfo::eFrameMinus1, CSeqLocInfo::eFramePlus1, eNa_strand_both, CSeq_loc::fMerge_All, CSeq_loc::fSort, CSeq_loc::fStrand_Ignore, CSeq_loc::GetStart(), ITERATE, CSeq_loc_Base::Reset(), CSeq_interval_Base::SetFrom(), CSeq_interval_Base::SetId(), CSeq_interval_Base::SetStrand(), CSeq_interval_Base::SetTo(), and tmp.
Referenced by Blast_FindWindowMaskerLoc().
◆ s_BuildResultsRemote()
|
static |
Build a result set from results in a remote blast search.
The remote blast object will be queried for results and these will be used to build a CSearchResultSet. If the search has not yet completed, this function will wait until it has.
- Parameters
-
rb The remote blast object representing the search.
- Returns
- The results of the search as a CSearchResultSet.
Definition at line 230 of file remote_search.cpp.
References eBlastSevError, CRemoteBlast::GetErrorVector(), CRemoteBlast::GetSeqAlignSets(), CRemoteBlast::GetWarningVector(), i, ITERATE, msg(), and s_SplitAlignVectorBySubjects().
Referenced by CRemoteSeqSearch::Run(), and CRemotePssmSearch::Run().
◆ s_BuildScoreList()
|
static |
Creates a list of score objects for a Seq-align, given an HSP structure.
- Parameters
-
hsp Structure containing HSP information [in] scores Linked list of score objects to put into a Seq-align [out] seqid_list List of GIs for the subject sequence.
Definition at line 1163 of file blast_seqalign.cpp.
References BlastHSP::bit_score, Blast_HSPGetQueryCoverage(), BlastHSP::comp_adjustment_method, BlastHSP::evalue, if(), ITERATE, kScore, BlastHSP::num, BlastHSP::num_ident, BlastHSP::num_positives, s_CalculateScoreVectorSize(), s_MakeScore(), BlastHSP::score, and SMALLEST_EVALUE.
Referenced by s_AddScoresToSeqAlign(), x_NonTranslatedHSPToStdSeg(), x_UngappedHSPToDenseDiag(), and x_UngappedHSPToStdSeg().
◆ s_BuildSearchInfoRequest()
|
static |
Definition at line 2334 of file remote_blast.cpp.
References CBlast4_request_body_Base::SetGet_search_info(), and rapidjson::value.
Referenced by CRemoteBlast::GetTitle(), CRemoteBlast::x_GetPsiIterationsFromServer(), and CRemoteBlast::x_GetSubjects().
◆ s_BuildSeqMasker()
| CSeqMasker* s_BuildSeqMasker | ( | const string & | lstat | ) |
Definition at line 99 of file winmask_filter.cpp.
References NCBI_THROW, NULL, and CException::what().
Referenced by Blast_FindWindowMaskerLoc().
◆ s_CalculateScoreVectorSize()
|
static |
Computes the exact size of a CSeq_align::TScore for a given HSP.
- Parameters
-
hsp HSP for which the score objects will be built, must be non-NULL [in] seqid_list list of IDs associated with this HSP [in]
Definition at line 1117 of file blast_seqalign.cpp.
References _ASSERT, BlastHSP::bit_score, BlastHSP::comp_adjustment_method, BlastHSP::evalue, if(), BlastHSP::num, BlastHSP::num_ident, BlastHSP::num_positives, BlastHSP::score, and SMALLEST_EVALUE.
Referenced by s_BuildScoreList().
◆ s_CheckAgainstNullData() [1/2]
|
static |
This function makes sure that none of the required data is returned as NULL or "empty".
- Parameters
-
pssm_input_msa interface which provides the data [in]
- Exceptions
-
CPssmEngineException in case of validation failure
Definition at line 69 of file pssm_engine.cpp.
References IPssmInputData::GetOptions(), IPssmInput_Base::GetQuery(), IPssmInput_Base::GetQueryLength(), and NCBI_THROW.
Referenced by CPssmEngine::CPssmEngine().
◆ s_CheckAgainstNullData() [2/2]
|
static |
This function makes sure that none of the required data is returned as NULL or "empty".
- Parameters
-
pssm_input_freqratios interface which provides the data [in]
- Exceptions
-
CPssmEngineException in case of validation failure
Definition at line 97 of file pssm_engine.cpp.
References BLASTAA_SIZE, CNcbiMatrix< T >::GetCols(), IPssmInputFreqRatios::GetData(), IPssmInput_Base::GetQuery(), IPssmInput_Base::GetQueryLength(), CNcbiMatrix< T >::GetRows(), NStr::IntToString(), and NCBI_THROW.
◆ s_CheckForBlastSeqSrcErrors()
|
static |
Checks if the BlastSeqSrc initialization succeeded.
- Exceptions
-
CBlastException if BlastSeqSrc initialization failed
Definition at line 110 of file local_db_adapter.cpp.
References BlastSeqSrcGetInitError(), msg(), NCBI_THROW, and sfree.
Referenced by CLocalDbAdapter::MakeSeqSrc().
◆ s_CheckMinWordSize()
| std::string s_CheckMinWordSize | ( | int | word_size | ) |
Definition at line 1098 of file blast_dbindex.cpp.
References CIndexedDb::Index_Set_Instance, NStr::IntToString(), kEmptyStr, CIndexedDb::MinIndexWordSize(), and CRef< C, Locker >::Reset().
Referenced by DbIndexInit().
◆ s_CollectSeqAlignData()
|
static |
Fills vectors of start positions, lengths and strands for all alignment segments.
Note that even though the edit_block is passed in, data for seqalign is collected from the esp_head argument for nsegs segments. This editing script may not be the full editing scripg if a discontinuous alignment is being built.
- Parameters
-
hsp HSP structure containing traceback information. [in] esp Traceback edit script [in] first first element of GapEditScript to use [in] nsegs Number of alignment segments [in] starts Vector of starting positions to fill [out] lengths Vector of segment lengths to fill [out] strands Vector of segment strands to fill [out] query_length Length of query sequence [in] subject_length Length of subject sequence [in] translate1 Is query translated? [in] translate2 Is subject translated? [in]
Definition at line 169 of file blast_seqalign.cpp.
References _ASSERT, eGapAlignDecline, eGapAlignDel, eGapAlignIns, eGapAlignSub, eNa_strand_unknown, first(), BlastSeg::frame, GAP_VALUE, int, kBlastAlignmentDim, NULL, GapEditScript::num, BlastSeg::offset, GapEditScript::op_type, BlastHSP::query, s_Frame2Strand(), s_GetAlignmentStart(), s_GetProteinFrameLength(), GapEditScript::size, and BlastHSP::subject.
Referenced by s_BlastHSP2SeqAlign().
◆ s_CombineDustMasksWithUserProvidedMasks()
| void s_CombineDustMasksWithUserProvidedMasks | ( | CSeqVector & | data, |
| CConstRef< CSeq_loc > | seqloc, | ||
| CRef< CScope > | scope, | ||
| CRef< CSeq_id > | query_id, | ||
| CRef< CSeq_loc > & | orig_query_mask, | ||
| Uint4 | level, | ||
| Uint4 | window, | ||
| Uint4 | linker | ||
| ) |
Definition at line 92 of file dust_filter.cpp.
References _ASSERT, CSeq_loc::Add(), CSeq_loc::ChangeToPackedInt(), data, eDiagFilter_Post, CSeq_loc::fMerge_All, CSeq_loc::fSort, CSeq_loc::fStrand_Ignore, GetLength(), CSymDustMasker::GetMaskedInts(), CSeq_loc_Base::IsEmpty(), CSeq_loc_Base::IsNull(), CSeq_loc_Base::IsPacked_int(), CSeq_loc_Base::IsWhole(), ITERATE, CSeq_loc_Mapper_Base::Map(), CSeq_loc::Merge(), CRef< C, Locker >::NotEmpty(), CRef< C, Locker >::Reset(), s_CreateSeqLocMapper(), SetDiagFilter(), and tmp.
Referenced by Blast_FindDustFilterLoc().
◆ s_CompareSeqAlignByEvalue()
|
static |
Definition at line 869 of file igblast.cpp.
References CSeq_id::eContent, CSeq_align::eScore_EValue, CSeq_align::eScore_Score, CSeq_align::GetAlignLength(), CSeq_id::GetLabel(), CSeq_align::GetNamedScore(), CSeq_align::GetSeq_id(), and NcbiEmptyString.
Referenced by CIgBlast::s_SortResultsByEvalue().
◆ s_CompareSeqAlignByScore()
|
static |
Definition at line 896 of file igblast.cpp.
References CSeq_align::eScore_Score, CSeq_align::GetAlignLength(), and CSeq_align::GetNamedScore().
Referenced by CIgBlast::x_FindDJAln().
◆ s_CompareSeqAlignByScoreAndName()
|
static |
Definition at line 530 of file igblast.cpp.
References CSeq_id::eContent, CSeq_align::eScore_Score, CSeq_align::GetAlignLength(), CSeq_id::GetLabel(), CSeq_align::GetNamedScore(), CSeq_align::GetSeq_id(), and NcbiEmptyString.
Referenced by CIgBlast::x_FindDJAln(), and CIgBlast::x_ProcessDGeneResult().
◆ s_CompareSeqAlignByScoreAndPosition()
|
inline |
Definition at line 432 of file igblast.hpp.
References abs, CSeq_id::eContent, eNa_strand_minus, CSeq_align::eScore_Score, CSeq_align::GetAlignLength(), CScope::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), CSeq_id::GetLabel(), CSeq_align::GetNamedScore(), CSeq_align::GetSeq_id(), CSeq_align::GetSeqStart(), CSeq_align::GetSeqStrand(), ly(), ScorePositionSort::min_J_position_diff, NcbiEmptyString, and ScorePositionSort::reliable_J_match_factor.
Referenced by ScorePositionSort::operator()().
◆ s_ComputeBtopAndIdentity()
|
static |
Definition at line 208 of file magicblast.cpp.
References _ASSERT, BLASTNA_TO_IUPACNA, BlastHSPMappingInfo::edits, JumperEditsBlock::edits, BlastSeg::end, HSPContainer::hsp, HSPChain::hsps, i, int, NStr::IntToString(), BlastHSPMappingInfo::left_edge, len, BlastHSP::map_info, MAPPER_SPLICE_SIGNAL, HSPContainer::next, NULL, JumperEditsBlock::num_edits, BlastSeg::offset, prev(), BlastHSP::query, JumperEdit::query_base, JumperEdit::query_pos, string, BlastHSP::subject, JumperEdit::subject_base, and tolower().
Referenced by s_CreateSeqAlign().
◆ s_ComputeStartEndContexts()
|
static |
Calculate the starting and ending contexts for a given strand.
- Parameters
-
strand strand to compute contexts for [in] num_contexts number of contexts [in] start starting context [out] end ending context [out]
Definition at line 284 of file blast_setup_cxx.cpp.
References abort(), eNa_strand_both, eNa_strand_minus, and eNa_strand_plus.
Referenced by s_AddMask().
◆ s_ConstBioseqSetToSeqLocs()
|
static |
Convert a constant reference to a Bioseq-set to IRemoteQueryData::TSeqLocs.
- Parameters
-
bioseq_set input data[in]
Definition at line 161 of file objmgrfree_query_data.cpp.
References ConstBegin(), eDetectLoops, CBlastQuerySourceBioseqSet::GetSeqLoc(), i, and CBlastQuerySourceBioseqSet::Size().
Referenced by CObjMgrFree_RemoteQueryData::GetSeqLocs().
◆ s_Convert_to_CBlast_ka_block()
|
static |
Definition at line 66 of file build_archive.cpp.
References Blast_KarlinBlk::H, Blast_KarlinBlk::K, and Blast_KarlinBlk::Lambda.
Referenced by s_BuildArchiveAll().
◆ s_ConvertBlastnMasks()
|
static |
Convert EBlastTypeBlastn CORE masks into TSeqLocInfoVector.
Definition at line 872 of file blast_aux.cpp.
References CSeqLocInfo::eFrameNotSet, i, ITERATE, Map(), mask, BlastSeqLoc::next, compile_time_bits::range(), s_GetBlastnMask(), CSeq_interval_Base::SetFrom(), CSeq_interval_Base::SetId(), and CSeq_interval_Base::SetTo().
Referenced by Blast_GetSeqLocInfoVector().
◆ s_CorrectUASequence()
Checks if any decline-to-align segments immediately follow an insertion or deletion, and swaps any such segments so indels are always to the right of the decline-to-align segments.
- Parameters
-
hsp HSP structure, containint traceback [in] [out]
Definition at line 375 of file blast_seqalign.cpp.
References eGapAlignDecline, eGapAlignDel, eGapAlignIns, BlastHSP::gap_info, GapEditScript::num, GapEditScript::op_type, and GapEditScript::size.
Referenced by s_BlastHSP2SeqAlign().
◆ s_CreateBlastMask()
|
static |
Creates a Blast4-mask which is supposed to contain all masked locations for a given query sequence and frame, all of which are in the packed_int argument.
Definition at line 1064 of file remote_blast.cpp.
References Blast_QueryIsNucleotide(), Blast_QueryIsTranslated(), eBlast4_frame_type_notset, eBlast4_frame_type_plus1, eNa_strand_minus, CPacked_seqint_Base::Get(), ITERATE, and CSeq_loc::SetPacked_int().
Referenced by CRemoteBlast::ConvertToRemoteMasks().
◆ s_CreateDenseg()
|
static |
Creates a Dense-seg object from the starts, lengths and strands vectors and two Seq-ids.
- Parameters
-
dense_seg the object to populate [in|out] master Query Seq-id [in] slave Subject Seq-ids [in] starts Vector of start positions for alignment segments [in] lengths Vector of alignment segments lengths [in] strands Vector of alignment segments strands [in]
- Returns
- The Dense-seg object.
Definition at line 272 of file blast_seqalign.cpp.
References _ASSERT, kBlastAlignmentDim, CDense_seg_Base::SetDim(), CDense_seg_Base::SetIds(), CDense_seg_Base::SetLens(), CDense_seg_Base::SetNumseg(), CDense_seg_Base::SetStarts(), and CDense_seg_Base::SetStrands().
Referenced by s_CreateSeqAlign().
◆ s_CreateRepeatsSearchOptions()
|
static |
Create an options handle with the defaults set for a search for repeats.
Definition at line 310 of file repeats_filter_cxx.cpp.
References _ASSERT, CBlastOptions::GetMBIndexLoaded(), CBlastOptionsHandle::GetOptions(), REPEATS_SEARCH_GAP_EXTEND, REPEATS_SEARCH_GAP_OPEN, REPEATS_SEARCH_MINSCORE, REPEATS_SEARCH_PENALTY, REPEATS_SEARCH_REWARD, REPEATS_SEARCH_WORD_SIZE, REPEATS_SEARCH_XDROP_FINAL, REPEATS_SEARCH_XDROP_UNGAPPED, CBlastOptionsHandle::SetCutoffScore(), CBlastNucleotideOptionsHandle::SetDustFiltering(), CBlastNucleotideOptionsHandle::SetGapExtensionCost(), CBlastNucleotideOptionsHandle::SetGapOpeningCost(), CBlastOptionsHandle::SetGapXDropoffFinal(), CBlastNucleotideOptionsHandle::SetMatchReward(), CBlastNucleotideOptionsHandle::SetMismatchPenalty(), CBlastNucleotideOptionsHandle::SetTraditionalBlastnDefaults(), CBlastNucleotideOptionsHandle::SetWordSize(), and CBlastNucleotideOptionsHandle::SetXDropoff().
Referenced by Blast_FindRepeatFilterLoc().
◆ s_CreateSeqAlign() [1/2]
|
static |
Definition at line 334 of file magicblast.cpp.
References _ASSERT, CUser_object::AddField(), CSeq_id::BlastRank(), HSPChain::context, BlastQueryInfo::contexts, HSPChain::count, CSeq_align::eScore_PercentIdentity_Gapped, CSeq_align::eScore_Score, CSeq_align_Base::eType_partial, CSeq_loc_CI::GetSeq_id(), ILocalQueryData::GetSeq_loc(), ILocalQueryData::GetSeqLength(), GetSequenceLengthAndId(), MakeSplicedSeg(), NUM_STRANDS, HSPChain::oid, s_ComputeBtopAndIdentity(), HSPChain::score, BlastContextInfo::segment_flags, SerialAssign(), CSeq_align_Base::SetDim(), CSeq_align_Base::SetExt(), CSeq_align::SetNamedScore(), CSeq_align_Base::SetSegs(), CUser_object_Base::SetType(), and CSeq_align_Base::SetType().
Referenced by CMagicBlast::x_CreateSeqAlignSet().
◆ s_CreateSeqAlign() [2/2]
|
static |
Creates a Seq-align for a single HSP from precalculated vectors of start positions, lengths and strands of segments, sequence identifiers and other information.
- Parameters
-
master Query sequence identifier [in] slave Subject sequence identifier [in] starts Start positions of alignment segments [in] lengths Lengths of alignment segments [in] strands Strands of alignment segments [in] translate_master Is query translated? [in] translate_slave Is subject translated? [in]
- Returns
- Resulting Seq-align object.
Definition at line 628 of file blast_seqalign.cpp.
References CSeq_align_Base::eType_partial, kBlastAlignmentDim, s_CreateDenseg(), s_CreateStdSegs(), CSeq_align_Base::SetDim(), CSeq_align_Base::SetSegs(), and CSeq_align_Base::SetType().
Referenced by s_BlastHSP2SeqAlign().
◆ s_CreateSeqLocMapper()
|
static |
Auxiliary function to create CSeq_loc_Mapper from a copy of the target Seq-loc.
Definition at line 75 of file dust_filter.cpp.
References _ASSERT, and CSeq_loc::SetWhole().
Referenced by s_CombineDustMasksWithUserProvidedMasks().
◆ s_CreateStdSegs()
|
static |
Creates a Std-seg object from the starts, lengths and strands vectors and two Seq-ids for a translated search.
- Parameters
-
master Query Seq-id [in] slave Subject Seq-ids [in] starts Vector of start positions for alignment segments [in] lengths Vector of alignment segments lengths [in] strands Vector of alignment segments strands [in] translate_master Is query sequence translated? [in] translate_slave Is subject sequenec translated? [in]
- Returns
- The Std-seg object.
Definition at line 307 of file blast_seqalign.cpp.
References _ASSERT, CODON_LENGTH, GAP_VALUE, i, int, kBlastAlignmentDim, CSeq_loc::SetEmpty(), and CSeq_loc::SetInt().
Referenced by s_CreateSeqAlign().
◆ s_DJNotCompatible()
|
static |
Definition at line 911 of file igblast.cpp.
References CSeq_align::GetSeqStart(), CSeq_align::GetSeqStop(), and ms().
Referenced by CIgBlast::x_FindDJAln(), and CIgBlast::x_ProcessDGeneResult().
◆ s_ExtractQueryIdsFromBioseqSet()
|
static |
Extract the query IDs from a CBioseq_set.
- Parameters
-
bss CBioseq_set object used as source [in] query_ids where the query_ids will be added [in|out]
Definition at line 2078 of file remote_blast.cpp.
References CSeq_id::BestRank(), ConstBegin(), eDetectLoops, and FindBestChoice().
Referenced by CRemoteBlast::x_ExtractQueryIds().
◆ s_ExtractSeqId()
|
static |
Find the first alignment in a set of blast results, and.
Definition at line 453 of file blast_results.cpp.
References CConstRef< C, Locker >::Empty(), CSeq_align_set_Base::Get(), CSeq_align_Base::C_Segs::GetDisc(), CSeq_align_Base::GetSegs(), CSeq_align::GetSeq_id(), CSeq_align_Base::C_Segs::IsDisc(), kQueryIndex, and CConstRef< C, Locker >::Reset().
Referenced by CSearchResultSet::CSearchResultSet().
◆ s_FillMaskLocFromBlastResults() [1/2]
|
static |
Fills the mask locations in the BlastSearchQuery structures, as if it was a lower case mask, given the results of a BLAST search against a database of repeats.
- Parameters
-
query Vector of queries [in] [out] results alignments returned from a BLAST search against a repeats database [in] program type of blast search [in]
Definition at line 237 of file repeats_filter_cxx.cpp.
References _ASSERT, BlastSeqLocCombine(), BlastSeqLocFree(), ITERATE, BlastSeqLoc::next, NULL, query, CRef< C, Locker >::Release(), REPEAT_MASK_LINK_VALUE, result, results, s_BlastSeqLoc2MaskedRegions(), and s_SeqAlignToBlastSeqLoc().
◆ s_FillMaskLocFromBlastResults() [2/2]
|
static |
Fills the mask locations in the query SSeqLoc structures, as if it was a lower case mask, given the results of a BLAST search against a database of repeats.
- Parameters
-
query Vector of query sequence locations structures [in] [out] results alignments returned from a BLAST search against a repeats database [in]
Definition at line 185 of file repeats_filter_cxx.cpp.
References _ASSERT, BlastSeqLocCombine(), BlastSeqLocFree(), CSeqLoc2BlastSeqLoc(), mask, NULL, query, REPEAT_MASK_LINK_VALUE, result, results, s_BlastSeqLoc2CSeqloc(), and s_SeqAlignToBlastSeqLoc().
Referenced by Blast_FindRepeatFilterLoc().
◆ s_FindPathToWM()
Find the path to the window masker files, first checking the (optionally set) value passed to the WindowMaskerPathInit function, then the environment variable WINDOW_MASKER_PATH, then the section WINDOW_MASKER, label WINDOW_MASKER_PATH in the NCBI configuration file.
If not found in either location, return the current working directory
- See also
- s_FindPathToGeneInfoFiles
Definition at line 372 of file winmask_filter.cpp.
References CCompoundRWRegistry::Add(), CEnvironmentRegistry::AddMapper(), CEnvironmentRegistry::ePriority_Max, CCompoundRWRegistry::ePriority_MaxUser, IRegistry::fWithNcbirc, IRegistry::Get(), CDir::GetCwd(), kEmptyStr, kSection, NStr::ReplaceInPlace(), NStr::StartsWith(), and WindowMaskerPathGet().
Referenced by GetTaxIdWithWindowMaskerSupport(), s_OldGetTaxIdWithWindowMaskerSupport(), and WindowMaskerTaxidToDb().
◆ s_FixNumIdent()
| void s_FixNumIdent | ( | BlastHSPList * | hsp_list, |
| bool | gapped_calculation | ||
| ) |
Definition at line 374 of file prelim_stage.cpp.
References BlastHSPList::hsp_array, BlastHSPList::hspcnt, i, and BlastHSP::num_ident.
Referenced by s_GetBitScores().
◆ s_Frame2Strand()
|
static |
Converts a frame into the appropriate strand.
Definition at line 75 of file blast_seqalign.cpp.
References eNa_strand_minus, eNa_strand_plus, and eNa_strand_unknown.
Referenced by MakeSplicedSeg(), s_CollectSeqAlignData(), s_OOFBlastHSP2SeqAlign(), x_NonTranslatedHSPToStdSeg(), x_UngappedHSPToDenseDiag(), and x_UngappedHSPToStdSeg().
◆ s_GetAlignmentStart()
|
static |
Finds the starting position of a sequence segment in an alignment, given an editing script.
- Parameters
-
curr_pos Current position on input, modified to next position on output [in] [out] num number of letters specified by traceback edit [in] strand Sequence strand [in] translate Is sequence translated? [in] length Sequence length [in] original_length Original (nucleotide) sequence length, if it is translated [in] frame Translating frame [in]
- Returns
- Start position of the current alignment segment.
Definition at line 115 of file blast_seqalign.cpp.
References CODON_LENGTH, eNa_strand_minus, and s_GetCurrPos().
Referenced by s_CollectSeqAlignData().
◆ s_GetBitScore()
Returns the bit_score from this score object.
- Parameters
-
score ASN.1 score object [in]
Definition at line 520 of file psiblast_aux_priv.cpp.
References BLAST_EXPECT_VALUE, CScore_Base::GetId(), CScore_Base::C_Value::GetReal(), CObject_id_Base::GetStr(), CScore_Base::GetValue(), and CScore_Base::C_Value::IsReal().
Referenced by GetLowestEvalue().
◆ s_GetBitScores()
| void s_GetBitScores | ( | BlastHitList * | hit_list, |
| bool | gapped_calculation, | ||
| const BlastScoreBlk * | sbp | ||
| ) |
Definition at line 387 of file prelim_stage.cpp.
References Blast_HSPListGetBitScores(), BlastHitList::hsplist_array, BlastHitList::hsplist_count, i, and s_FixNumIdent().
Referenced by CBlastPrelimSearch::x_BuildStdSegList().
◆ s_GetBlastnMask()
|
static |
Return the masked locations for a given query as well as whether the linked list's elements should be reverted or not (true in the case of negative only strand) The first element of the returned pair is the linked list of masked locations The second element of the returned pair is true if the linked list needs to be reversed.
Definition at line 853 of file blast_aux.cpp.
References _ASSERT, eBlastTypeBlastn, GetNumberOfContexts(), and mask.
Referenced by s_ConvertBlastnMasks().
◆ s_GetCStringOfMatrixPath()
Get the path to the matrix, without the actual matrix name.
- Parameters
-
full_path including the matrix name, this string will be modified [in] matrix_name name of matrix (e.g., BLOSUM62) [in]
- Returns
- char* to matrix path
Definition at line 1293 of file blast_setup_cxx.cpp.
References strdup.
Referenced by BlastFindMatrixPath().
◆ s_GetCurrPos()
Advances position in a sequence, according to an edit script instruction.
- Parameters
-
pos Current position on input, next position on output [in] [out] pos2advance How much the position should be advanced? [in]
- Returns
- Current position.
Definition at line 90 of file blast_seqalign.cpp.
Referenced by s_GetAlignmentStart(), and s_OOFBlastHSP2SeqAlign().
◆ s_GetEvalue()
Returns the evalue from this score object.
- Parameters
-
score ASN.1 score object [in]
Definition at line 508 of file psiblast_aux_priv.cpp.
References CScore_Base::GetId(), CScore_Base::C_Value::GetReal(), CObject_id_Base::GetStr(), CScore_Base::GetValue(), CScore_Base::C_Value::IsReal(), and max().
Referenced by GetLowestEvalue().
◆ s_GetMinimumSupportedWordSizeByIndex()
Definition at line 926 of file blast_dbindex.cpp.
References ERR_POST, CMemoryFile::GetPtr(), SIndexHeader::hkey_width_, Info(), ReadIndexHeader< false >(), and SIndexHeader::stride_.
Referenced by CIndexedDb_Old::MinIndexWordSize(), and CIndexedDb_New::MinIndexWordSize().
◆ s_GetPartsFromReply()
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static |
Extract information from the get-seq-parts reply object.
- Parameters
-
reply The reply object from blast4. ids All Seq-ids for the requested sequences. seq_data Seq_data for the sequences in question. errors Any error messages found in the reply. warnings Any warnings found in the reply.
Definition at line 592 of file blast_services.cpp.
References NON_CONST_ITERATE, and s_ProcessErrorsFromReply().
Referenced by CBlastServices::GetSequenceParts().
◆ s_GetProteinFrameLength()
Finds length of a protein frame given a nucleotide length and a frame number.
- Parameters
-
nuc_length Nucleotide sequence length [in] frame Translation frame [in]
- Returns
- Length of the translated sequence.
Definition at line 148 of file blast_seqalign.cpp.
References ABS, and CODON_LENGTH.
Referenced by s_CollectSeqAlignData().
◆ s_GetQuerySequenceData()
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static |
Auxiliary function to retrieve the sequence data in NCBI-stdaa format from the bioseq.
- Parameters
-
bioseq Bioseq to extract the data from [in] query_length size of the query [in] retval return value of this function [in|out]
- See also
- CPssm::GetQuerySequenceData
Definition at line 151 of file msa_pssm_input.cpp.
References CSeqportUtil::Convert(), copy(), CSeq_data_Base::e_Ncbistdaa, CAliasBase< TPrim >::Get(), CBioseq_Base::GetInst(), CSeq_data_Base::GetNcbistdaa(), CSeq_inst_Base::GetSeq_data(), CSeq_data_Base::IsNcbistdaa(), and CAliasBase< TPrim >::Set().
Referenced by CPsiBlastInputClustalW::x_ExtractQueryForPssm().
◆ s_GetRestrictedBlastSeqLocs()
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static |
Extract the masking locations for a single query into a CBlastQueryFilteredFrames object and adjust the masks so that they correspond to the range specified by the Seq-loc in queries.
- Parameters
-
queries all query sequences [in] query_index index of the query of interest in queries [in] qinfo BlastQueryInfo structure for the queries above [in] program BLAST program being executed [in]
Definition at line 440 of file blast_setup_cxx.cpp.
References BlastSeqLoc_RestrictToInterval(), eExtreme_Positional, CRef< C, Locker >::Empty(), IBlastQuerySource::GetMaskedRegions(), IBlastQuerySource::GetSeqLoc(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), and s_RestrictSeqLocs_Multiframe().
Referenced by SetupQueries_OMF().
◆ s_GetSeqsFromReply()
|
static |
Get bioseqs from a sequence fetching reply.
This method reads the reply from a sequence fetching request and extracts the bioseqs, errors and warnings from it.
- Parameters
-
reply The reply from a sequence fetching request. bioseqs The returned list of bioseqs from the request. errors Returned string containing any errors encountered. warnings Returned string containing any warnigns encountered.
Definition at line 118 of file blast_services.cpp.
References ITERATE, and s_ProcessErrorsFromReply().
Referenced by s_GetSequences().
◆ s_GetSequences()
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static |
Main function to issue a Blast4-get-sequences-request and collect its results from the remote BLAST server.
- Parameters
-
seqids The seqids of the sequences to fetch. [in] database The database or databases containing the desired sequences. [in] seqtype Either 'p' or 'n' for protein or nucleotide. [in] bioseqs The vector used to return the requested Bioseqs. [out] errors Returned string containing any errors encountered. [out] warnings A null-separated list of warning. [out] skip_seq_data If true, the sequence data will NOT be fetched [in] verbose Produce verbose output. [in]
Definition at line 252 of file blast_services.cpp.
References CBlast4Client_Base::Ask(), database, CRef< C, Locker >::Empty(), MSerial_AsnText, NCBI_THROW, NcbiCout, s_BuildGetSeqRequest(), and s_GetSeqsFromReply().
Referenced by CBlastServices::GetSequences(), and CBlastServices::GetSequencesInfo().
◆ s_GuessProgram()
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static |
Auxiliary function to help guess the program type from a CSeq-loc.
This should only be used in the context of CObjMgr_QueryFactory::ExtractUserSpecifiedMasks
Definition at line 431 of file objmgr_query_data.cpp.
References eBlastTypeBlastn, eNa_strand_unknown, and mask.
Referenced by CObjMgr_QueryFactory::ExtractUserSpecifiedMasks().
◆ s_InitializeGumbelBlk()
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static |
Definition at line 62 of file blast_results.cpp.
References _ASSERT, and calloc().
Referenced by CBlastAncillaryData::CBlastAncillaryData(), and CBlastAncillaryData::do_copy().
◆ s_InitializeKarlinBlk()
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static |
Definition at line 51 of file blast_results.cpp.
References _ASSERT, Blast_KarlinBlkCopy(), Blast_KarlinBlkNew(), and Blast_KarlinBlk::Lambda.
Referenced by CBlastAncillaryData::CBlastAncillaryData().
◆ s_InitNewSeqDbSrc()
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static |
Initializes the data structure and function pointers in a SeqDb based BlastSeqSrc.
- Parameters
-
retval Structure to populate [in] [out] seqdb Reference to a CSeqDB object [in]
Definition at line 645 of file seqsrc_seqdb.cpp.
References _ASSERT, _BlastSeqSrcImpl_SetCopyFnPtr(), _BlastSeqSrcImpl_SetDataStructure(), _BlastSeqSrcImpl_SetDeleteFnPtr(), _BlastSeqSrcImpl_SetGetAvgSeqLen(), _BlastSeqSrcImpl_SetGetIsProt(), _BlastSeqSrcImpl_SetGetMaxSeqLen(), _BlastSeqSrcImpl_SetGetMinSeqLen(), _BlastSeqSrcImpl_SetGetName(), _BlastSeqSrcImpl_SetGetNumSeqs(), _BlastSeqSrcImpl_SetGetNumSeqsStats(), _BlastSeqSrcImpl_SetGetSeqLen(), _BlastSeqSrcImpl_SetGetSequence(), _BlastSeqSrcImpl_SetGetSupportsPartialFetching(), _BlastSeqSrcImpl_SetGetTotLen(), _BlastSeqSrcImpl_SetGetTotLenStats(), _BlastSeqSrcImpl_SetIterNext(), _BlastSeqSrcImpl_SetReleaseSequence(), _BlastSeqSrcImpl_SetResetChunkIterator(), _BlastSeqSrcImpl_SetSetNumberOfThreads(), _BlastSeqSrcImpl_SetSetSeqRange(), s_SeqDbGetAvgLength(), s_SeqDbGetIsProt(), s_SeqDbGetMaxLength(), s_SeqDbGetMinLength(), s_SeqDbGetName(), s_SeqDbGetNumSeqs(), s_SeqDbGetNumSeqsStats(), s_SeqDbGetSeqLen(), s_SeqDbGetSequence(), s_SeqDbGetSupportsPartialFetching(), s_SeqDbGetTotLen(), s_SeqDbGetTotLenStats(), s_SeqDbIteratorNext(), s_SeqDbReleaseSequence(), s_SeqDbResetChunkIterator(), s_SeqDbSetNumberOfThreads(), s_SeqDbSetRanges(), s_SeqDbSrcCopy(), and s_SeqDbSrcFree().
Referenced by s_SeqDbSrcNew(), and s_SeqDbSrcSharedNew().
◆ s_InitSeqInfoSrc()
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static |
FIXME: this should be removed as soon as we safely can We will be able to do this once we are guaranteed that every constructor to CLocalBlast takes or can construct a IBlastSeqInfoSrc on it's own.
This function is dangerous as it assumes that the BlastSeqSrc is based upon CSeqDB, which is not guaranteed.
Definition at line 150 of file local_blast.cpp.
References BlastSeqSrcGetIsProt(), BlastSeqSrcGetName(), NCBI_THROW, and true.
Referenced by CLocalBlast::Run().
◆ s_InvalidateQueryContexts()
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static |
Mark the contexts corresponding to the query identified by query_index as invalid.
- Parameters
-
qinfo BlastQueryInfo structure to modify [in] query_index index of the query, assumes it's in the BlastQueryInfo structure above [in]
Definition at line 474 of file blast_setup_cxx.cpp.
References _ASSERT, BlastQueryInfo::contexts, FALSE, BlastQueryInfo::first_context, i, BlastContextInfo::is_valid, and BlastContextInfo::query_index.
Referenced by SetupQueries_OMF().
◆ s_IsNumericId()
Definition at line 149 of file uniform_search.cpp.
References NStr::fConvErr_NoThrow, and NStr::StringToNumeric().
Referenced by CSearchDatabase::SetFilteringAlgorithm().
◆ s_IsSeqAlignAsGood()
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static |
Definition at line 791 of file igblast.cpp.
References CSeq_align::eScore_EValue, CSeq_align::eScore_Score, CSeq_align::GetAlignLength(), and CSeq_align::GetNamedScore().
Referenced by s_MakeTopHitsId().
◆ s_IsValidResidue()
Tests if a number represents a valid residue.
- Parameters
-
res Value to test [in]
- Returns
- TRUE if value is a valid residue
Definition at line 867 of file blast_setup_cxx.cpp.
References BLASTAA_SIZE.
Referenced by GetSequenceProtein().
◆ s_LocalQueryData2Packed_seqint()
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static |
Auxiliary function to extract the Seq-ids from the ILocalQueryData and bundle them in a Packed-seqint.
- Parameters
-
query_data input query data [in]
- Returns
- Packed-seqint with query Seq-locs
Definition at line 95 of file setup_factory.cpp.
References ILocalQueryData::GetNumQueries(), ILocalQueryData::GetSeq_loc(), ILocalQueryData::GetSeqLength(), i, and len.
Referenced by CSetupFactory::CreateScoreBlock().
◆ s_MakeScore()
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static |
Creates and initializes CScore with a given name, and with integer or double value.
Integer value is used if it is not zero, otherwise double value is assigned.
- Parameters
-
ident_string Score type name [in] d Real value of the score [in] i Integer value of the score. [in]
- Returns
- Resulting CScore object.
Definition at line 1099 of file blast_seqalign.cpp.
References i.
Referenced by s_BuildScoreList().
◆ s_MakeTopHitsId()
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static |
Definition at line 815 of file igblast.cpp.
References count, ITERATE, NcbiEmptyString, s_IsSeqAlignAsGood(), and s_RemoveLocalPrefix().
Referenced by CIgBlast::x_AnnotateC(), CIgBlast::x_AnnotateD(), CIgBlast::x_AnnotateDJ(), CIgBlast::x_AnnotateJ(), and CIgBlast::x_AnnotateV().
◆ s_MB_IdbCheckOid()
Definition at line 1216 of file blast_dbindex.cpp.
References _ASSERT, CIndexedDb::CheckOid(), and CIndexedDb::Index_Set_Instance.
Referenced by IndexedDbSetQueryInfo().
◆ s_MB_IdbGetResults()
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static |
Get the seed search results for a give subject id and chunk number.
- Parameters
-
idb_v [I] Database and index data. oid_i [I] Subject id. chunk_i [I] Chunk number. init_hitlist [I/O] Results are returned here.
- Returns
- Word size used for search.
Definition at line 1223 of file blast_dbindex.cpp.
References _ASSERT, CIndexedDb::GetResults(), and CIndexedDb::Index_Set_Instance.
Referenced by IndexedDbSetQueryInfo().
◆ s_MB_IdxEndSearchIndication()
Definition at line 1210 of file blast_dbindex.cpp.
References CIndexedDb::EndSearchIndication(), and CIndexedDb::Index_Set_Instance.
Referenced by IndexedDbSetQueryInfo().
◆ s_MergeCBlast4_parameters()
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static |
Convenience function to merge all lists into one object to facilitate invoking AdjustProgram.
Definition at line 650 of file blast_options_builder.cpp.
Referenced by CBlastOptionsBuilder::GetSearchOptions().
◆ s_MultiSeqGetAvgLength()
Retrieves the length of the longest sequence in the BlastSeqSrc.
- Parameters
-
multiseq_handle Pointer to the structure containing sequences [in]
Definition at line 245 of file seqsrc_multiseq.cpp.
References _ASSERT, and CRef< C, Locker >::NotEmpty().
Referenced by s_MultiSeqSrcNew().
◆ s_MultiSeqGetIsProt()
Answers whether this object is for protein or nucleotide sequences.
- Parameters
-
multiseq_handle Pointer to the structure containing sequences [in]
Definition at line 317 of file seqsrc_multiseq.cpp.
References _ASSERT, and CRef< C, Locker >::NotEmpty().
Referenced by s_MultiSeqSrcNew().
◆ s_MultiSeqGetMaxLength()
The following functions interact with the C API, and have to be declared extern "C".
Retrieves the length of the longest sequence in the BlastSeqSrc.
- Parameters
-
multiseq_handle Pointer to the structure containing sequences [in]
Definition at line 203 of file seqsrc_multiseq.cpp.
References _ASSERT, MAX, and CRef< C, Locker >::NotEmpty().
Referenced by s_MultiSeqSrcNew().
◆ s_MultiSeqGetMinLength()
Retrieves the length of the longest sequence in the BlastSeqSrc.
- Parameters
-
multiseq_handle Pointer to the structure containing sequences [in]
Definition at line 226 of file seqsrc_multiseq.cpp.
References BLAST_SEQSRC_MINLENGTH, INT4_MAX, and MIN.
Referenced by s_MultiSeqSrcNew().
◆ s_MultiSeqGetName()
Always returns NcbiEmptyCStr.
Definition at line 309 of file seqsrc_multiseq.cpp.
References NcbiEmptyCStr.
Referenced by s_MultiSeqSrcNew().
◆ s_MultiSeqGetNextChunk()
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static |
Mirrors the database iteration interface.
Next chunk of indices retrieval is really just a check that current index has not reached the end.
- Parameters
-
multiseq_handle Pointer to the multiple sequence object [in] itr Iterator over multiseq_handle [in] [out]
- Returns
- Status.
Definition at line 412 of file seqsrc_multiseq.cpp.
References _ASSERT, BLAST_SEQSRC_EOF, BLAST_SEQSRC_SUCCESS, BlastSeqSrcIterator::current_pos, CRef< C, Locker >::NotEmpty(), and UINT4_MAX.
Referenced by s_MultiSeqIteratorNext().
◆ s_MultiSeqGetNumSeqs()
Retrieves the number of sequences in the BlastSeqSrc.
- Parameters
-
multiseq_handle Pointer to the structure containing sequences [in]
Definition at line 273 of file seqsrc_multiseq.cpp.
References _ASSERT, and CRef< C, Locker >::NotEmpty().
Referenced by s_MultiSeqSrcNew().
◆ s_MultiSeqGetNumSeqsStats()
Returns zero as this implementation does not support alias files.
Definition at line 285 of file seqsrc_multiseq.cpp.
Referenced by s_MultiSeqSrcNew().
◆ s_MultiSeqGetSeqLen()
Retrieve length of a given sequence.
- Parameters
-
multiseq_handle Pointer to the structure containing sequences [in] args Pointer to integer indicating index into the sequences vector [in]
- Returns
- Length of the sequence or BLAST_SEQSRC_ERROR.
Definition at line 388 of file seqsrc_multiseq.cpp.
References _ASSERT, and CRef< C, Locker >::NotEmpty().
Referenced by s_MultiSeqSrcNew().
◆ s_MultiSeqGetSequence()
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static |
Retrieves the sequence for a given index, in a given encoding.
- Parameters
-
multiseq_handle Pointer to the structure containing sequences [in] args Pointer to BlastSeqSrcGetSeqArg structure, containing sequence index and encoding. [in]
- Returns
- return codes defined in blast_seqsrc.h
Definition at line 334 of file seqsrc_multiseq.cpp.
References _ASSERT, BLAST_SEQSRC_EOF, BLAST_SEQSRC_ERROR, BLAST_SEQSRC_SUCCESS, BlastSequenceBlkCopy(), eBlastEncodingNcbi4na, eBlastEncodingNucleotide, BlastSeqSrcGetSeqArg::encoding, FALSE, BLAST_SequenceBlk::lcase_mask, BLAST_SequenceBlk::lcase_mask_allocated, CRef< C, Locker >::NotEmpty(), NULL, BLAST_SequenceBlk::oid, BlastSeqSrcGetSeqArg::oid, BlastSeqSrcGetSeqArg::seq, BLAST_SequenceBlk::sequence, and BLAST_SequenceBlk::sequence_start.
Referenced by s_MultiSeqSrcNew().
◆ s_MultiSeqGetTotLen()
Returns total length in db scan mode.
Returns 0 as total length, indicating that this is not a database search.
Definition at line 293 of file seqsrc_multiseq.cpp.
Referenced by s_MultiSeqSrcNew().
◆ s_MultiSeqGetTotLenStats()
Returns 0 as this implementation does not use alias files.
Definition at line 302 of file seqsrc_multiseq.cpp.
Referenced by s_MultiSeqSrcNew().
◆ s_MultiSeqIteratorNext()
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static |
Gets the next sequence index, given a BlastSeqSrc pointer.
- Parameters
-
multiseq_handle Handle to access the underlying object over which iteration occurs. [in] itr Iterator over seqsrc [in] [out]
- Returns
- Next index in the sequence set
Definition at line 444 of file seqsrc_multiseq.cpp.
References _ASSERT, BLAST_SEQSRC_EOF, BlastSeqSrcIterator::current_pos, and s_MultiSeqGetNextChunk().
Referenced by s_MultiSeqSrcNew().
◆ s_MultiSeqReleaseSequence()
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static |
Deallocates the uncompressed sequence buffer if necessary.
- Parameters
-
args Pointer to BlastSeqSrcGetSeqArg structure [in]
Definition at line 375 of file seqsrc_multiseq.cpp.
References _ASSERT, BlastSeqSrcGetSeqArg::seq, BLAST_SequenceBlk::sequence_start, BLAST_SequenceBlk::sequence_start_allocated, and sfree.
Referenced by s_MultiSeqSrcNew().
◆ s_MultiSeqResetChunkIter()
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static |
Resets the internal bookmark iterator (N/A in this case)
Definition at line 433 of file seqsrc_multiseq.cpp.
Referenced by s_MultiSeqSrcNew().
◆ s_MultiSeqSrcCopy()
|
static |
Multi-sequence sequence source copier: creates a new reference to the CMultiSeqInfo object and copies the rest of the BlastSeqSrc structure.
- Parameters
-
seq_src BlastSeqSrc structure to copy [in]
- Returns
- Pointer to the new BlastSeqSrc.
Definition at line 490 of file seqsrc_multiseq.cpp.
References _BlastSeqSrcImpl_GetDataStructure(), _BlastSeqSrcImpl_SetDataStructure(), and NULL.
Referenced by s_MultiSeqSrcNew().
◆ s_MultiSeqSrcFree()
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static |
Multi sequence source destructor: frees its internal data structure.
- Parameters
-
seq_src BlastSeqSrc structure to free [in]
- Returns
- NULL
Definition at line 475 of file seqsrc_multiseq.cpp.
References _BlastSeqSrcImpl_GetDataStructure(), and NULL.
Referenced by s_MultiSeqSrcNew().
◆ s_MultiSeqSrcNew()
|
static |
Multi-sequence source constructor.
- Parameters
-
retval BlastSeqSrc structure (already allocated) to populate [in] args Pointer to MultiSeqSrcNewArgs structure above [in]
- Returns
- Updated bssp structure (with all function pointers initialized
Definition at line 508 of file seqsrc_multiseq.cpp.
References _ASSERT, _BlastSeqSrcImpl_SetCopyFnPtr(), _BlastSeqSrcImpl_SetDataStructure(), _BlastSeqSrcImpl_SetDeleteFnPtr(), _BlastSeqSrcImpl_SetGetAvgSeqLen(), _BlastSeqSrcImpl_SetGetIsProt(), _BlastSeqSrcImpl_SetGetMaxSeqLen(), _BlastSeqSrcImpl_SetGetMinSeqLen(), _BlastSeqSrcImpl_SetGetName(), _BlastSeqSrcImpl_SetGetNumSeqs(), _BlastSeqSrcImpl_SetGetNumSeqsStats(), _BlastSeqSrcImpl_SetGetSeqLen(), _BlastSeqSrcImpl_SetGetSequence(), _BlastSeqSrcImpl_SetGetTotLen(), _BlastSeqSrcImpl_SetGetTotLenStats(), _BlastSeqSrcImpl_SetInitErrorStr(), _BlastSeqSrcImpl_SetIterNext(), _BlastSeqSrcImpl_SetReleaseSequence(), _BlastSeqSrcImpl_SetResetChunkIterator(), SMultiSeqSrcNewArgs::dbscan_mode, SMultiSeqSrcNewArgs::program, CRef< C, Locker >::Reset(), s_MultiSeqGetAvgLength(), s_MultiSeqGetIsProt(), s_MultiSeqGetMaxLength(), s_MultiSeqGetMinLength(), s_MultiSeqGetName(), s_MultiSeqGetNumSeqs(), s_MultiSeqGetNumSeqsStats(), s_MultiSeqGetSeqLen(), s_MultiSeqGetSequence(), s_MultiSeqGetTotLen(), s_MultiSeqGetTotLenStats(), s_MultiSeqIteratorNext(), s_MultiSeqReleaseSequence(), s_MultiSeqResetChunkIter(), s_MultiSeqSrcCopy(), s_MultiSeqSrcFree(), SMultiSeqSrcNewArgs::seq_vector, and strdup.
Referenced by MultiSeqBlastSeqSrcInit().
◆ s_Ncbi4naToNcbi2na()
Definition at line 427 of file blast_objmgr_tools.cpp.
References _ASSERT, b, base_length, ctable, CRandom::GetRand(), and i.
Referenced by CBlastSeqVectorOM::GetCompressedPlusStrand().
◆ s_OldGetTaxIdWithWindowMaskerSupport()
Definition at line 431 of file winmask_filter.cpp.
References set< Key, Compare >::clear(), NStr::fConvErr_NoThrow, fFF_File, FindFiles(), CDirEntry::GetPathSeparator(), set< Key, Compare >::insert(), NON_CONST_ITERATE, s_FindPathToWM(), s_WINDOW_MASKER_STAT_FILE_NAME(), and NStr::StringToInt().
Referenced by GetTaxIdWithWindowMaskerSupport().
◆ s_OOFBlastHSP2SeqAlign()
|
static |
This function is used for out-of-frame traceback conversion Converts an OOF editing script chain to a Seq-align of type Std-seg.
- Parameters
-
program BLAST program: blastx or tblastn. hsp HSP structure containing traceback produced by an out-of-frame gapped extension [in] query_id Query sequence identifier [in] subject_id Subject sequence identifier [in] query_length Length of query sequence [in] subject_length Length of subject sequence [in]
Definition at line 769 of file blast_seqalign.cpp.
References _ASSERT, eBlastTypeBlastx, eGapAlignDel, eGapAlignDel1, eGapAlignDel2, eGapAlignIns, eGapAlignIns1, eGapAlignIns2, eGapAlignSub, eNa_strand_minus, CSeq_align_Base::eType_partial, FALSE, BlastSeg::frame, BlastHSP::gap_info, CSeq_interval_Base::GetFrom(), CRef< C, Locker >::GetPointer(), CSeq_interval_Base::GetTo(), kBlastAlignmentDim, MIN, NULL, GapEditScript::num, BlastSeg::offset, GapEditScript::op_type, BlastHSP::query, CRef< C, Locker >::Reset(), s_Frame2Strand(), s_GetCurrPos(), CSeq_align_Base::SetDim(), CSeq_loc::SetEmpty(), CSeq_interval_Base::SetFrom(), CSeq_loc::SetInt(), CSeq_align_Base::SetSegs(), CSeq_interval_Base::SetTo(), CSeq_align_Base::SetType(), GapEditScript::size, BlastHSP::subject, and TRUE.
Referenced by BLASTHspListToSeqAlign().
◆ s_PrintVector()
Auxiliary function to print a vector.
- Parameters
-
data2print vector to print [in]
Definition at line 256 of file split_query_aux_priv.hpp.
Referenced by operator<<().
◆ s_ProcessErrorsFromReply()
|
static |
Process error messages from a reply object.
Every reply object from blast4 has a space for error and warning messages. This function extracts such messages and returns them to the user in two strings. All warnings are returned in one string, concatenated together with a newline as the delimiter, and all error messages are concatenated together in another string in the same way. If there are no warnings or errors, the resulting strings will be empty.
- Parameters
-
reply The reply object from blast4. errors Concatenated error messages (if any). warnings Concatenated warning messages (if any).
Definition at line 73 of file blast_services.cpp.
References eBlast4_error_flags_warning, and ITERATE.
Referenced by s_GetPartsFromReply(), and s_GetSeqsFromReply().
◆ s_QueryFactoryBlastSeqSrcInit()
|
static |
Definition at line 540 of file seqsrc_query_factory.cpp.
References BlastSeqSrcNew(), BlastSeqSrcNewInfo::constructor, BlastSeqSrcNewInfo::ctor_argument, CRef< C, Locker >::Empty(), NCBI_THROW, NULL, and s_QueryFactorySrcNew().
Referenced by QueryFactoryBlastSeqSrcInit().
◆ s_QueryFactoryGetAvgLength()
Retrieves the average length of the sequence in the BlastSeqSrc.
- Parameters
-
multiseq_handle Pointer to the structure containing sequences [in]
Definition at line 239 of file seqsrc_query_factory.cpp.
References _ASSERT.
Referenced by s_QueryFactorySrcNew().
◆ s_QueryFactoryGetIsProt()
Answers whether this object is for protein or nucleotide sequences.
- Parameters
-
multiseq_handle Pointer to the structure containing sequences [in]
Definition at line 300 of file seqsrc_query_factory.cpp.
References _ASSERT.
Referenced by s_QueryFactorySrcNew().
◆ s_QueryFactoryGetMaxLength()
The following functions interact with the C API, and have to be declared extern "C".
Retrieves the length of the longest sequence in the BlastSeqSrc.
- Parameters
-
multiseq_handle Pointer to the structure containing sequences [in]
Definition at line 217 of file seqsrc_query_factory.cpp.
References _ASSERT.
Referenced by s_QueryFactorySrcNew().
◆ s_QueryFactoryGetMinLength()
Retrieves the length of the longest sequence in the BlastSeqSrc.
- Parameters
-
multiseq_handle Pointer to the structure containing sequences [in]
Definition at line 228 of file seqsrc_query_factory.cpp.
References _ASSERT.
Referenced by s_QueryFactorySrcNew().
◆ s_QueryFactoryGetName()
Always returns NcbiEmptyCStr.
Definition at line 292 of file seqsrc_query_factory.cpp.
References NcbiEmptyCStr.
Referenced by s_QueryFactorySrcNew().
◆ s_QueryFactoryGetNextChunk()
|
static |
Mirrors the database iteration interface.
Next chunk of indices retrieval is really just a check that current index has not reached the end.
- Parameters
-
multiseq_handle Pointer to the multiple sequence object [in] itr Iterator over multiseq_handle [in] [out]
- Returns
- Status.
Definition at line 391 of file seqsrc_query_factory.cpp.
References _ASSERT, BLAST_SEQSRC_EOF, BLAST_SEQSRC_SUCCESS, BlastSeqSrcIterator::current_pos, and UINT4_MAX.
Referenced by s_QueryFactoryIteratorNext().
◆ s_QueryFactoryGetNumSeqs()
Retrieves the number of sequences in the BlastSeqSrc.
- Parameters
-
multiseq_handle Pointer to the structure containing sequences [in]
Definition at line 260 of file seqsrc_query_factory.cpp.
References _ASSERT.
Referenced by s_QueryFactorySrcNew().
◆ s_QueryFactoryGetNumSeqsStats()
Returns zero as this implementation does not use an alias file.
Definition at line 271 of file seqsrc_query_factory.cpp.
Referenced by s_QueryFactorySrcNew().
◆ s_QueryFactoryGetSeqLen()
Retrieve length of a given sequence.
- Parameters
-
multiseq_handle Pointer to the structure containing sequences [in] args Pointer to integer indicating index into the sequences vector [in]
- Returns
- Length of the sequence or BLAST_SEQSRC_ERROR.
Definition at line 368 of file seqsrc_query_factory.cpp.
References _ASSERT.
Referenced by s_QueryFactorySrcNew().
◆ s_QueryFactoryGetSequence()
|
static |
Retrieves the sequence for a given index, in a given encoding.
- Parameters
-
multiseq_handle Pointer to the structure containing sequences [in] args Pointer to BlastSeqSrcGetSeqArg structure, containing sequence index and encoding. [in]
- Returns
- return codes defined in blast_seqsrc.h
Definition at line 314 of file seqsrc_query_factory.cpp.
References _ASSERT, BLAST_SEQSRC_EOF, BLAST_SEQSRC_ERROR, BLAST_SEQSRC_SUCCESS, BlastSequenceBlkCopy(), eBlastEncodingNcbi4na, eBlastEncodingNucleotide, BlastSeqSrcGetSeqArg::encoding, FALSE, BLAST_SequenceBlk::lcase_mask, BLAST_SequenceBlk::lcase_mask_allocated, NULL, BLAST_SequenceBlk::oid, BlastSeqSrcGetSeqArg::oid, BlastSeqSrcGetSeqArg::seq, BLAST_SequenceBlk::sequence, and BLAST_SequenceBlk::sequence_start.
Referenced by s_QueryFactorySrcNew().
◆ s_QueryFactoryGetTotLen()
Returns 0 as total length, indicating that this is NOT a database!
Definition at line 278 of file seqsrc_query_factory.cpp.
Referenced by s_QueryFactorySrcNew().
◆ s_QueryFactoryGetTotLenStats()
Returns 0 as total statistic length, as this implementation does not use alias files.
Definition at line 285 of file seqsrc_query_factory.cpp.
Referenced by s_QueryFactorySrcNew().
◆ s_QueryFactoryIteratorNext()
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static |
Gets the next sequence index, given a BlastSeqSrc pointer.
- Parameters
-
multiseq_handle Handle to access the underlying object over which iteration occurs. [in] itr Iterator over seqsrc [in] [out]
- Returns
- Next index in the sequence set
Definition at line 421 of file seqsrc_query_factory.cpp.
References _ASSERT, BLAST_SEQSRC_EOF, BlastSeqSrcIterator::current_pos, and s_QueryFactoryGetNextChunk().
Referenced by s_QueryFactorySrcNew().
◆ s_QueryFactoryReleaseSequence()
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static |
Deallocates the uncompressed sequence buffer if necessary.
- Parameters
-
args Pointer to BlastSeqSrcGetSeqArg structure [in]
Definition at line 355 of file seqsrc_query_factory.cpp.
References _ASSERT, BlastSeqSrcGetSeqArg::seq, BLAST_SequenceBlk::sequence_start, BLAST_SequenceBlk::sequence_start_allocated, and sfree.
Referenced by s_QueryFactorySrcNew().
◆ s_QueryFactoryResetChunkIter()
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static |
Resets the internal bookmark iterator (N/A in this case)
Definition at line 410 of file seqsrc_query_factory.cpp.
Referenced by s_QueryFactorySrcNew().
◆ s_QueryFactorySrcCopy()
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static |
Multi-sequence sequence source copier: creates a new reference to the CQueryFactoryInfo object and copies the rest of the BlastSeqSrc structure.
- Parameters
-
seq_src BlastSeqSrc structure to copy [in]
- Returns
- Pointer to the new BlastSeqSrc.
Definition at line 470 of file seqsrc_query_factory.cpp.
References _BlastSeqSrcImpl_GetDataStructure(), _BlastSeqSrcImpl_SetDataStructure(), and NULL.
Referenced by s_QueryFactorySrcNew().
◆ s_QueryFactorySrcFree()
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static |
Multi sequence source destructor: frees its internal data structure.
- Parameters
-
seq_src BlastSeqSrc structure to free [in]
- Returns
- NULL
Definition at line 455 of file seqsrc_query_factory.cpp.
References _BlastSeqSrcImpl_GetDataStructure(), and NULL.
Referenced by s_QueryFactorySrcNew().
◆ s_QueryFactorySrcNew()
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static |
Multi-sequence source constructor.
- Parameters
-
retval BlastSeqSrc structure (already allocated) to populate [in] args Pointer to QueryFactorySrcNewArgs structure above [in]
- Returns
- Updated bssp structure (with all function pointers initialized
Definition at line 488 of file seqsrc_query_factory.cpp.
References _ASSERT, _BlastSeqSrcImpl_SetCopyFnPtr(), _BlastSeqSrcImpl_SetDataStructure(), _BlastSeqSrcImpl_SetDeleteFnPtr(), _BlastSeqSrcImpl_SetGetAvgSeqLen(), _BlastSeqSrcImpl_SetGetIsProt(), _BlastSeqSrcImpl_SetGetMaxSeqLen(), _BlastSeqSrcImpl_SetGetMinSeqLen(), _BlastSeqSrcImpl_SetGetName(), _BlastSeqSrcImpl_SetGetNumSeqs(), _BlastSeqSrcImpl_SetGetNumSeqsStats(), _BlastSeqSrcImpl_SetGetSeqLen(), _BlastSeqSrcImpl_SetGetSequence(), _BlastSeqSrcImpl_SetGetTotLen(), _BlastSeqSrcImpl_SetGetTotLenStats(), _BlastSeqSrcImpl_SetInitErrorStr(), _BlastSeqSrcImpl_SetIterNext(), _BlastSeqSrcImpl_SetReleaseSequence(), _BlastSeqSrcImpl_SetResetChunkIterator(), NULL, SQueryFactorySrcNewArgs::program, SQueryFactorySrcNewArgs::query_factory, CRef< C, Locker >::Reset(), s_QueryFactoryGetAvgLength(), s_QueryFactoryGetIsProt(), s_QueryFactoryGetMaxLength(), s_QueryFactoryGetMinLength(), s_QueryFactoryGetName(), s_QueryFactoryGetNumSeqs(), s_QueryFactoryGetNumSeqsStats(), s_QueryFactoryGetSeqLen(), s_QueryFactoryGetSequence(), s_QueryFactoryGetTotLen(), s_QueryFactoryGetTotLenStats(), s_QueryFactoryIteratorNext(), s_QueryFactoryReleaseSequence(), s_QueryFactoryResetChunkIter(), s_QueryFactorySrcCopy(), s_QueryFactorySrcFree(), strdup, and SQueryFactorySrcNewArgs::subj_seqs.
Referenced by s_QueryFactoryBlastSeqSrcInit().
◆ s_QueryInfo_SetContext()
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static |
Set field values for one element of the context array of a concatenated query.
All previous contexts should have already been assigned correct values.
- Parameters
-
qinfo Query info structure containing contexts. [in/out] index Index of the context to fill. [in] length Length of this context. [in]
Definition at line 65 of file blast_setup_cxx.cpp.
References _ASSERT, BlastQueryInfo::contexts, BlastContextInfo::is_valid, BlastQueryInfo::last_context, BlastContextInfo::query_length, and BlastContextInfo::query_offset.
Referenced by SetupQueryInfo_OMF().
◆ s_QueryVectorToBioseqSet()
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static |
Produces a BioseqSet from a CBlastQueryVector.
- Parameters
-
queries queries as a CBlastQueryVector
- Return values
-
CRef to BioseqSet
Definition at line 61 of file objmgr_query_data.cpp.
References CBioseq_Handle::GetBioseqCore(), CScope::GetBioseqHandle(), CBlastQueryVector::GetQuerySeqLoc(), CBlastQueryVector::GetScope(), i, CRef< C, Locker >::Reset(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), and CBlastQueryVector::Size().
Referenced by CObjMgr_RemoteQueryData::GetBioseqSet().
◆ s_QueryVectorToTSeqLocs()
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static |
Produces a vector of SeqLocs from a CBlastQueryVector.
- Parameters
-
queries queries as a CBlastQueryVector
- Return values
-
vector of SeqLocs.
Definition at line 135 of file objmgr_query_data.cpp.
References CBlastQueryVector::GetQuerySeqLoc(), i, and CBlastQueryVector::Size().
Referenced by CObjMgr_RemoteQueryData::GetSeqLocs().
◆ s_ReadLinesFromFile()
Definition at line 65 of file igblast.cpp.
Referenced by CIgAnnotationInfo::CIgAnnotationInfo().
◆ s_RemapToSubjectLoc()
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static |
Remap subject alignment if its location specified the reverse strand or a starting location other than the beginning of the sequence.
- Parameters
-
subj_aligns Seq-align containing HSPs for a given query-subject alignment [in|out] subj_loc Location of the subject sequence searched. [in]
Definition at line 1537 of file blast_seqalign.cpp.
References _ASSERT, CSeq_loc_Base::IsInt(), CSeq_loc_Base::IsWhole(), RemapAlignToLoc(), and CRef< C, Locker >::Reset().
Referenced by BlastHitList2SeqAlign_OMF(), and s_BLAST_OneSubjectResults2CSeqAlign().
◆ s_RemoveLocalPrefix()
Definition at line 809 of file igblast.cpp.
Referenced by s_MakeTopHitsId(), CIgBlast::x_AnnotateD(), CIgBlast::x_AnnotateDJ(), CIgBlast::x_AnnotateDomain(), CIgBlast::x_AnnotateJ(), and CIgBlast::x_FillJDomain().
◆ s_RestrictSeqLocs_Multiframe()
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static |
Restricts the masked locations in frame_to_bsl for the case when the BLAST program requires the query to be translated into multiple frames.
- Parameters
-
frame_to_bsl query filtered frames to adjust [out] queries all query sequences [in] query_index index of the query of interest in queries [in] qinfo BlastQueryInfo structure for the queries above [in]
Definition at line 399 of file blast_setup_cxx.cpp.
References _ASSERT, BlastSeqLoc_RestrictToInterval(), BlastQueryInfo::contexts, eExtreme_Positional, BlastContextInfo::frame, CBlastQueryFilteredFrames::GetNumFrames(), IBlastQuerySource::GetSeqLoc(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), ITERATE, CBlastQueryFilteredFrames::ListFrames(), and BlastContextInfo::query_index.
Referenced by s_GetRestrictedBlastSeqLocs().
◆ s_SearchPending()
Determine whether the search is still running.
- Parameters
-
reply Reply from get-search-results request.
- Returns
- True if search needs more time, false if done or failed.
Definition at line 85 of file remote_blast.cpp.
References eBlast4_error_code_search_pending, and i.
Referenced by CRemoteBlast::x_CheckResults(), and CRemoteBlast::x_CheckResultsDC().
◆ s_SeqAlignInSet()
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static |
Definition at line 858 of file igblast.cpp.
References CSeq_align::GetSeq_id(), CSeq_align::GetSeqStart(), CSeq_align::GetSeqStop(), and ITERATE.
Referenced by CIgBlast::s_AppendResults().
◆ s_SeqAlignToBlastSeqLoc()
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static |
Build a list of BlastSeqLoc's from a set of Dense-seg contained in a Seq-align-set.
This function processes Dense-segs, and adds the range of each hit to a list of BlastSeqLoc structures. Frame information is used to translate hit coordinates hits to the plus strand. All of the HSPs should refer to the same query; both the query and subject in the HSP are ignored. This is used to construct a set of filtered areas from hits against a repeats database.
- Parameters
-
alignment Seq-align-set containing Dense-segs which specify the ranges of hits. [in] locs Filtered areas for this query are added here. [out]
Definition at line 144 of file repeats_filter_cxx.cpp.
References _ASSERT, BlastSeqLocNew(), CSeq_align_set_Base::Get(), CDense_seg_Base::GetDim(), CDense_seg_Base::GetLens(), CDense_seg_Base::GetNumseg(), CDense_seg_Base::GetStarts(), CDense_seg_Base::GetStrands(), and ITERATE.
Referenced by s_FillMaskLocFromBlastResults().
◆ s_SeqDbGetAvgLength()
Retrieves the average length of sequences in the BlastSeqSrc.
- Parameters
-
seqdb_handle Pointer to initialized CSeqDB object [in] ignoreme Unused by this implementation [in]
Definition at line 203 of file seqsrc_seqdb.cpp.
References MAX, s_SeqDbGetNumSeqs(), and s_SeqDbGetTotLen().
Referenced by s_InitNewSeqDbSrc().
◆ s_SeqDbGetIsProt()
Checks whether database is protein or nucleotide.
- Parameters
-
seqdb_handle Pointer to initialized CSeqDB object [in]
- Returns
- TRUE if database is protein, FALSE if nucleotide.
Definition at line 224 of file seqsrc_seqdb.cpp.
Referenced by s_InitNewSeqDbSrc().
◆ s_SeqDbGetMaxLength()
Retrieves the length of the longest sequence in the BlastSeqSrc.
- Parameters
-
seqdb_handle Pointer to initialized CSeqDB object [in]
Definition at line 137 of file seqsrc_seqdb.cpp.
References CSeqDB::GetMaxLength().
Referenced by s_InitNewSeqDbSrc().
◆ s_SeqDbGetMinLength()
Retrieves the length of the shortest sequence in the BlastSeqSrc.
- Parameters
-
seqdb_handle Pointer to initialized CSeqDB object [in]
Definition at line 146 of file seqsrc_seqdb.cpp.
References CSeqDB::GetMinLength().
Referenced by s_InitNewSeqDbSrc().
◆ s_SeqDbGetName()
Retrieves the name of the BLAST database.
- Parameters
-
seqdb_handle Pointer to initialized CSeqDB object [in]
Definition at line 214 of file seqsrc_seqdb.cpp.
References CSeqDB::GetDBNameList().
Referenced by s_InitNewSeqDbSrc().
◆ s_SeqDbGetNextChunk()
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static |
Assigns next chunk of the database to the sequence source iterator.
- Parameters
-
seqdb_handle Reference to the database object, cast to void* to satisfy the signature requirement. [in] itr Iterator over the database sequence source. [in|out]
Definition at line 465 of file seqsrc_seqdb.cpp.
References BLAST_SEQSRC_EOF, BLAST_SEQSRC_ERROR, BLAST_SEQSRC_SUCCESS, BlastSeqSrcIterator::chunk_sz, BlastSeqSrcIterator::current_pos, eOidList, CSeqDB::eOidList, eOidRange, CSeqDB::eOidRange, CSeqDB::GetNextOIDChunk(), BlastSeqSrcIterator::itr_type, malloc(), BlastSeqSrcIterator::oid_list, BlastSeqSrcIterator::oid_range, and sfree.
Referenced by s_SeqDbIteratorNext().
◆ s_SeqDbGetNumSeqs()
Retrieves the number of sequences in the BlastSeqSrc.
- Parameters
-
seqdb_handle Pointer to initialized CSeqDB object [in]
Definition at line 164 of file seqsrc_seqdb.cpp.
References CSeqDB::GetNumSeqs().
Referenced by s_InitNewSeqDbSrc(), and s_SeqDbGetAvgLength().
◆ s_SeqDbGetNumSeqsStats()
Retrieves the number of sequences from alias file to be used for.
- Parameters
-
seqdb_handle Pointer to initialized CSeqDB object [in]
Definition at line 174 of file seqsrc_seqdb.cpp.
References CSeqDB::GetNumSeqsStats().
Referenced by s_InitNewSeqDbSrc().
◆ s_SeqDbGetSeqLen()
Retrieve length of a given database sequence.
- Parameters
-
seqdb_handle Pointer to initialized CSeqDB object [in] args Pointer to integer indicating ordinal id [in]
- Returns
- Length of the database sequence or BLAST_SEQSRC_ERROR.
Definition at line 449 of file seqsrc_seqdb.cpp.
References BLAST_SEQSRC_ERROR, and CSeqDB::GetSeqLength().
Referenced by s_InitNewSeqDbSrc().
◆ s_SeqDbGetSequence()
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static |
Retrieves the sequence meeting the criteria defined by its second argument.
- Parameters
-
seqdb_handle Pointer to initialized CSeqDB object [in] args Pointer to BlastSeqSrcGetSeqArg structure [in]
- Returns
- return codes defined in blast_seqsrc.h
Definition at line 287 of file seqsrc_seqdb.cpp.
References ASSERT, CSeqDBIdSet::Blank(), BLAST_SEQSRC_ERROR, BLAST_SEQSRC_EXCLUDED, BLAST_SEQSRC_SUCCESS, BlastSeqBlkSetSeqRanges(), BlastSeqSrcSetRangesArgFree(), BlastSequenceBlkClean(), BlastSetUp_SeqBlkNew(), buf, BlastSeqSrcGetSeqArg::check_oid_exclusion, eBlastEncodingNcbi4na, eBlastEncodingNucleotide, eHardSubjMasking, eMalloc, BlastSeqSrcGetSeqArg::encoding, eNoSubjMasking, CSeqDB::TOffsetPair::first, CSeqDB::GetAmbigPartialSeq(), CSeqDB::GetAmbigSeqAlloc(), CSeqDB::GetIdSet(), CSeqDB::GetMaskData(), CSeqDB::GetSeqIDs(), CSeqDB::GetSequence(), i, len, NULL, BlastSeqSrcSetRangesArg::num_ranges, BLAST_SequenceBlk::oid, BlastSeqSrcGetSeqArg::oid, CSeqDB::TSequenceRanges::push_back(), BlastSeqSrcSetRangesArg::ranges, BlastSeqSrcGetSeqArg::ranges, BlastSeqSrcGetSeqArg::reset_ranges, CSeqDB::TOffsetPair::second, BlastSeqSrcGetSeqArg::seq, BLAST_SequenceBlk::sequence, BLAST_SequenceBlk::sequence_allocated, BLAST_SequenceBlk::sequence_start, and TRUE.
Referenced by s_InitNewSeqDbSrc().
◆ s_SeqDbGetSupportsPartialFetching()
Determine if partial fetching should be enabled.
- Parameters
-
seqdb_handle Pointer to initialized CSeqDB object [in]
Definition at line 234 of file seqsrc_seqdb.cpp.
References CSeqDB::GetMaxLength(), CSeqDB::GetNumSeqs(), CSeqDB::GetTotalLength(), and MAX.
Referenced by s_InitNewSeqDbSrc().
◆ s_SeqDbGetTotLen()
Retrieves the total length of all sequences in the BlastSeqSrc.
- Parameters
-
seqdb_handle Pointer to initialized CSeqDB object [in]
Definition at line 183 of file seqsrc_seqdb.cpp.
References CSeqDB::GetTotalLength().
Referenced by s_InitNewSeqDbSrc(), and s_SeqDbGetAvgLength().
◆ s_SeqDbGetTotLenStats()
Retrieves the total length of all sequences from alias file.
- Parameters
-
seqdb_handle Pointer to initialized CSeqDB object [in]
Definition at line 193 of file seqsrc_seqdb.cpp.
References CSeqDB::GetTotalLengthStats().
Referenced by s_InitNewSeqDbSrc().
◆ s_SeqDbIteratorNext()
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static |
Finds the next not searched ordinal id in the iteration over BLAST database.
- Parameters
-
seqdb_handle Reference to the database object, cast to void* to satisfy the signature requirement. [in] itr Iterator of the BlastSeqSrc pointed by ptr. [in]
- Returns
- Next ordinal id.
Definition at line 511 of file seqsrc_seqdb.cpp.
References _ASSERT, abort(), BLAST_SEQSRC_EOF, BLAST_SEQSRC_ERROR, BLAST_SEQSRC_SUCCESS, BlastSeqSrcIterator::chunk_sz, BlastSeqSrcIterator::current_pos, eOidList, eOidRange, BlastSeqSrcIterator::itr_type, BlastSeqSrcIterator::oid_list, BlastSeqSrcIterator::oid_range, s_SeqDbGetNextChunk(), and UINT4_MAX.
Referenced by s_InitNewSeqDbSrc().
◆ s_SeqDbReleaseSequence()
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static |
Returns the memory allocated for the sequence buffer to the CSeqDB interface.
- Parameters
-
seqdb_handle Pointer to initialized CSeqDB object [in] args Pointer to the BlastSeqSrcGetSeqArgs structure, containing sequence block with the buffer that needs to be deallocated. [in]
Definition at line 417 of file seqsrc_seqdb.cpp.
References _ASSERT, BlastSeqSrcSetRangesArgFree(), FALSE, NULL, BlastSeqSrcGetSeqArg::ranges, CSeqDB::RetSequence(), BlastSeqSrcGetSeqArg::seq, BLAST_SequenceBlk::sequence, BLAST_SequenceBlk::sequence_allocated, BLAST_SequenceBlk::sequence_start, BLAST_SequenceBlk::sequence_start_allocated, and sfree.
Referenced by s_InitNewSeqDbSrc().
◆ s_SeqDbResetChunkIterator()
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static |
Resets CSeqDB's internal chunk bookmark.
- Parameters
-
seqdb_handle Reference to the database object, cast to void* to satisfy the signature requirement. [in]
Definition at line 554 of file seqsrc_seqdb.cpp.
References _ASSERT, CSeqDB::FlushOffsetRangeCache(), and CSeqDB::ResetInternalChunkBookmark().
Referenced by s_InitNewSeqDbSrc().
◆ s_SeqDbSetNumberOfThreads()
Setting number of threads in MT mode.
- Parameters
-
n_threads number of threads [in]
Definition at line 155 of file seqsrc_seqdb.cpp.
References n, and CSeqDB::SetNumberOfThreads().
Referenced by s_InitNewSeqDbSrc().
◆ s_SeqDbSetRanges()
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static |
Set sequence ranges for partial fetching.
- Parameters
-
seqdb_handle Pointer to initialized CSeqDB object [in] args Pointer to BlastSeqSrcSetRangesArg structure [in]
Definition at line 268 of file seqsrc_seqdb.cpp.
References i, set< Key, Compare >::insert(), BlastSeqSrcSetRangesArg::num_ranges, BlastSeqSrcSetRangesArg::oid, BlastSeqSrcSetRangesArg::ranges, and CSeqDB::SetOffsetRanges().
Referenced by s_InitNewSeqDbSrc().
◆ s_SeqDbSrcCopy()
|
static |
SeqDb sequence source copier: creates a new reference to the CSeqDB object and copies the rest of the BlastSeqSrc structure.
- Parameters
-
seq_src BlastSeqSrc structure to copy [in]
- Returns
- Pointer to the new BlastSeqSrc.
Definition at line 627 of file seqsrc_seqdb.cpp.
References _BlastSeqSrcImpl_GetDataStructure(), _BlastSeqSrcImpl_SetDataStructure(), and NULL.
Referenced by s_InitNewSeqDbSrc().
◆ s_SeqDbSrcFree()
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static |
SeqDb sequence source destructor: frees its internal data structure.
- Parameters
-
seq_src BlastSeqSrc structure to free [in]
- Returns
- NULL
Definition at line 610 of file seqsrc_seqdb.cpp.
References _BlastSeqSrcImpl_GetDataStructure(), and NULL.
Referenced by s_InitNewSeqDbSrc().
◆ s_SeqDbSrcNew()
|
static |
SeqDb sequence source constructor.
- Parameters
-
retval BlastSeqSrc structure (already allocated) to populate [in] args Pointer to internal CSeqDbSrcNewArgs structure (
- See also
- CSeqDbSrcNewArgs) [in]
- Returns
- Updated seq_src structure (with all function pointers initialized
Definition at line 701 of file seqsrc_seqdb.cpp.
References _ASSERT, _BlastSeqSrcImpl_SetInitErrorStr(), eDPF_ErrCodeExplanation, CSeqDB::eNucleotide, CSeqDB::eProtein, CSeqDB::GetAvailableMaskAlgorithms(), CSeqDbSrcNewArgs::GetDbName(), CSeqDbSrcNewArgs::GetDbType(), CSeqDbSrcNewArgs::GetFinalOid(), CSeqDbSrcNewArgs::GetFirstOid(), CSeqDbSrcNewArgs::GetMaskAlgoId(), CSeqDbSrcNewArgs::GetMaskType(), msg(), s_InitNewSeqDbSrc(), CSeqDB::SetIterationRange(), and strdup.
Referenced by SeqDbBlastSeqSrcInit().
◆ s_SeqDbSrcSharedNew()
|
static |
Populates a BlastSeqSrc, creating a new reference to the already existing SeqDb object.
- Parameters
-
retval Original BlastSeqSrc [in] args Pointer to a reference to CSeqDB object [in]
- Returns
- retval
Definition at line 683 of file seqsrc_seqdb.cpp.
References _ASSERT, and s_InitNewSeqDbSrc().
Referenced by SeqDbBlastSeqSrcInit().
◆ s_SeqIntervalToSeqLocInfo()
|
static |
Definition at line 110 of file seqinfosrc_seqvec.cpp.
References COpenRange< TSeqPos >::GetEmpty(), CSeq_interval_Base::GetFrom(), CSeq_interval_Base::GetTo(), and COpenRange< Position >::IntersectingWith().
Referenced by CSeqVecSeqInfoSrc::GetMasks().
◆ s_SeqLoc2MaskedSubjRanges()
|
static |
Definition at line 661 of file blast_setup_cxx.cpp.
References _ASSERT, CSeq_loc_Base::e_not_set, CSeqDB::TOffsetPair::first, CPacked_seqint_Base::Get(), CSeq_loc_mix_Base::Get(), CSeq_interval_Base::GetFrom(), CSeq_loc_Base::GetInt(), CSeq_loc_Base::GetMix(), CSeq_loc_Base::GetPacked_int(), CSeq_interval_Base::GetTo(), CSeq_loc_Base::IsEmpty(), CSeq_loc_Base::IsInt(), CSeq_loc_Base::IsMix(), CSeq_loc_Base::IsNull(), CSeq_loc_Base::IsPacked_int(), ITERATE, MIN, NCBI_THROW, offset, output, compile_time_bits::range(), CSeqDB::TOffsetPair::second, and CSeq_loc_Base::Which().
Referenced by SetupSubjects_OMF().
◆ s_SeqTypeToResidue()
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static |
Definition at line 142 of file blast_services.cpp.
References eBlast4_residue_type_nucleotide, eBlast4_residue_type_protein, and eBlast4_residue_type_unknown.
Referenced by s_BuildGetSeqPartsRequest(), and s_BuildGetSeqRequest().
◆ s_SortResultsByEvalue()
|
staticprivate |
Sort blast results according to evalue.
Definition at line 1935 of file igblast.cpp.
References ITERATE, result, results, s_CompareSeqAlignByEvalue(), and CSeq_align_set_Base::Set().
Referenced by CIgBlast::Run().
◆ s_SplitAlignVectorBySubjects()
|
static |
CRemoteBlast does not separate each hit to the query in discontinuous Seq-aligns, so we do it here.
This functionality might be merged with CRemoteBlast::GetSeqAlignSets() in the future
Definition at line 183 of file remote_search.cpp.
References CSeq_id::Compare(), CSeq_id_Base::e_Gi, CSeq_id::e_NO, CSeq_align_Base::eType_disc, CSeq_align_set_Base::Get(), ITERATE, NON_CONST_ITERATE, CRef< C, Locker >::NotEmpty(), CRef< C, Locker >::Reset(), CSeq_align_set_Base::Set(), CSeq_align_Base::SetDim(), CSeq_align_Base::SetSegs(), and CSeq_align_Base::SetType().
Referenced by s_BuildResultsRemote().
◆ s_TransposeSeqAlignVector()
|
static |
Transpose the (linearly organized) seqalign set matrix from (q1 s1 q2 s1 ...
qN s1, ..., q1 sM q2 sM ... qN sM) to (q1 s1 q1 s2 ... q1 sM, ..., qN s1 qN s2 ... qN sM) this method only reorganizes the seqalign sets, does not copy them.
- Parameters
-
alnvec data structure to reorganize [in] num_queries number of queries [in] num_subjects number of subjects [in]
- Return values
-
transposed data structure
Definition at line 1875 of file blast_seqalign.cpp.
References _ASSERT.
Referenced by s_BlastResults2SeqAlignSequenceCmp_OMF().
◆ s_TSeqLocVectorToBioseqSet()
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static |
Produces a BioseqSet from a TSeqLocVector.
- Parameters
-
queries queries as a TSeqLocVector
- Return values
-
Cref to BioseqSet
Definition at line 92 of file objmgr_query_data.cpp.
References ITERATE, query, CSeq_entry_Base::SetSeq(), and CBioseq_set_Base::SetSeq_set().
Referenced by CObjMgr_RemoteQueryData::GetBioseqSet().
◆ s_TSeqLocVectorToTSeqLocs()
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static |
Produces a vector of SeqLocs from a TSeqLocVector.
- Parameters
-
queries queries as a TSeqLocVector
- Return values
-
vector of SeqLocs.
Definition at line 119 of file objmgr_query_data.cpp.
References ITERATE, and query.
Referenced by CObjMgr_RemoteQueryData::GetSeqLocs().
◆ s_Validate() [1/3]
|
static |
Performs validation on data provided before invoking the CORE PSSM engine.
Should be called after invoking Process() on its argument
- Exceptions
-
CPssmEngineException if validation fails
Definition at line 153 of file pssm_engine.cpp.
References _ASSERT, Blast_MessageFree(), IPssmInputCdd::GetData(), IPssmInputCdd::GetOptions(), Blast_Message::message, msg(), NCBI_THROW, NULL, PSIBlastOptionsValidate(), and string.
◆ s_Validate() [2/3]
|
static |
Performs validation on data provided before invoking the CORE PSSM engine.
Should be called after invoking Process() on its argument
- Exceptions
-
CPssmEngineException if validation fails
Definition at line 131 of file pssm_engine.cpp.
References _ASSERT, Blast_MessageFree(), IPssmInputData::GetData(), IPssmInputData::GetOptions(), Blast_Message::message, msg(), NCBI_THROW, NULL, PSIBlastOptionsValidate(), and string.
Referenced by CPssmEngine::x_CreatePssmFromCDD(), CPssmEngine::x_CreatePssmFromFreqRatios(), and CPssmEngine::x_CreatePssmFromMsa().
◆ s_Validate() [3/3]
|
static |
Performs validation on data provided before invoking the CORE PSSM engine.
Should be called after invoking Process() on its argument
- Exceptions
-
CPssmEngineException if validation fails
Definition at line 176 of file pssm_engine.cpp.
References _ASSERT, IPssmInputFreqRatios::GetData(), ITERATE, and NCBI_THROW.
◆ s_ValidateExon()
|
static |
Definition at line 400 of file blast_seqalign.cpp.
References CSeq_id::AsFastaString(), CSpliced_exon_chunk_Base::e_Genomic_ins, CSpliced_exon_chunk_Base::e_Match, CSpliced_exon_chunk_Base::e_Mismatch, CSpliced_exon_chunk_Base::e_Product_ins, g(), CSpliced_exon_Base::GetGenomic_end(), CSpliced_exon_Base::GetGenomic_start(), CProduct_pos_Base::GetNucpos(), CSpliced_exon_Base::GetParts(), CSpliced_exon_Base::GetProduct_end(), and CSpliced_exon_Base::GetProduct_start().
Referenced by MakeSplicedSeg().
◆ s_WINDOW_MASKER_PATH()
Referenced by WindowMaskerPathGet(), WindowMaskerPathInit(), and WindowMaskerPathReset().
◆ s_WINDOW_MASKER_STAT_FILE_NAME()
◆ SafeSetupQueries()
| BLAST_SequenceBlk * SafeSetupQueries | ( | IBlastQuerySource & | queries, |
| const CBlastOptions * | options, | ||
| BlastQueryInfo * | query_info, | ||
| TSearchMessages & | messages | ||
| ) |
Wrapper around SetupQueries.
- Parameters
-
queries interface to obtain query data [in] options BLAST algorithm options [in] query_info BlastQueryInfo structure [in|out] messages error/warning messages are returned here [in|out]
Definition at line 1471 of file blast_setup_cxx.cpp.
References _ASSERT, IBlastQuerySource::Empty(), CBlastOptions::GetProgramType(), CBlastOptions::GetStrandOption(), CBLAST_SequenceBlk::Release(), and SetupQueries_OMF().
Referenced by CObjMgr_LocalQueryData::GetSequenceBlk(), and CObjMgrFree_LocalQueryData::GetSequenceBlk().
◆ SafeSetupQueryInfo()
| BlastQueryInfo * SafeSetupQueryInfo | ( | const IBlastQuerySource & | queries, |
| const CBlastOptions * | options | ||
| ) |
Wrapper around SetupQueryInfo.
- Parameters
-
queries interface to obtain query data [in] options BLAST algorithm options [in]
Definition at line 1488 of file blast_setup_cxx.cpp.
References _ASSERT, IBlastQuerySource::Empty(), CBlastQueryInfo::Get(), CBlastOptions::GetProgramType(), CBlastOptions::GetStrandOption(), NCBI_THROW, NULL, CBlastQueryInfo::Release(), and SetupQueryInfo_OMF().
Referenced by CObjMgr_LocalQueryData::GetQueryInfo(), and CObjMgrFree_LocalQueryData::GetQueryInfo().
◆ SBlast4ParamFinder()
|
inline |
Definition at line 576 of file blast_options_builder.cpp.
◆ SBlastSequence() [1/3]
|
inline |
Default constructor.
Definition at line 69 of file blast_setup.hpp.
◆ SBlastSequence() [2/3]
|
inline |
Allocates a sequence buffer of the specified length.
- Parameters
-
buf_len number of bytes to allocate [in]
Definition at line 75 of file blast_setup.hpp.
References SBlastSequence::data, NStr::IntToString(), and NCBI_THROW.
◆ SBlastSequence() [3/3]
Parametrized constructor.
- Parameters
-
d buffer containing sequence data [in] l length of buffer above [in]
Definition at line 88 of file blast_setup.hpp.
◆ SBlastSetupData()
|
inline |
Definition at line 103 of file blast_aux_priv.hpp.
◆ ScorePositionSort()
Definition at line 428 of file igblast.hpp.
References ScorePositionSort::m_scope.
◆ SDatabaseScanData()
| SDatabaseScanData::SDatabaseScanData | ( | ) |
Default ctor.
Definition at line 471 of file setup_factory.cpp.
References SDatabaseScanData::kNoPhiBlastPattern, and SDatabaseScanData::m_NumPatOccurInDB.
◆ SeqDbBlastSeqSrcInit() [1/2]
| BlastSeqSrc * SeqDbBlastSeqSrcInit | ( | const string & | dbname, |
| bool | is_prot, | ||
| Uint4 | first_seq = 0, |
||
| Uint4 | last_seq = 0, |
||
| Int4 | mask_algo_id = -1, |
||
| ESubjectMaskingType | mask_type = eNoSubjMasking |
||
| ) |
Initialize the sequence source structure.
- Parameters
-
dbname BLAST database name [in] is_prot Is this a protein or nucleotide database? [in] first_seq First ordinal id in the database to search [in] last_seq Last ordinal id in the database to search (full database if 0) [in] mask_algo_id Database masking algorithm ID (-1 if not applicable) [in] mask_type Type of database masking [in]
Definition at line 764 of file seqsrc_seqdb.cpp.
References BlastSeqSrcNew(), BlastSeqSrcNewInfo::constructor, BlastSeqSrcNewInfo::ctor_argument, dbname(), NULL, and s_SeqDbSrcNew().
Referenced by BOOST_AUTO_TEST_CASE(), CSetupFactory::CreateBlastSeqSrc(), and CTracebackSearchTestFixture::x_Traceback().
◆ SeqDbBlastSeqSrcInit() [2/2]
| BlastSeqSrc * SeqDbBlastSeqSrcInit | ( | CSeqDB * | seqdb, |
| Int4 | mask_algo_id = -1, |
||
| ESubjectMaskingType | mask_type = eNoSubjMasking |
||
| ) |
Initialize the sequence source structure using an existing SeqDB object.
- Parameters
-
seqdb CSeqDB object [in] mask_algo_id Database masking algorithm ID (-1 if not applicable) [in] mask_type Type of database masking [in]
Definition at line 780 of file seqsrc_seqdb.cpp.
References BlastSeqSrcNew(), BlastSeqSrcNewInfo::constructor, BlastSeqSrcNewInfo::ctor_argument, data, NULL, and s_SeqDbSrcSharedNew().
◆ SetAvgLength() [1/2]
|
inline |
Sets average length.
Definition at line 97 of file seqsrc_multiseq.cpp.
References CMultiSeqInfo::m_iAvgLength.
◆ SetAvgLength() [2/2]
|
inline |
Sets average length.
Definition at line 180 of file seqsrc_query_factory.cpp.
References CQueryFactoryInfo::m_AvgLength.
◆ SetBatchNumber()
|
inline |
Definition at line 116 of file local_blast.hpp.
References CLocalBlast::m_batch_num_str, NStr::NumericToString(), and string.
Referenced by CBlastnApp::x_RunMTBySplitDB().
◆ SetBestHitOverhang() [1/2]
| void CBlastOptions::SetBestHitOverhang | ( | double | overhang | ) |
Definition at line 1876 of file blast_options_cxx.cpp.
References eBlastOpt_BestHitOverhang, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetBestHitOverhang(), and CBlastOptionsRemote::SetValue().
Referenced by BOOST_AUTO_TEST_CASE(), CHspFilteringArgs::ExtractAlgorithmOptions(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetBestHitOverhang() [2/2]
|
inline |
Definition at line 1385 of file blast_options_local_priv.hpp.
References _ASSERT, BlastHSPFilteringOptions::best_hit, BlastHSPBestHitOptionsNew(), BlastHSPFilteringOptions_AddBestHit(), BlastHSPFilteringOptionsNew(), eBoth, BlastHitSavingOptions::hsp_filt_opt, kBestHit_ScoreEdgeDflt, CBlastOptionsLocal::m_HitSaveOpts, NULL, and BlastHSPBestHitOptions::overhang.
Referenced by CBlastOptions::SetBestHitOverhang().
◆ SetBestHitScoreEdge() [1/2]
| void CBlastOptions::SetBestHitScoreEdge | ( | double | score_edge | ) |
Definition at line 1895 of file blast_options_cxx.cpp.
References eBlastOpt_BestHitScoreEdge, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetBestHitScoreEdge(), and CBlastOptionsRemote::SetValue().
Referenced by BOOST_AUTO_TEST_CASE(), CHspFilteringArgs::ExtractAlgorithmOptions(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetBestHitScoreEdge() [2/2]
|
inline |
Definition at line 1355 of file blast_options_local_priv.hpp.
References _ASSERT, BlastHSPFilteringOptions::best_hit, BlastHSPBestHitOptionsNew(), BlastHSPFilteringOptions_AddBestHit(), BlastHSPFilteringOptionsNew(), eBoth, BlastHitSavingOptions::hsp_filt_opt, kBestHit_OverhangDflt, CBlastOptionsLocal::m_HitSaveOpts, NULL, and BlastHSPBestHitOptions::score_edge.
Referenced by CBlastOptions::SetBestHitScoreEdge().
◆ SetCandidateSeqs()
|
inline |
Sets the max number of candidate matches to process with BLAST @candidates max number of target sequences to process with BLAST [in].
Definition at line 87 of file blastp_kmer_options.hpp.
Referenced by CBlastKmerThread::Main(), and CBlastKmerApplication::Run().
◆ SetChaining() [1/3]
| void CBlastOptions::SetChaining | ( | bool | ch | ) |
Definition at line 1760 of file blast_options_cxx.cpp.
References CBlastOptions::m_Local, CBlastOptionsLocal::SetChaining(), and CBlastOptions::x_Throwx().
◆ SetChaining() [2/3]
|
inline |
Enables/disables chaining.
- Parameters
-
ch Chaining enabled, if ch is true [in]
Definition at line 134 of file blast_prot_options.hpp.
Referenced by CBlastOptionsFactory::CreateTask().
◆ SetChaining() [3/3]
|
inline |
Definition at line 1262 of file blast_options_local_priv.hpp.
References BlastExtensionOptions::chaining, and CBlastOptionsLocal::m_ExtnOpts.
Referenced by CBlastOptions::SetChaining().
◆ SetChunkBounds()
| void CSplitQueryBlk::SetChunkBounds | ( | size_t | chunk_num, |
| const TChunkRange & | chunk_range | ||
| ) |
Set the boundaries of a chunk in the concatenated query.
- Parameters
-
chunk_num desired chunk [in] chunk_range range in the concatenated query for this chunk [in]
Definition at line 150 of file split_query_blk.cpp.
References COpenRange< Position >::GetFrom(), COpenRange< Position >::GetToOpen(), CSplitQueryBlk::m_SplitQueryBlk, and SplitQueryBlk_SetChunkBounds().
Referenced by CQuerySplitter::x_ComputeChunkRanges().
◆ SetChunkOverlapSize()
| void CSplitQueryBlk::SetChunkOverlapSize | ( | size_t | size | ) |
Sets the size (# of bases/residues) of overlap between query chunks.
- Parameters
-
size value to set [in]
Definition at line 200 of file split_query_blk.cpp.
References CSplitQueryBlk::m_SplitQueryBlk, ncbi::grid::netcache::search::fields::size, and SplitQueryBlk_SetChunkOverlapSize().
Referenced by CQuerySplitter::x_ComputeChunkRanges().
◆ SetClientId()
Sets the client ID used by this object to send requests.
Definition at line 463 of file remote_blast.hpp.
References CRemoteBlast::m_ClientId.
Referenced by BOOST_AUTO_TEST_CASE(), and InitializeRemoteBlast().
◆ SetCoding() [1/3]
|
inlinevirtual |
@inheritDoc
Definition at line 494 of file blast_objmgr_tools.cpp.
References CBlastSeqVectorOM::m_SeqVector, and CSeqVector::SetCoding().
◆ SetCoding() [2/3]
|
virtual |
@inheritDoc
Implements IBlastSeqVector.
Definition at line 131 of file bioseq_extract_data_priv.cpp.
References _ASSERT, CSeqConvert::Convert(), CSeq_data_Base::e_Ncbi2na, CSeq_data_Base::e_Ncbi4na, CSeq_data_Base::e_Ncbistdaa, CBlastSeqVectorFromCSeq_data::m_Encoding, CBlastSeqVectorFromCSeq_data::m_SequenceData, NCBI_THROW, IBlastSeqVector::size(), tmp, and CBlastSeqVectorFromCSeq_data::x_Encoding_CSeq_data2CSeqUtil().
Referenced by CBlastSeqVectorFromCSeq_data::GetCompressedPlusStrand().
◆ SetCoding() [3/3]
|
pure virtual |
Sets the encoding for the sequence data.
Two encodings are really necessary: ncbistdaa and ncbi4na, both use 1 byte per residue/base
Implemented in CBlastSeqVectorFromCSeq_data.
Referenced by GetSequenceCompressedNucleotide(), GetSequenceProtein(), and GetSequenceSingleNucleotideStrand().
◆ SetComplexityAdjMode() [1/3]
Definition at line 2127 of file blast_options_cxx.cpp.
References eBlastOpt_ComplexityAdjMode, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetComplexityAdjMode(), and CBlastOptionsRemote::SetValue().
Referenced by CRMBlastNArg::ExtractAlgorithmOptions(), CBlastOptionsHandle::SetComplexityAdjMode(), and CMagicBlastOptionsHandle::SetScoringOptionsDefaults().
◆ SetComplexityAdjMode() [2/3]
Sets ComplexityAdjMode -RMH-.
- Parameters
-
m ComplexityAdjMode [in]
Definition at line 297 of file blast_options_handle.hpp.
References CBlastOptionsHandle::m_Opts, and CBlastOptions::SetComplexityAdjMode().
Referenced by CBlastNucleotideOptionsHandle::SetMBScoringOptionsDefaults(), and CBlastNucleotideOptionsHandle::SetScoringOptionsDefaults().
◆ SetComplexityAdjMode() [3/3]
Definition at line 1615 of file blast_options_local_priv.hpp.
References BlastScoringOptions::complexity_adjusted_scoring, and CBlastOptionsLocal::m_ScoringOpts.
Referenced by CBlastOptions::SetComplexityAdjMode().
◆ SetCompositionBasedStats() [1/5]
|
inline |
Set composition based statistics mode.
- Parameters
-
mode Composition based statistics mode
Definition at line 110 of file blast_rps_options.hpp.
References eCompositionBasedStats, and eNoCompositionBasedStats.
Referenced by BOOST_AUTO_TEST_CASE(), RpsTestFixture::NuclSearch(), and CBlastRPSOptionsHandle::SetGappedExtensionDefaults().
◆ SetCompositionBasedStats() [2/5]
|
inline |
Sets this mode, which mostly specifies whether composition of db sequence is taken into account when calculating expect values.
- Parameters
-
mode composition-based statistics mode [in]
Definition at line 77 of file blast_advprot_options.hpp.
Referenced by CdBlaster::blast(), BOOST_FIXTURE_TEST_CASE(), CSimpleB2SWrapper::InitializeToDefaults(), CdBlaster::psiBlast(), and CSimpleB2SWrapper::SetCompoAdjustMode().
◆ SetCompositionBasedStats() [3/5]
| void CBlastOptions::SetCompositionBasedStats | ( | ECompoAdjustModes | mode | ) |
Definition at line 1654 of file blast_options_cxx.cpp.
References eBlastOpt_CompositionBasedStats, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetCompositionBasedStats(), and CBlastOptionsRemote::SetValue().
Referenced by BOOST_AUTO_TEST_CASE(), CheckForFreqRatioFile(), CIgBlast::Run(), CPsiBlastApp::Run(), s_SetCompositionBasedStats(), CBlastAdvancedProteinOptionsHandle::SetGappedExtensionDefaults(), CBlastxOptionsHandle::SetGappedExtensionDefaults(), CDeltaBlastOptionsHandle::SetGappedExtensionDefaults(), CTBlastnOptionsHandle::SetGappedExtensionDefaults(), CIgBlastpAppArgs::x_CreateOptionsHandle(), CBlastOptionsBuilder::x_ProcessOneOption(), and CIgBlast::x_SetupVSearch().
◆ SetCompositionBasedStats() [4/5]
|
inline |
Sets this mode, which mostly specifies whether composition of db sequence is taken into account when calculating expect values.
- Parameters
-
mode composition-based statistics mode [in]
Definition at line 111 of file blastx_options.hpp.
◆ SetCompositionBasedStats() [5/5]
|
inline |
Definition at line 1196 of file blast_options_local_priv.hpp.
References BlastExtensionOptions::compositionBasedStats, and CBlastOptionsLocal::m_ExtnOpts.
Referenced by CBlastOptions::SetCompositionBasedStats().
◆ SetCullingLimit() [1/3]
| void CBlastOptions::SetCullingLimit | ( | int | s | ) |
Definition at line 1837 of file blast_options_cxx.cpp.
References eBlastOpt_CullingLimit, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetCullingLimit(), and CBlastOptionsRemote::SetValue().
Referenced by CHspFilteringArgs::ExtractAlgorithmOptions(), CBlastOptionsHandle::SetCullingLimit(), CBlastOptionsBuilder::x_ApplyInteractions(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetCullingLimit() [2/3]
|
inline |
Sets Culling limit.
- Parameters
-
s CullingLimit [in]
Definition at line 285 of file blast_options_handle.hpp.
References CBlastOptionsHandle::m_Opts, and CBlastOptions::SetCullingLimit().
Referenced by BOOST_FIXTURE_TEST_CASE().
◆ SetCullingLimit() [3/3]
|
inline |
Definition at line 1320 of file blast_options_local_priv.hpp.
References _ASSERT, BlastHSPCullingOptionsNew(), BlastHSPFilteringOptions_AddCulling(), BlastHSPFilteringOptionsNew(), BlastHitSavingOptions::culling_limit, BlastHSPFilteringOptions::culling_opts, eBoth, BlastHitSavingOptions::hsp_filt_opt, CBlastOptionsLocal::m_HitSaveOpts, BlastHSPCullingOptions::max_hits, and NULL.
Referenced by CBlastOptions::SetCullingLimit().
◆ SetCutoffScore() [1/4]
| void CBlastOptions::SetCutoffScore | ( | int | s | ) |
Definition at line 1933 of file blast_options_cxx.cpp.
References eBlastOpt_CutoffScore, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetCutoffScore(), and CBlastOptionsRemote::SetValue().
Referenced by CRMBlastNArg::ExtractAlgorithmOptions(), CDiscontiguousMegablastArgs::ExtractAlgorithmOptions(), CMappingArgs::ExtractAlgorithmOptions(), and CBlastOptionsHandle::SetCutoffScore().
◆ SetCutoffScore() [2/4]
|
inline |
Sets CutoffScore.
- Parameters
-
s CutoffScore [in]
Definition at line 255 of file blast_options_handle.hpp.
References CBlastOptionsHandle::m_Opts, and CBlastOptions::SetCutoffScore().
Referenced by BOOST_FIXTURE_TEST_CASE(), s_CreateRepeatsSearchOptions(), CBlastNucleotideOptionsHandle::SetHitSavingOptionsDefaults(), CBlastProteinOptionsHandle::SetHitSavingOptionsDefaults(), CBlastRPSOptionsHandle::SetHitSavingOptionsDefaults(), CBlastNucleotideOptionsHandle::SetMBHitSavingOptionsDefaults(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetCutoffScore() [3/4]
|
inline |
Set a single alignment cutoff score.
- Parameters
-
s cutoff score [in]
Definition at line 178 of file magicblast_options.hpp.
Referenced by CMagicBlastOptionsHandle::SetHitSavingOptionsDefaults().
◆ SetCutoffScore() [4/4]
|
inline |
Definition at line 1450 of file blast_options_local_priv.hpp.
References BlastHitSavingOptions::cutoff_score, and CBlastOptionsLocal::m_HitSaveOpts.
Referenced by CBlastOptions::SetCutoffScore().
◆ SetCutoffScoreCoeffs() [1/3]
| void CBlastOptions::SetCutoffScoreCoeffs | ( | const vector< double > & | c | ) |
Definition at line 1952 of file blast_options_cxx.cpp.
References CBlastOptions::m_Local, CBlastOptionsLocal::SetCutoffScoreCoeffs(), and CBlastOptions::x_Throwx().
Referenced by CMappingArgs::ExtractAlgorithmOptions().
◆ SetCutoffScoreCoeffs() [2/3]
|
inline |
Set coefficients for alignment cutoff score as a linear function of query length: x[0] + x[1] * length.
- Parameters
-
c function coefficients [in]
Definition at line 188 of file magicblast_options.hpp.
Referenced by CMagicBlastOptionsHandle::SetHitSavingOptionsDefaults().
◆ SetCutoffScoreCoeffs() [3/3]
|
inline |
Definition at line 1465 of file blast_options_local_priv.hpp.
References BlastHitSavingOptions::cutoff_score_fun, int, and CBlastOptionsLocal::m_HitSaveOpts.
Referenced by CBlastOptions::SetCutoffScoreCoeffs().
◆ SetDatabase()
Set the name of the database to search against.
Definition at line 1555 of file remote_blast.cpp.
References CRemoteBlast::eSubject, CRemoteBlast::m_NeedConfig, CRemoteBlast::m_QSR, NCBI_THROW, CBlast4_subject_Base::SetDatabase(), and CRemoteBlast::x_SetDatabase().
Referenced by BOOST_AUTO_TEST_CASE(), CRemoteBlast::x_Init(), CRemoteSeqSearch::x_RemoteBlast(), and CRemotePssmSearch::x_RemoteBlast().
◆ SetDatabaseName()
Mutator for the database name.
- Parameters
-
dbname database name [in]
Definition at line 64 of file uniform_search.cpp.
References dbname(), and CSearchDatabase::m_DbName.
◆ SetDbFilteringAlgorithmId()
| void CRemoteBlast::SetDbFilteringAlgorithmId | ( | int | algo_id, |
| ESubjectMaskingType | mask_type = eSoftSubjMasking |
||
| ) |
Sets the filtering algorithm ID to be applied to the BLAST database (not supported by server yet)
- Parameters
-
algo_id algorithm ID to use (ignored if -1)
Definition at line 1482 of file remote_blast.cpp.
References eBlastOpt_DbFilteringAlgorithmId, eBlastOpt_SubjectMaskingType, CBlast4Field::Get(), int, CRemoteBlast::m_DbFilteringAlgorithmId, CRemoteBlast::m_SubjectMaskingType, mask, and CRemoteBlast::x_SetOneParam().
Referenced by CRemoteBlast::x_Init().
◆ SetDbFilteringAlgorithmKey()
| void CRemoteBlast::SetDbFilteringAlgorithmKey | ( | string | algo_key, |
| ESubjectMaskingType | mask_type = eSoftSubjMasking |
||
| ) |
Sets the filtering algorithm key to be applied to the BLAST database (not supported by server yet)
- Parameters
-
algo_id algorithm ID to use (ignored if -1)
Definition at line 1494 of file remote_blast.cpp.
References eBlastOpt_DbFilteringAlgorithmKey, eBlastOpt_SubjectMaskingType, CBlast4Field::Get(), int, kEmptyStr, ncbi::grid::netcache::search::fields::key, CRemoteBlast::m_DbFilteringAlgorithmKey, CRemoteBlast::m_SubjectMaskingType, mask, and CRemoteBlast::x_SetOneParam().
Referenced by CRemoteBlast::x_Init().
◆ SetDbGeneticCode() [1/5]
| void CBlastOptions::SetDbGeneticCode | ( | int | gc | ) |
Definition at line 2411 of file blast_options_cxx.cpp.
References CAutomaticGenCodeSingleton::AddGeneticCode(), eBlastOpt_DbGeneticCode, CBlastOptions::m_GenCodeSingletonVar, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetDbGeneticCode(), and CBlastOptionsRemote::SetValue().
Referenced by CGeneticCodeArgs::ExtractAlgorithmOptions(), CPSIBlastOptionsHandle::SetPSITblastnDefaults(), CTBlastxOptionsHandle::SetSubjectSequenceOptionsDefaults(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetDbGeneticCode() [2/5]
|
inline |
Sets DbGeneticCode.
- Parameters
-
gc DbGeneticCode [in]
Definition at line 68 of file rpstblastn_options.hpp.
◆ SetDbGeneticCode() [3/5]
|
inline |
Sets DbGeneticCode.
- Parameters
-
gc DbGeneticCode [in]
Definition at line 89 of file tblastn_options.hpp.
Referenced by CTBlastnOptionsHandle::SetSubjectSequenceOptionsDefaults().
◆ SetDbGeneticCode() [4/5]
|
inline |
Sets DbGeneticCode.
- Parameters
-
gc DbGeneticCode [in]
Definition at line 82 of file tblastx_options.hpp.
◆ SetDbGeneticCode() [5/5]
| void CBlastOptionsLocal::SetDbGeneticCode | ( | int | gc | ) |
Definition at line 347 of file blast_options_local_priv.cpp.
References BlastDatabaseOptions::genetic_code, and CBlastOptionsLocal::m_DbOpts.
Referenced by CBlastOptions::SetDbGeneticCode().
◆ SetDbLength() [1/3]
| void CBlastOptions::SetDbLength | ( | Int8 | l | ) |
Definition at line 2340 of file blast_options_cxx.cpp.
References eBlastOpt_DbLength, l(), CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetDbLength(), and CBlastOptionsRemote::SetValue().
Referenced by CBlastDatabaseArgs::ExtractAlgorithmOptions(), CBlastOptionsHandle::SetDbLength(), CMagicBlastOptionsHandle::SetEffectiveLengthsOptionsDefaults(), and CLocalVDBBlast::x_AdjustDbSize().
◆ SetDbLength() [2/3]
|
inline |
Definition at line 1701 of file blast_options_local_priv.hpp.
References BlastEffectiveLengthsOptions::db_length, l(), and CBlastOptionsLocal::m_EffLenOpts.
Referenced by CBlastOptions::SetDbLength().
◆ SetDbLength() [3/3]
|
inline |
Sets DbLength.
- Parameters
-
len DbLength [in]
Definition at line 309 of file blast_options_handle.hpp.
References len, CBlastOptionsHandle::m_Opts, and CBlastOptions::SetDbLength().
Referenced by CdBlaster::blast(), BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), CSimpleB2SWrapper::InitializeToDefaults(), CdBlaster::psiBlast(), CBlastKmerSearch::Run(), CSimpleB2SWrapper::SetDbLength(), CBlastNucleotideOptionsHandle::SetEffectiveLengthsOptionsDefaults(), CBlastProteinOptionsHandle::SetEffectiveLengthsOptionsDefaults(), CBlastRPSOptionsHandle::SetEffectiveLengthsOptionsDefaults(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetDBScanInfo()
| void CBlastTracebackSearch::SetDBScanInfo | ( | CRef< SDatabaseScanData > | dbscan_info | ) |
Sets the m_DBscanInfo field.
Definition at line 120 of file traceback_stage.cpp.
References CBlastTracebackSearch::m_DBscanInfo.
Referenced by CBlastTracebackSearch::CBlastTracebackSearch().
◆ SetDbSeqNum() [1/3]
| void CBlastOptions::SetDbSeqNum | ( | unsigned int | n | ) |
Definition at line 2359 of file blast_options_cxx.cpp.
References eBlastOpt_DbSeqNum, CBlastOptions::m_Local, CBlastOptions::m_Remote, n, CBlastOptionsLocal::SetDbSeqNum(), and CBlastOptionsRemote::SetValue().
Referenced by CBlastOptionsHandle::SetDbSeqNum(), CMagicBlastOptionsHandle::SetEffectiveLengthsOptionsDefaults(), and CLocalVDBBlast::x_AdjustDbSize().
◆ SetDbSeqNum() [2/3]
|
inline |
Definition at line 1713 of file blast_options_local_priv.hpp.
References BlastEffectiveLengthsOptions::dbseq_num, CBlastOptionsLocal::m_EffLenOpts, and n.
Referenced by CBlastOptions::SetDbSeqNum().
◆ SetDbSeqNum() [3/3]
|
inline |
Sets DbSeqNum.
- Parameters
-
num DbSeqNum [in]
Definition at line 315 of file blast_options_handle.hpp.
References CBlastOptionsHandle::m_Opts, and CBlastOptions::SetDbSeqNum().
Referenced by CdBlaster::blast(), BOOST_FIXTURE_TEST_CASE(), CSimpleB2SWrapper::InitializeToDefaults(), CdBlaster::psiBlast(), CBlastNucleotideOptionsHandle::SetEffectiveLengthsOptionsDefaults(), CBlastProteinOptionsHandle::SetEffectiveLengthsOptionsDefaults(), and CBlastRPSOptionsHandle::SetEffectiveLengthsOptionsDefaults().
◆ SetDefaults() [1/3]
|
virtual |
Sets Defaults.
Reimplemented from CBlastOptionsHandle.
Definition at line 62 of file blast_nucl_options.cpp.
References CBlastOptionsHandle::m_Opts, CBlastOptions::SetDefaultsMode(), and CBlastNucleotideOptionsHandle::SetTraditionalMegablastDefaults().
◆ SetDefaults() [2/3]
|
virtual |
Resets the state of the object to all default values.
This is a template method (design pattern).
Reimplemented in CMagicBlastOptionsHandle, and CBlastNucleotideOptionsHandle.
Definition at line 74 of file blast_options_handle.cpp.
References CBlastOptions::eRemote, CBlastOptions::GetLocality(), CBlastOptionsHandle::m_Opts, CBlastOptions::SetDefaultsMode(), CBlastOptionsHandle::SetEffectiveLengthsOptionsDefaults(), CBlastOptionsHandle::SetGappedExtensionDefaults(), CBlastOptionsHandle::SetHitSavingOptionsDefaults(), CBlastOptionsHandle::SetInitialWordOptionsDefaults(), CBlastOptionsHandle::SetLookupTableDefaults(), CBlastOptionsHandle::SetQueryOptionDefaults(), CBlastOptionsHandle::SetRemoteProgramAndService_Blast3(), CBlastOptionsHandle::SetScoringOptionsDefaults(), and CBlastOptionsHandle::SetSubjectSequenceOptionsDefaults().
Referenced by CSplignApp::x_SetupBlastOptions().
◆ SetDefaults() [3/3]
|
virtual |
Sets Defaults.
Reimplemented from CBlastOptionsHandle.
Definition at line 62 of file magicblast_options.cpp.
References CBlastOptionsHandle::m_Opts, CBlastOptions::SetDefaultsMode(), and CMagicBlastOptionsHandle::SetRNAToGenomeDefaults().
◆ SetDefaultsMode() [1/2]
| void CBlastOptions::SetDefaultsMode | ( | bool | dmode | ) |
If this is true, remote options will ignore "Set" calls.
Definition at line 2705 of file blast_options_cxx.cpp.
References CBlastOptions::m_Remote, and CBlastOptionsRemote::SetDefaultsMode().
Referenced by CBlastNucleotideOptionsHandle::SetDefaults(), CBlastOptionsHandle::SetDefaults(), CMagicBlastOptionsHandle::SetDefaults(), CMagicBlastOptionsHandle::SetGenomeToGenomeDefaults(), CDiscNucleotideOptionsHandle::SetMBInitialWordOptionsDefaults(), CDiscNucleotideOptionsHandle::SetMBLookupTableDefaults(), CMagicBlastOptionsHandle::SetRNAToGenomeDefaults(), CMagicBlastOptionsHandle::SetRNAToRNADefaults(), CBlastNucleotideOptionsHandle::SetTraditionalBlastnDefaults(), CBlastNucleotideOptionsHandle::SetTraditionalMegablastDefaults(), and CBlastNucleotideOptionsHandle::SetVecScreenDefaults().
◆ SetDefaultsMode() [2/2]
|
inline |
Definition at line 138 of file blast_options_cxx.cpp.
References CBlastOptionsRemote::m_DefaultsMode.
Referenced by CBlastOptions::DoneDefaults(), and CBlastOptions::SetDefaultsMode().
◆ SetDeltaBlastDefaults()
|
protected |
Sets Delta Blast defaults.
Definition at line 63 of file deltablast_options.cpp.
References DELTA_INCLUSION_ETHRESH, CBlastOptionsHandle::m_Opts, PSI_PSEUDO_COUNT_CONST, CBlastOptions::SetInclusionThreshold(), and CBlastOptions::SetPseudoCount().
◆ SetDomainInclusionThreshold() [1/3]
|
inline |
Definition at line 1823 of file blast_options_local_priv.hpp.
References PSIBlastOptions::inclusion_ethresh, and CBlastOptionsLocal::m_DeltaBlastOpts.
Referenced by CBlastOptions::SetDomainInclusionThreshold().
◆ SetDomainInclusionThreshold() [2/3]
| void CBlastOptions::SetDomainInclusionThreshold | ( | double | th | ) |
Definition at line 2522 of file blast_options_cxx.cpp.
References eBlastOpt_DomainInclusionThreshold, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetDomainInclusionThreshold(), CBlastOptionsRemote::SetValue(), and th.
Referenced by CPssmEngineArgs::ExtractAlgorithmOptions(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetDomainInclusionThreshold() [3/3]
|
inline |
Set e-value threshold for including domains in Pssm calculation.
- Parameters
-
th E-value cutoff for domains [in]
Definition at line 70 of file deltablast_options.hpp.
References th.
◆ SetDustFiltering() [1/3]
|
inline |
Enable dust filtering.
- Parameters
-
val enable dust filtering [in]
Definition at line 106 of file blast_nucl_options.hpp.
References val.
Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), s_CreateRepeatsSearchOptions(), and CBlastNucleotideOptionsHandle::SetQueryOptionDefaults().
◆ SetDustFiltering() [2/3]
Definition at line 1161 of file blast_options_cxx.cpp.
References eBlastOpt_DustFiltering, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetDustFiltering(), CBlastOptionsRemote::SetValue(), and val.
Referenced by BOOST_AUTO_TEST_CASE(), CBlastOptions::ClearFilterOptions(), CFilteringArgs::ExtractAlgorithmOptions(), CMagicBlastOptionsHandle::SetQueryOptionDefaults(), CBlastNucleotideOptionsHandle::SetVecScreenDefaults(), CBlastOptionsBuilder::x_ProcessOneOption(), and CSplignApp::x_SetupBlastOptions().
◆ SetDustFiltering() [3/3]
Definition at line 759 of file blast_options_local_priv.hpp.
References SBlastFilterOptions::dustOptions, QuerySetUpOptions::filtering_options, CBlastOptionsLocal::m_QueryOpts, SDustOptionsFree(), SDustOptionsNew(), and val.
Referenced by CBlastOptions::SetDustFiltering().
◆ SetDustFilteringLevel() [1/3]
|
inline |
Set level parameter for dust.
Acceptable values: 2 < level < 64
- Parameters
-
level dust filtering parameter level [in]
Definition at line 112 of file blast_nucl_options.hpp.
Referenced by BOOST_FIXTURE_TEST_CASE().
◆ SetDustFilteringLevel() [2/3]
| void CBlastOptions::SetDustFilteringLevel | ( | int | m | ) |
Definition at line 1180 of file blast_options_cxx.cpp.
References eBlastOpt_DustFilteringLevel, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetDustFilteringLevel(), and CBlastOptionsRemote::SetValue().
Referenced by CFilteringArgs::ExtractAlgorithmOptions(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetDustFilteringLevel() [3/3]
|
inline |
Definition at line 783 of file blast_options_local_priv.hpp.
References SBlastFilterOptions::dustOptions, QuerySetUpOptions::filtering_options, SDustOptions::level, CBlastOptionsLocal::m_QueryOpts, NULL, and SDustOptionsNew().
Referenced by CBlastOptions::SetDustFilteringLevel().
◆ SetDustFilteringLinker() [1/3]
|
inline |
Set linker parameter for dust.
Acceptable values: 1 < linker < 32
- Parameters
-
linker dust filtering parameter linker [in]
Definition at line 124 of file blast_nucl_options.hpp.
Referenced by BOOST_FIXTURE_TEST_CASE().
◆ SetDustFilteringLinker() [2/3]
| void CBlastOptions::SetDustFilteringLinker | ( | int | m | ) |
Definition at line 1218 of file blast_options_cxx.cpp.
References eBlastOpt_DustFilteringLinker, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetDustFilteringLinker(), and CBlastOptionsRemote::SetValue().
Referenced by CFilteringArgs::ExtractAlgorithmOptions(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetDustFilteringLinker() [3/3]
|
inline |
Definition at line 821 of file blast_options_local_priv.hpp.
References SBlastFilterOptions::dustOptions, QuerySetUpOptions::filtering_options, SDustOptions::linker, CBlastOptionsLocal::m_QueryOpts, NULL, and SDustOptionsNew().
Referenced by CBlastOptions::SetDustFilteringLinker().
◆ SetDustFilteringWindow() [1/3]
| void CBlastOptions::SetDustFilteringWindow | ( | int | m | ) |
Definition at line 1199 of file blast_options_cxx.cpp.
References eBlastOpt_DustFilteringWindow, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetDustFilteringWindow(), and CBlastOptionsRemote::SetValue().
Referenced by CFilteringArgs::ExtractAlgorithmOptions(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetDustFilteringWindow() [2/3]
|
inline |
Definition at line 802 of file blast_options_local_priv.hpp.
References SBlastFilterOptions::dustOptions, QuerySetUpOptions::filtering_options, CBlastOptionsLocal::m_QueryOpts, NULL, SDustOptionsNew(), and SDustOptions::window.
Referenced by CBlastOptions::SetDustFilteringWindow().
◆ SetDustFilteringWindow() [3/3]
|
inline |
Set window parameter for dust.
Acceptable values: 8 < windowsize < 64
- Parameters
-
window dust filtering parameter window [in]
Definition at line 118 of file blast_nucl_options.hpp.
Referenced by BOOST_FIXTURE_TEST_CASE().
◆ SetEffectiveLengthsOptionsDefaults() [1/5]
|
protectedvirtual |
Overrides EffectiveLengthsOptionsDefaults for nucleotide options.
Implements CBlastOptionsHandle.
Definition at line 273 of file blast_nucl_options.cpp.
References CBlastOptionsHandle::SetDbLength(), CBlastOptionsHandle::SetDbSeqNum(), and CBlastOptionsHandle::SetEffectiveSearchSpace().
Referenced by CBlastNucleotideOptionsHandle::SetTraditionalBlastnDefaults(), and CBlastNucleotideOptionsHandle::SetTraditionalMegablastDefaults().
◆ SetEffectiveLengthsOptionsDefaults() [2/5]
|
protectedvirtual |
Overrides EffectiveLengthsOptionsDefaults for protein options.
Implements CBlastOptionsHandle.
Definition at line 151 of file blast_prot_options.cpp.
References CBlastOptionsHandle::SetDbLength(), CBlastOptionsHandle::SetDbSeqNum(), and CBlastOptionsHandle::SetEffectiveSearchSpace().
◆ SetEffectiveLengthsOptionsDefaults() [3/5]
|
protectedvirtual |
Overrides EffectiveLengthsOptionsDefaults for RPS-BLAST options.
Implements CBlastOptionsHandle.
Definition at line 125 of file blast_rps_options.cpp.
References CBlastOptionsHandle::SetDbLength(), CBlastOptionsHandle::SetDbSeqNum(), and CBlastOptionsHandle::SetEffectiveSearchSpace().
◆ SetEffectiveLengthsOptionsDefaults() [4/5]
|
protectedvirtual |
Overrides EffectiveLengthsOptionsDefaults for nucleotide options.
Implements CBlastOptionsHandle.
Definition at line 220 of file magicblast_options.cpp.
References CBlastOptionsHandle::m_Opts, CBlastOptions::SetDbLength(), CBlastOptions::SetDbSeqNum(), and CBlastOptions::SetEffectiveSearchSpace().
Referenced by CMagicBlastOptionsHandle::SetGenomeToGenomeDefaults(), CMagicBlastOptionsHandle::SetRNAToGenomeDefaults(), and CMagicBlastOptionsHandle::SetRNAToRNADefaults().
◆ SetEffectiveLengthsOptionsDefaults() [5/5]
|
protectedpure virtual |
Sets EffectiveLengthsOptionsDefaults.
Implemented in CMagicBlastOptionsHandle, CBlastRPSOptionsHandle, CBlastProteinOptionsHandle, and CBlastNucleotideOptionsHandle.
Referenced by CBlastOptionsHandle::SetDefaults().
◆ SetEffectiveSearchSpace() [1/5]
Definition at line 2388 of file blast_options_cxx.cpp.
References _ASSERT, eBlastOpt_EffectiveSearchSpace, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetEffectiveSearchSpace(), and CBlastOptionsRemote::SetValue().
◆ SetEffectiveSearchSpace() [2/5]
Definition at line 1742 of file blast_options_local_priv.hpp.
References copy(), CBlastOptionsLocal::m_EffLenOpts, malloc(), BlastEffectiveLengthsOptions::num_searchspaces, BlastEffectiveLengthsOptions::searchsp_eff, and sfree.
◆ SetEffectiveSearchSpace() [3/5]
| void CBlastOptions::SetEffectiveSearchSpace | ( | Int8 | eff | ) |
Definition at line 2378 of file blast_options_cxx.cpp.
References eBlastOpt_EffectiveSearchSpace, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetEffectiveSearchSpace(), and CBlastOptionsRemote::SetValue().
Referenced by CGenericSearchArgs::ExtractAlgorithmOptions(), CMagicBlastOptionsHandle::SetEffectiveLengthsOptionsDefaults(), CBlastOptionsHandle::SetEffectiveSearchSpace(), CBlastNucleotideOptionsHandle::SetVecScreenDefaults(), and SplitQuery_SetEffectiveSearchSpace().
◆ SetEffectiveSearchSpace() [4/5]
|
inline |
Sets EffectiveSearchSpace.
- Parameters
-
eff EffectiveSearchSpace [in]
Definition at line 323 of file blast_options_handle.hpp.
References CBlastOptionsHandle::m_Opts, and CBlastOptions::SetEffectiveSearchSpace().
Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), CBlastNucleotideOptionsHandle::SetEffectiveLengthsOptionsDefaults(), CBlastProteinOptionsHandle::SetEffectiveLengthsOptionsDefaults(), CBlastRPSOptionsHandle::SetEffectiveLengthsOptionsDefaults(), CSimpleB2SWrapper::SetEffSearchSpace(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetEffectiveSearchSpace() [5/5]
|
inline |
Definition at line 1728 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_EffLenOpts, malloc(), BlastEffectiveLengthsOptions::num_searchspaces, BlastEffectiveLengthsOptions::searchsp_eff, and sfree.
Referenced by CBlastOptions::SetEffectiveSearchSpace().
◆ SetEntrezQuery()
| void CRemoteBlast::SetEntrezQuery | ( | const char * | x | ) |
Restrict search to sequences matching this Entrez query.
Definition at line 1606 of file remote_blast.cpp.
References eBlastOpt_EntrezQuery, CBlast4Field::Get(), CRemoteBlast::m_EntrezQuery, NCBI_THROW, and CRemoteBlast::x_SetOneParam().
Referenced by CIgBlast::Run(), CRemoteBlast::x_Init(), CRemoteSeqSearch::x_RemoteBlast(), and CRemotePssmSearch::x_RemoteBlast().
◆ SetEntrezQueryLimitation()
Mutator for the entrez query.
- Parameters
-
entrez_query entrez query string [in]
Definition at line 88 of file uniform_search.cpp.
References CSearchDatabase::m_EntrezQueryLimitation.
Referenced by CBlastDatabaseArgs::ExtractAlgorithmOptions(), and s_ImportDatabase().
◆ SetEvalueThreshold() [1/3]
| void CBlastOptions::SetEvalueThreshold | ( | double | eval | ) |
Definition at line 1914 of file blast_options_cxx.cpp.
References eBlastOpt_EvalueThreshold, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetEvalueThreshold(), and CBlastOptionsRemote::SetValue().
Referenced by CGenericSearchArgs::ExtractAlgorithmOptions(), CBlastOptionsHandle::SetEvalueThreshold(), CMagicBlastOptionsHandle::SetHitSavingOptionsDefaults(), and CBlastNucleotideOptionsHandle::SetVecScreenDefaults().
◆ SetEvalueThreshold() [2/3]
|
inline |
Sets EvalueThreshold.
- Parameters
-
eval EvalueThreshold [in]
Definition at line 250 of file blast_options_handle.hpp.
References CBlastOptionsHandle::m_Opts, and CBlastOptions::SetEvalueThreshold().
Referenced by CdBlaster::blast(), BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), CBlastOptionsFactory::CreateTask(), CSimpleB2SWrapper::InitializeToDefaults(), CBlastDemoApplication::ProcessCommandLineArgs(), CIgBlast::Run(), RunMultipleProteinSearch(), CSimpleB2SWrapper::SetEValueThreshold(), CBlastNucleotideOptionsHandle::SetHitSavingOptionsDefaults(), CBlastProteinOptionsHandle::SetHitSavingOptionsDefaults(), CBlastRPSOptionsHandle::SetHitSavingOptionsDefaults(), CBlastNucleotideOptionsHandle::SetMBHitSavingOptionsDefaults(), CDeltaBlast::x_FindDomainHits(), CMultiAligner::x_FindRPSHits(), CBlastOptionsBuilder::x_ProcessOneOption(), CIgBlast::x_SetupCRegionSearch(), CIgBlast::x_SetupDJSearch(), CIgBlast::x_SetupNoOverlapDSearch(), and CIgBlast::x_SetupVSearch().
◆ SetEvalueThreshold() [3/3]
|
inline |
Definition at line 1438 of file blast_options_local_priv.hpp.
References BlastHitSavingOptions::expect_value, and CBlastOptionsLocal::m_HitSaveOpts.
Referenced by CBlastOptions::SetEvalueThreshold().
◆ SetFilteredQueryRegions()
| void CSearchResultSet::SetFilteredQueryRegions | ( | const TSeqLocInfoVector & | masks | ) |
Sets the filtered query regions.
If results are of type eSequenceComparison, the masks can be one for each query and they will be duplicated as necessary to meet this class' pre-conditions.
Definition at line 523 of file blast_results.cpp.
References _ASSERT, copy(), eSequenceComparison, i, CSearchResultSet::m_IsPhiBlast, CSearchResultSet::m_QueryMasks, CSearchResultSet::m_Results, and CSearchResultSet::m_ResultType.
Referenced by CLocalBlast::Run(), and CSearchResultSet::x_Init().
◆ SetFilteringAlgorithm() [1/3]
| void CSearchDatabase::SetFilteringAlgorithm | ( | const string & | filt_algorithm, |
| ESubjectMaskingType | mask_type | ||
| ) |
Mutator for the filtering algorithm.
- Parameters
-
filt_algorithm filtering algorithm string [in] mask_type type of mask [in]
Definition at line 156 of file uniform_search.cpp.
References eNoSubjMasking, CSearchDatabase::m_FilteringAlgorithmId, CSearchDatabase::m_FilteringAlgorithmString, CSearchDatabase::m_MaskType, CSearchDatabase::m_NeedsFilteringTranslation, s_IsNumericId(), NStr::StringToInt(), and CSearchDatabase::x_ValidateMaskingAlgorithm().
◆ SetFilteringAlgorithm() [2/3]
| void CSearchDatabase::SetFilteringAlgorithm | ( | int | filt_algorithm_id | ) |
Temporary fix for backwards compatibility with other 6.0 SCs.
Definition at line 175 of file uniform_search.cpp.
References eSoftSubjMasking.
Referenced by BOOST_AUTO_TEST_CASE(), CBlastFormat::CBlastFormat(), CBlastDbSet::CreateLocalDbAdapter(), CBlastDatabaseArgs::ExtractAlgorithmOptions(), and s_ImportDatabase().
◆ SetFilteringAlgorithm() [3/3]
| void CSearchDatabase::SetFilteringAlgorithm | ( | int | filt_algorithm_id, |
| ESubjectMaskingType | mask_type | ||
| ) |
Mutator for the filtering algorithm.
- Parameters
-
filt_algorithm_id filtering algorithm ID [in] mask_type type of mask [in]
Definition at line 181 of file uniform_search.cpp.
References eNoSubjMasking, CSearchDatabase::m_FilteringAlgorithmId, CSearchDatabase::m_FilteringAlgorithmString, CSearchDatabase::m_MaskType, CSearchDatabase::m_NeedsFilteringTranslation, and CSearchDatabase::x_ValidateMaskingAlgorithm().
◆ SetFilteringAlgorithmId()
| void CSeqDbSeqInfoSrc::SetFilteringAlgorithmId | ( | int | algo_id | ) |
Sets the filtering algorithm ID used in the search.
- Parameters
-
algo_id filtering algorithm ID [in]
Definition at line 92 of file seqinfosrc_seqdb.cpp.
References CSeqDbSeqInfoSrc::m_FilteringAlgoId.
Referenced by CSeqDbSeqInfoSrc::CSeqDbSeqInfoSrc().
◆ SetFilterString() [1/3]
|
inline |
Definition at line 695 of file blast_options_local_priv.hpp.
References BlastFilteringOptionsFromString(), eBlastTypeBlastn, eBlastTypeMapping, f, QuerySetUpOptions::filter_string, QuerySetUpOptions::filtering_options, CBlastOptionsLocal::GetProgramType(), CBlastOptionsLocal::m_QueryOpts, NULL, SBlastFilterOptions::repeatFilterOptions, SBlastFilterOptionsFree(), SBlastFilterOptionsMerge(), sfree, SRepeatFilterOptionsFree(), and strdup.
Referenced by CBlastOptions::SetFilterString().
◆ SetFilterString() [2/3]
Definition at line 1042 of file blast_options_cxx.cpp.
References Blast_QueryIsNucleotide(), Blast_QueryIsProtein(), Blast_QueryIsTranslated(), CBlastOptions::ClearFilterOptions(), NStr::CompareNocase(), eBlastOpt_DustFiltering, eBlastOpt_DustFilteringLevel, eBlastOpt_DustFilteringLinker, eBlastOpt_DustFilteringWindow, eBlastOpt_MaskAtHash, eBlastOpt_RepeatFiltering, eBlastOpt_RepeatFilteringDB, eBlastOpt_SegFiltering, eBlastOpt_SegFilteringHicut, eBlastOpt_SegFilteringLocut, eBlastOpt_SegFilteringWindow, f, CBlast4Field::Get(), CBlastOptionsLocal::GetDustFiltering(), CBlastOptionsLocal::GetDustFilteringLevel(), CBlastOptionsLocal::GetDustFilteringLinker(), CBlastOptionsLocal::GetDustFilteringWindow(), CBlastOptionsLocal::GetMaskAtHash(), CBlastOptions::GetProgramType(), CBlastOptionsLocal::GetRepeatFiltering(), CBlastOptionsLocal::GetRepeatFilteringDB(), CBlastOptionsLocal::GetSegFiltering(), CBlastOptionsLocal::GetSegFilteringHicut(), CBlastOptionsLocal::GetSegFilteringLocut(), CBlastOptionsLocal::GetSegFilteringWindow(), CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsRemote::ResetValue(), CBlastOptionsLocal::SetFilterString(), and CBlastOptionsRemote::SetValue().
Referenced by BOOST_AUTO_TEST_CASE(), and CBlastOptionsHandle::SetFilterString().
◆ SetFilterString() [3/3]
Sets FilterString.
- Parameters
-
f FilterString [in]
Definition at line 104 of file blast_options_handle.cpp.
References f, CBlastOptionsHandle::m_Opts, and CBlastOptions::SetFilterString().
Referenced by BOOST_AUTO_TEST_CASE(), RpsTestFixture::NuclSearch(), CIgBlastnAppArgs::x_CreateOptionsHandle(), CIgBlastpAppArgs::x_CreateOptionsHandle(), CDeltaBlast::x_FindDomainHits(), CMultiAligner::x_FindRPSHits(), CBlastOptionsBuilder::x_ProcessOneOption(), CIgBlast::x_SetupCRegionSearch(), CIgBlast::x_SetupDJSearch(), CIgBlast::x_SetupNoOverlapDSearch(), and CIgBlast::x_SetupVSearch().
◆ SetFrameShiftPenalty() [1/4]
| void CBlastOptions::SetFrameShiftPenalty | ( | int | p | ) |
Definition at line 2301 of file blast_options_cxx.cpp.
References eBlastOpt_FrameShiftPenalty, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetFrameShiftPenalty(), and CBlastOptionsRemote::SetValue().
Referenced by CFrameShiftArgs::ExtractAlgorithmOptions(), CBlastNucleotideOptionsHandle::SetMBScoringOptionsDefaults(), CBlastNucleotideOptionsHandle::SetScoringOptionsDefaults(), CBlastProteinOptionsHandle::SetScoringOptionsDefaults(), CBlastRPSOptionsHandle::SetScoringOptionsDefaults(), and CMagicBlastOptionsHandle::SetScoringOptionsDefaults().
◆ SetFrameShiftPenalty() [2/4]
|
inline |
Sets FrameShiftPenalty.
- Parameters
-
p FrameShiftPenalty [in]
Definition at line 91 of file blastx_options.hpp.
◆ SetFrameShiftPenalty() [3/4]
|
inline |
Sets FrameShiftPenalty.
- Parameters
-
p FrameShiftPenalty [in]
Definition at line 74 of file tblastn_options.hpp.
◆ SetFrameShiftPenalty() [4/4]
|
inline |
Definition at line 1676 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_ScoringOpts, and BlastScoringOptions::shift_pen.
Referenced by CBlastOptions::SetFrameShiftPenalty().
◆ SetGapExtensionCost() [1/5]
|
inline |
Sets GapExtensionCost.
- Parameters
-
e GapExtensionCost [in]
Definition at line 210 of file blast_nucl_options.hpp.
Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), s_CreateRepeatsSearchOptions(), CBlastNucleotideOptionsHandle::SetMBScoringOptionsDefaults(), and CBlastNucleotideOptionsHandle::SetScoringOptionsDefaults().
◆ SetGapExtensionCost() [2/5]
| void CBlastOptions::SetGapExtensionCost | ( | int | e | ) |
Definition at line 2282 of file blast_options_cxx.cpp.
References eBlastOpt_GapExtensionCost, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetGapExtensionCost(), and CBlastOptionsRemote::SetValue().
Referenced by BOOST_AUTO_TEST_CASE(), CSetupFactory::CreateRpsStructures(), CGenericSearchArgs::ExtractAlgorithmOptions(), CIgBlast::Run(), CBlastNucleotideOptionsHandle::SetVecScreenDefaults(), CIgBlastnAppArgs::x_CreateOptionsHandle(), CBlastOptionsBuilder::x_ProcessOneOption(), CIgBlast::x_SetupCRegionSearch(), CIgBlast::x_SetupDJSearch(), CIgBlast::x_SetupNoOverlapDSearch(), and CIgBlast::x_SetupVSearch().
◆ SetGapExtensionCost() [3/5]
|
inline |
Sets GapExtensionCost.
- Parameters
-
e GapExtensionCost [in]
Definition at line 127 of file blast_prot_options.hpp.
Referenced by BOOST_FIXTURE_TEST_CASE(), CBlastOptionsFactory::CreateTask(), and CBlastProteinOptionsHandle::SetScoringOptionsDefaults().
◆ SetGapExtensionCost() [4/5]
|
inline |
Definition at line 1664 of file blast_options_local_priv.hpp.
References BlastScoringOptions::gap_extend, and CBlastOptionsLocal::m_ScoringOpts.
Referenced by CBlastOptions::SetGapExtensionCost().
◆ SetGapExtensionCost() [5/5]
|
inline |
Sets gap extension cost.
- Parameters
-
g gap extension cost [in]
Definition at line 171 of file magicblast_options.hpp.
References g().
Referenced by CMagicBlastOptionsHandle::SetGenomeToGenomeDefaults(), CMagicBlastOptionsHandle::SetRNAToRNADefaults(), and CMagicBlastOptionsHandle::SetScoringOptionsDefaults().
◆ SetGapExtnAlgorithm() [1/3]
| void CBlastOptions::SetGapExtnAlgorithm | ( | EBlastPrelimGapExt | a | ) |
Definition at line 1614 of file blast_options_cxx.cpp.
References a, eBlastOpt_GapExtnAlgorithm, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetGapExtnAlgorithm(), and CBlastOptionsRemote::SetValue().
Referenced by CNuclArgs::ExtractAlgorithmOptions(), CBlastProteinOptionsHandle::SetGappedExtensionDefaults(), CBlastRPSOptionsHandle::SetGappedExtensionDefaults(), CMagicBlastOptionsHandle::SetGappedExtensionDefaults(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetGapExtnAlgorithm() [2/3]
|
inline |
Definition at line 1172 of file blast_options_local_priv.hpp.
References a, BlastExtensionOptions::ePrelimGapExt, and CBlastOptionsLocal::m_ExtnOpts.
Referenced by CBlastOptions::SetGapExtnAlgorithm().
◆ SetGapExtnAlgorithm() [3/3]
|
inline |
Sets GapExtnAlgorithm.
- Parameters
-
algo GapExtnAlgorithm [in]
Definition at line 172 of file blast_nucl_options.hpp.
References algo.
Referenced by BOOST_FIXTURE_TEST_CASE(), CBlastNucleotideOptionsHandle::SetGappedExtensionDefaults(), CBlastNucleotideOptionsHandle::SetMBGappedExtensionDefaults(), and CDiscNucleotideOptionsHandle::SetMBGappedExtensionDefaults().
◆ SetGapOpeningCost() [1/5]
|
inline |
Sets GapOpeningCost.
- Parameters
-
g GapOpeningCost [in]
Definition at line 204 of file blast_nucl_options.hpp.
References g().
Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), s_CreateRepeatsSearchOptions(), CBlastNucleotideOptionsHandle::SetMBScoringOptionsDefaults(), and CBlastNucleotideOptionsHandle::SetScoringOptionsDefaults().
◆ SetGapOpeningCost() [2/5]
| void CBlastOptions::SetGapOpeningCost | ( | int | g | ) |
Definition at line 2263 of file blast_options_cxx.cpp.
References eBlastOpt_GapOpeningCost, g(), CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetGapOpeningCost(), and CBlastOptionsRemote::SetValue().
Referenced by BOOST_AUTO_TEST_CASE(), CSetupFactory::CreateRpsStructures(), CGenericSearchArgs::ExtractAlgorithmOptions(), CIgBlast::Run(), CBlastNucleotideOptionsHandle::SetVecScreenDefaults(), CIgBlastnAppArgs::x_CreateOptionsHandle(), CBlastOptionsBuilder::x_ProcessOneOption(), CIgBlast::x_SetupCRegionSearch(), CIgBlast::x_SetupDJSearch(), CIgBlast::x_SetupNoOverlapDSearch(), and CIgBlast::x_SetupVSearch().
◆ SetGapOpeningCost() [3/5]
|
inline |
Sets GapOpeningCost.
- Parameters
-
g GapOpeningCost [in]
Definition at line 121 of file blast_prot_options.hpp.
References g().
Referenced by BOOST_FIXTURE_TEST_CASE(), CBlastOptionsFactory::CreateTask(), and CBlastProteinOptionsHandle::SetScoringOptionsDefaults().
◆ SetGapOpeningCost() [4/5]
|
inline |
Set gap opening cost.
- Parameters
-
g gap opening cost [in]
Definition at line 164 of file magicblast_options.hpp.
References g().
Referenced by CMagicBlastOptionsHandle::SetScoringOptionsDefaults().
◆ SetGapOpeningCost() [5/5]
|
inline |
Definition at line 1652 of file blast_options_local_priv.hpp.
References g(), BlastScoringOptions::gap_open, and CBlastOptionsLocal::m_ScoringOpts.
Referenced by CBlastOptions::SetGapOpeningCost().
◆ SetGappedExtensionDefaults() [1/11]
|
protectedvirtual |
Overrides SetGappedExtensionDefaults for advanced blastp options.
Reimplemented from CBlastProteinOptionsHandle.
Reimplemented in CTBlastnOptionsHandle, and CDeltaBlastOptionsHandle.
Definition at line 54 of file blast_advprot_options.cpp.
References _ASSERT, eCompositionMatrixAdjust, CBlastOptions::GetSegFiltering(), CBlastOptionsHandle::m_Opts, CBlastOptions::SetCompositionBasedStats(), CBlastProteinOptionsHandle::SetGappedExtensionDefaults(), and CBlastOptions::SetSmithWatermanMode().
Referenced by CDeltaBlastOptionsHandle::SetGappedExtensionDefaults().
◆ SetGappedExtensionDefaults() [2/11]
|
protectedvirtual |
Overrides GappedExtensionDefaults for nucleotide options.
Implements CBlastOptionsHandle.
Definition at line 177 of file blast_nucl_options.cpp.
References BLAST_GAP_TRIGGER_NUCL, BLAST_GAP_X_DROPOFF_FINAL_NUCL, BLAST_GAP_X_DROPOFF_NUCL, eDynProgScoreOnly, eDynProgTbck, CBlastNucleotideOptionsHandle::SetGapExtnAlgorithm(), CBlastNucleotideOptionsHandle::SetGapTracebackAlgorithm(), CBlastOptionsHandle::SetGapTrigger(), CBlastOptionsHandle::SetGapXDropoff(), and CBlastOptionsHandle::SetGapXDropoffFinal().
Referenced by CBlastNucleotideOptionsHandle::SetTraditionalBlastnDefaults().
◆ SetGappedExtensionDefaults() [3/11]
|
protectedvirtual |
Overrides GappedExtensionDefaults for protein options.
Implements CBlastOptionsHandle.
Reimplemented in CTBlastxOptionsHandle, CTBlastnOptionsHandle, CDeltaBlastOptionsHandle, CBlastxOptionsHandle, and CBlastAdvancedProteinOptionsHandle.
Definition at line 108 of file blast_prot_options.cpp.
References BLAST_GAP_TRIGGER_PROT, BLAST_GAP_X_DROPOFF_FINAL_PROT, BLAST_GAP_X_DROPOFF_PROT, eDynProgScoreOnly, eDynProgTbck, CBlastOptionsHandle::m_Opts, CBlastOptions::SetGapExtnAlgorithm(), CBlastOptions::SetGapTracebackAlgorithm(), CBlastOptionsHandle::SetGapTrigger(), CBlastOptionsHandle::SetGapXDropoff(), and CBlastOptionsHandle::SetGapXDropoffFinal().
Referenced by CBlastAdvancedProteinOptionsHandle::SetGappedExtensionDefaults(), CBlastxOptionsHandle::SetGappedExtensionDefaults(), CTBlastnOptionsHandle::SetGappedExtensionDefaults(), and CTBlastxOptionsHandle::SetGappedExtensionDefaults().
◆ SetGappedExtensionDefaults() [4/11]
|
protectedvirtual |
Overrides GappedExtensionDefaults for RPS-BLAST options.
Implements CBlastOptionsHandle.
Reimplemented in CRPSTBlastnOptionsHandle.
Definition at line 85 of file blast_rps_options.cpp.
References BLAST_GAP_TRIGGER_PROT, BLAST_GAP_X_DROPOFF_FINAL_PROT, BLAST_GAP_X_DROPOFF_PROT, eDynProgScoreOnly, eDynProgTbck, CBlastOptionsHandle::m_Opts, CBlastRPSOptionsHandle::SetCompositionBasedStats(), CBlastOptions::SetGapExtnAlgorithm(), CBlastOptions::SetGapTracebackAlgorithm(), CBlastOptionsHandle::SetGapTrigger(), CBlastOptionsHandle::SetGapXDropoff(), and CBlastOptionsHandle::SetGapXDropoffFinal().
Referenced by CRPSTBlastnOptionsHandle::SetGappedExtensionDefaults().
◆ SetGappedExtensionDefaults() [5/11]
|
protectedvirtual |
Overrides SetGappedExtensionDefaults for blastx option.
Reimplemented from CBlastProteinOptionsHandle.
Definition at line 71 of file blastx_options.cpp.
References _ASSERT, eCompositionMatrixAdjust, CBlastOptions::GetSegFiltering(), CBlastOptionsHandle::m_Opts, CBlastOptions::SetCompositionBasedStats(), CBlastProteinOptionsHandle::SetGappedExtensionDefaults(), and CBlastOptions::SetSmithWatermanMode().
◆ SetGappedExtensionDefaults() [6/11]
|
protectedvirtual |
Override the parent class' defaults for gapped extension (i.e.
: composition based statistics 1)
Reimplemented from CBlastAdvancedProteinOptionsHandle.
Definition at line 69 of file deltablast_options.cpp.
References eCompositionBasedStats, CBlastOptionsHandle::m_Opts, CBlastOptions::SetCompositionBasedStats(), and CBlastAdvancedProteinOptionsHandle::SetGappedExtensionDefaults().
◆ SetGappedExtensionDefaults() [7/11]
|
protectedvirtual |
Overrides GappedExtensionDefaults for nucleotide options.
Implements CBlastOptionsHandle.
Definition at line 168 of file magicblast_options.cpp.
References eJumperWithTraceback, CBlastOptionsHandle::m_Opts, CBlastOptions::SetGapExtnAlgorithm(), CMagicBlastOptionsHandle::SetGapXDropoff(), CBlastOptions::SetMaxMismatches(), CBlastOptions::SetMismatchWindow(), and CMagicBlastOptionsHandle::SetSpliceAlignments().
Referenced by CMagicBlastOptionsHandle::SetGenomeToGenomeDefaults(), CMagicBlastOptionsHandle::SetRNAToGenomeDefaults(), and CMagicBlastOptionsHandle::SetRNAToRNADefaults().
◆ SetGappedExtensionDefaults() [8/11]
|
protectedvirtual |
Overrides SetGappedExtensionDefaults for RPS-TBLASTN options.
Reimplemented from CBlastRPSOptionsHandle.
Definition at line 54 of file rpstblastn_options.cpp.
References CBlastRPSOptionsHandle::SetGappedExtensionDefaults().
◆ SetGappedExtensionDefaults() [9/11]
|
protectedvirtual |
Overrides SetGappedExtensionDefaults for tblastn options.
Reimplemented from CBlastAdvancedProteinOptionsHandle.
Definition at line 74 of file tblastn_options.cpp.
References eCompositionMatrixAdjust, CBlastOptionsHandle::m_Opts, CBlastOptions::SetCompositionBasedStats(), CBlastProteinOptionsHandle::SetGappedExtensionDefaults(), and CBlastOptions::SetSmithWatermanMode().
◆ SetGappedExtensionDefaults() [10/11]
|
protectedvirtual |
Overrides GappedExtensionDefaults for tblastx options.
Reimplemented from CBlastProteinOptionsHandle.
Definition at line 84 of file tblastx_options.cpp.
References BLAST_GAP_X_DROPOFF_FINAL_TBLASTX, BLAST_GAP_X_DROPOFF_TBLASTX, CBlastOptionsHandle::m_Opts, CBlastProteinOptionsHandle::SetGappedExtensionDefaults(), CBlastOptions::SetGapXDropoff(), and CBlastOptions::SetGapXDropoffFinal().
◆ SetGappedExtensionDefaults() [11/11]
|
protectedpure virtual |
Sets GappedExtensionDefaults.
Implemented in CTBlastxOptionsHandle, CTBlastnOptionsHandle, CRPSTBlastnOptionsHandle, CMagicBlastOptionsHandle, CDeltaBlastOptionsHandle, CBlastxOptionsHandle, CBlastRPSOptionsHandle, CBlastProteinOptionsHandle, CBlastNucleotideOptionsHandle, and CBlastAdvancedProteinOptionsHandle.
Referenced by CBlastOptionsHandle::SetDefaults().
◆ SetGappedMode() [1/3]
Definition at line 2083 of file blast_options_cxx.cpp.
References eBlastOpt_GappedMode, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetGappedMode(), and CBlastOptionsRemote::SetValue().
Referenced by CGappedArgs::ExtractAlgorithmOptions(), CBlastOptionsHandle::SetGappedMode(), CMagicBlastOptionsHandle::SetScoringOptionsDefaults(), and CTBlastxOptionsHandle::SetScoringOptionsDefaults().
◆ SetGappedMode() [2/3]
Sets GappedMode.
- Parameters
-
m GappedMode [in]
Definition at line 279 of file blast_options_handle.hpp.
References CBlastOptionsHandle::m_Opts, and CBlastOptions::SetGappedMode().
Referenced by BOOST_FIXTURE_TEST_CASE(), CBlastNucleotideOptionsHandle::SetMBScoringOptionsDefaults(), CBlastNucleotideOptionsHandle::SetScoringOptionsDefaults(), CBlastProteinOptionsHandle::SetScoringOptionsDefaults(), CBlastRPSOptionsHandle::SetScoringOptionsDefaults(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetGappedMode() [3/3]
Definition at line 1550 of file blast_options_local_priv.hpp.
References BlastScoringOptions::gapped_calculation, and CBlastOptionsLocal::m_ScoringOpts.
Referenced by CBlastOptions::SetGappedMode().
◆ SetGapTracebackAlgorithm() [1/3]
| void CBlastOptions::SetGapTracebackAlgorithm | ( | EBlastTbackExt | a | ) |
Definition at line 1634 of file blast_options_cxx.cpp.
References a, eBlastOpt_GapTracebackAlgorithm, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetGapTracebackAlgorithm(), and CBlastOptionsRemote::SetValue().
Referenced by CNuclArgs::ExtractAlgorithmOptions(), CBlastProteinOptionsHandle::SetGappedExtensionDefaults(), CBlastRPSOptionsHandle::SetGappedExtensionDefaults(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetGapTracebackAlgorithm() [2/3]
|
inline |
Definition at line 1184 of file blast_options_local_priv.hpp.
References a, BlastExtensionOptions::eTbackExt, and CBlastOptionsLocal::m_ExtnOpts.
Referenced by CBlastOptions::SetGapTracebackAlgorithm().
◆ SetGapTracebackAlgorithm() [3/3]
|
inline |
Sets GapTracebackAlgorithm.
- Parameters
-
algo GapTracebackAlgorithm [in]
Definition at line 179 of file blast_nucl_options.hpp.
References algo.
Referenced by BOOST_FIXTURE_TEST_CASE(), CBlastNucleotideOptionsHandle::SetGappedExtensionDefaults(), CBlastNucleotideOptionsHandle::SetMBGappedExtensionDefaults(), and CDiscNucleotideOptionsHandle::SetMBGappedExtensionDefaults().
◆ SetGapTrigger() [1/3]
| void CBlastOptions::SetGapTrigger | ( | double | g | ) |
Definition at line 1595 of file blast_options_cxx.cpp.
References eBlastOpt_GapTrigger, g(), CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetGapTrigger(), and CBlastOptionsRemote::SetValue().
Referenced by CGapTriggerArgs::ExtractAlgorithmOptions(), CBlastOptionsHandle::SetGapTrigger(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetGapTrigger() [2/3]
|
inline |
Sets GapTrigger.
- Parameters
-
g GapTrigger [in]
Definition at line 213 of file blast_options_handle.hpp.
References g(), CBlastOptionsHandle::m_Opts, and CBlastOptions::SetGapTrigger().
Referenced by BOOST_FIXTURE_TEST_CASE(), CBlastNucleotideOptionsHandle::SetGappedExtensionDefaults(), CBlastProteinOptionsHandle::SetGappedExtensionDefaults(), CBlastRPSOptionsHandle::SetGappedExtensionDefaults(), CBlastNucleotideOptionsHandle::SetMBGappedExtensionDefaults(), and CDiscNucleotideOptionsHandle::SetMBGappedExtensionDefaults().
◆ SetGapTrigger() [3/3]
|
inline |
Definition at line 1135 of file blast_options_local_priv.hpp.
References g(), BlastInitialWordOptions::gap_trigger, and CBlastOptionsLocal::m_InitWordOpts.
Referenced by CBlastOptions::SetGapTrigger().
◆ SetGapXDropoff() [1/4]
| void CBlastOptions::SetGapXDropoff | ( | double | x | ) |
Definition at line 1557 of file blast_options_cxx.cpp.
References eBlastOpt_GapXDropoff, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetGapXDropoff(), and CBlastOptionsRemote::SetValue().
Referenced by CGenericSearchArgs::ExtractAlgorithmOptions(), CTBlastxOptionsHandle::SetGappedExtensionDefaults(), CBlastOptionsHandle::SetGapXDropoff(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetGapXDropoff() [2/4]
|
inline |
Sets GapXDropoff.
- Parameters
-
x GapXDropoff [in]
Definition at line 207 of file blast_options_handle.hpp.
References CBlastOptionsHandle::m_Opts, and CBlastOptions::SetGapXDropoff().
Referenced by BOOST_FIXTURE_TEST_CASE(), CBlastNucleotideOptionsHandle::SetGappedExtensionDefaults(), CBlastProteinOptionsHandle::SetGappedExtensionDefaults(), CBlastRPSOptionsHandle::SetGappedExtensionDefaults(), CBlastNucleotideOptionsHandle::SetMBGappedExtensionDefaults(), and CDiscNucleotideOptionsHandle::SetMBGappedExtensionDefaults().
◆ SetGapXDropoff() [3/4]
|
inline |
Definition at line 1148 of file blast_options_local_priv.hpp.
References BlastExtensionOptions::gap_x_dropoff, and CBlastOptionsLocal::m_ExtnOpts.
Referenced by CBlastOptions::SetGapXDropoff().
◆ SetGapXDropoff() [4/4]
|
inline |
Set x-dropoff parameter for gapped alignment.
- Parameters
-
d x-dropoff value [in]
Definition at line 148 of file magicblast_options.hpp.
Referenced by CMagicBlastOptionsHandle::SetGappedExtensionDefaults().
◆ SetGapXDropoffFinal() [1/3]
| void CBlastOptions::SetGapXDropoffFinal | ( | double | x | ) |
Definition at line 1576 of file blast_options_cxx.cpp.
References eBlastOpt_GapXDropoffFinal, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetGapXDropoffFinal(), and CBlastOptionsRemote::SetValue().
Referenced by CGenericSearchArgs::ExtractAlgorithmOptions(), CTBlastxOptionsHandle::SetGappedExtensionDefaults(), CBlastOptionsHandle::SetGapXDropoffFinal(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetGapXDropoffFinal() [2/3]
|
inline |
Sets GapXDropoffFinal.
- Parameters
-
x GapXDropoffFinal [in]
Definition at line 221 of file blast_options_handle.hpp.
References CBlastOptionsHandle::m_Opts, and CBlastOptions::SetGapXDropoffFinal().
Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), s_CreateRepeatsSearchOptions(), CBlastNucleotideOptionsHandle::SetGappedExtensionDefaults(), CBlastProteinOptionsHandle::SetGappedExtensionDefaults(), CBlastRPSOptionsHandle::SetGappedExtensionDefaults(), CBlastNucleotideOptionsHandle::SetMBGappedExtensionDefaults(), and CDiscNucleotideOptionsHandle::SetMBGappedExtensionDefaults().
◆ SetGapXDropoffFinal() [3/3]
|
inline |
Definition at line 1160 of file blast_options_local_priv.hpp.
References BlastExtensionOptions::gap_x_dropoff_final, and CBlastOptionsLocal::m_ExtnOpts.
Referenced by CBlastOptions::SetGapXDropoffFinal().
◆ SetGenomeToGenomeDefaults()
|
virtual |
Definition at line 110 of file magicblast_options.cpp.
References eMapper, CBlastOptionsHandle::m_Opts, CBlastOptions::SetDefaultsMode(), CMagicBlastOptionsHandle::SetEffectiveLengthsOptionsDefaults(), CMagicBlastOptionsHandle::SetGapExtensionCost(), CMagicBlastOptionsHandle::SetGappedExtensionDefaults(), CMagicBlastOptionsHandle::SetHitSavingOptionsDefaults(), CMagicBlastOptionsHandle::SetInitialWordOptionsDefaults(), CMagicBlastOptionsHandle::SetLookupDbFilter(), CMagicBlastOptionsHandle::SetLookupTableDefaults(), CMagicBlastOptionsHandle::SetMismatchPenalty(), CBlastOptions::SetProgram(), CMagicBlastOptionsHandle::SetQueryOptionDefaults(), CMagicBlastOptionsHandle::SetScoringOptionsDefaults(), CMagicBlastOptionsHandle::SetSpliceAlignments(), CMagicBlastOptionsHandle::SetSubjectSequenceOptionsDefaults(), and CMagicBlastOptionsHandle::SetWordSize().
Referenced by CBlastOptionsFactory::CreateTask().
◆ SetGIList()
This restricts the subject database to this list of GIs (this is not supported yet on the server end).
- Parameters
-
gi_list list of GIs to restrict the search to [in]
Definition at line 1460 of file remote_blast.cpp.
References copy(), eBlastOpt_GiList, CBlast4Field::Get(), GI_TO, ITERATE, CRemoteBlast::m_GiList, NCBI_THROW, and CRemoteBlast::x_SetOneParam().
Referenced by CRemoteBlast::x_Init(), CRemoteSeqSearch::x_RemoteBlast(), and CRemotePssmSearch::x_RemoteBlast().
◆ SetGiList()
| void CSearchDatabase::SetGiList | ( | CSeqDBGiList * | gilist | ) |
Mutator for the gi list.
- Parameters
-
gilist list of gis [in]
Definition at line 100 of file uniform_search.cpp.
References CSearchDatabase::m_GiList, CSearchDatabase::m_GiListSet, NCBI_THROW, and CRef< C, Locker >::Reset().
Referenced by BOOST_AUTO_TEST_CASE(), CBlastDbSet::CreateLocalDbAdapter(), CBlastDatabaseArgs::ExtractAlgorithmOptions(), CIgBlastArgs::ExtractAlgorithmOptions(), CMagicBlastThread::Main(), CBlastFormatterApp::PrintFormattedOutput(), s_GetTaxIDList(), and s_ImportDatabase().
◆ SetHitlistSize() [1/3]
| void CBlastOptions::SetHitlistSize | ( | int | s | ) |
Definition at line 1780 of file blast_options_cxx.cpp.
References eBlastOpt_HitlistSize, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetHitlistSize(), and CBlastOptionsRemote::SetValue().
Referenced by CFormattingArgs::ExtractAlgorithmOptions(), CLocalVDBBlast::Run(), CBlastOptionsHandle::SetHitlistSize(), and CMagicBlastOptionsHandle::SetHitSavingOptionsDefaults().
◆ SetHitlistSize() [2/3]
|
inline |
Sets HitlistSize.
- Parameters
-
s HitlistSize [in]
Definition at line 228 of file blast_options_handle.hpp.
References CBlastOptionsHandle::m_Opts, and CBlastOptions::SetHitlistSize().
Referenced by CdBlaster::blast(), BOOST_FIXTURE_TEST_CASE(), CSimpleB2SWrapper::InitializeToDefaults(), CdBlaster::psiBlast(), CIgBlast::Run(), CVectorScreen::Run(), RunMultipleProteinSearch(), CSimpleB2SWrapper::SetHitlistSize(), CBlastNucleotideOptionsHandle::SetHitSavingOptionsDefaults(), CBlastProteinOptionsHandle::SetHitSavingOptionsDefaults(), CBlastRPSOptionsHandle::SetHitSavingOptionsDefaults(), CBlastNucleotideOptionsHandle::SetMBHitSavingOptionsDefaults(), CMultiAligner::x_FindRPSHits(), CBl2Seq::x_InitCLocalBlast(), CBlastOptionsBuilder::x_ProcessOneOption(), CIgBlast::x_SetupCRegionSearch(), CIgBlast::x_SetupDJSearch(), CIgBlast::x_SetupNoOverlapDSearch(), and CIgBlast::x_SetupVSearch().
◆ SetHitlistSize() [3/3]
|
inline |
Definition at line 1275 of file blast_options_local_priv.hpp.
References BlastHitSavingOptions::hitlist_size, and CBlastOptionsLocal::m_HitSaveOpts.
Referenced by CBlastOptions::SetHitlistSize().
◆ SetHitSavingOptionsDefaults() [1/8]
|
protectedvirtual |
Overrides HitSavingOptionsDefaults for nucleotide options.
Implements CBlastOptionsHandle.
Definition at line 231 of file blast_nucl_options.cpp.
References BLAST_EXPECT_VALUE, CBlastOptionsHandle::SetCutoffScore(), CBlastOptionsHandle::SetEvalueThreshold(), CBlastOptionsHandle::SetHitlistSize(), CBlastOptionsHandle::SetLowScorePerc(), CBlastOptionsHandle::SetMaskLevel(), CBlastOptionsHandle::SetMaxHspsPerSubject(), CBlastOptionsHandle::SetMaxNumHspPerSequence(), CBlastOptionsHandle::SetMinDiagSeparation(), CBlastOptionsHandle::SetPercentIdentity(), and CBlastOptionsHandle::SetQueryCovHspPerc().
Referenced by CBlastNucleotideOptionsHandle::SetTraditionalBlastnDefaults().
◆ SetHitSavingOptionsDefaults() [2/8]
|
protectedvirtual |
Overrides HitSavingOptionsDefaults for protein options.
Implements CBlastOptionsHandle.
Reimplemented in CTBlastxOptionsHandle, CTBlastnOptionsHandle, and CBlastxOptionsHandle.
Definition at line 134 of file blast_prot_options.cpp.
References BLAST_EXPECT_VALUE, CBlastOptionsHandle::SetCutoffScore(), CBlastOptionsHandle::SetEvalueThreshold(), CBlastOptionsHandle::SetHitlistSize(), CBlastOptionsHandle::SetMaxHspsPerSubject(), CBlastOptionsHandle::SetMaxNumHspPerSequence(), CBlastOptionsHandle::SetMinDiagSeparation(), CBlastOptionsHandle::SetPercentIdentity(), and CBlastOptionsHandle::SetQueryCovHspPerc().
Referenced by CBlastxOptionsHandle::SetHitSavingOptionsDefaults(), CTBlastnOptionsHandle::SetHitSavingOptionsDefaults(), and CTBlastxOptionsHandle::SetHitSavingOptionsDefaults().
◆ SetHitSavingOptionsDefaults() [3/8]
|
protectedvirtual |
Overrides HitSavingOptionsDefaults for RPS-BLAST options.
Implements CBlastOptionsHandle.
Definition at line 106 of file blast_rps_options.cpp.
References BLAST_EXPECT_VALUE, CBlastOptionsHandle::m_Opts, CBlastOptionsHandle::SetCutoffScore(), CBlastOptionsHandle::SetEvalueThreshold(), CBlastOptionsHandle::SetHitlistSize(), CBlastOptionsHandle::SetMaxHspsPerSubject(), CBlastOptionsHandle::SetMaxNumHspPerSequence(), CBlastOptionsHandle::SetMinDiagSeparation(), CBlastOptionsHandle::SetPercentIdentity(), CBlastOptionsHandle::SetQueryCovHspPerc(), and CBlastOptions::SetSumStatisticsMode().
◆ SetHitSavingOptionsDefaults() [4/8]
|
protectedvirtual |
Overrides HitSavingOptionsDefaults for blastx options.
Reimplemented from CBlastProteinOptionsHandle.
Definition at line 86 of file blastx_options.cpp.
References CBlastOptionsHandle::m_Opts, CBlastProteinOptionsHandle::SetHitSavingOptionsDefaults(), and CBlastOptions::SetSumStatisticsMode().
◆ SetHitSavingOptionsDefaults() [5/8]
|
protectedvirtual |
Overrides HitSavingOptionsDefaults for nucleotide options.
Implements CBlastOptionsHandle.
Definition at line 197 of file magicblast_options.cpp.
References BLAST_EXPECT_VALUE, INT4_MAX, CBlastOptionsHandle::m_Opts, CMagicBlastOptionsHandle::SetCutoffScore(), CMagicBlastOptionsHandle::SetCutoffScoreCoeffs(), CBlastOptions::SetEvalueThreshold(), CBlastOptions::SetHitlistSize(), CMagicBlastOptionsHandle::SetLongestIntronLength(), CBlastOptions::SetLowScorePerc(), CMagicBlastOptionsHandle::SetMaxEditDistance(), CBlastOptions::SetMaxHspsPerSubject(), CBlastOptions::SetMaxNumHspPerSequence(), CBlastOptions::SetPercentIdentity(), and CBlastOptions::SetQueryCovHspPerc().
Referenced by CMagicBlastOptionsHandle::SetGenomeToGenomeDefaults(), CMagicBlastOptionsHandle::SetRNAToGenomeDefaults(), and CMagicBlastOptionsHandle::SetRNAToRNADefaults().
◆ SetHitSavingOptionsDefaults() [6/8]
|
protectedvirtual |
Sets HitSavingOptionsDefaults for tblastn options.
Reimplemented from CBlastProteinOptionsHandle.
Definition at line 67 of file tblastn_options.cpp.
References CBlastOptionsHandle::m_Opts, CBlastProteinOptionsHandle::SetHitSavingOptionsDefaults(), and CBlastOptions::SetSumStatisticsMode().
◆ SetHitSavingOptionsDefaults() [7/8]
|
protectedvirtual |
Overrides HitSavingOptionsDefaults for tblastx options.
Reimplemented from CBlastProteinOptionsHandle.
Definition at line 77 of file tblastx_options.cpp.
References CBlastOptionsHandle::m_Opts, CBlastProteinOptionsHandle::SetHitSavingOptionsDefaults(), and CBlastOptions::SetSumStatisticsMode().
◆ SetHitSavingOptionsDefaults() [8/8]
|
protectedpure virtual |
Sets HitSavingOptionsDefaults.
Implemented in CTBlastxOptionsHandle, CTBlastnOptionsHandle, CMagicBlastOptionsHandle, CBlastxOptionsHandle, CBlastRPSOptionsHandle, CBlastProteinOptionsHandle, and CBlastNucleotideOptionsHandle.
Referenced by CBlastOptionsHandle::SetDefaults().
◆ SetIgAnnotation()
|
inline |
Definition at line 210 of file igblast.hpp.
References CIgBlastResults::m_Annotation.
Referenced by CIgBlast::x_SetAnnotation().
◆ SetIgnoreMsaMaster() [1/2]
| void CBlastOptions::SetIgnoreMsaMaster | ( | bool | val | ) |
Definition at line 2501 of file blast_options_cxx.cpp.
References eBlastOpt_IgnoreMsaMaster, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetIgnoreMsaMaster(), CBlastOptionsRemote::SetValue(), and val.
Referenced by CPsiBlastArgs::ExtractAlgorithmOptions(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetIgnoreMsaMaster() [2/2]
|
inline |
Definition at line 1796 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_PSIBlastOpts, PSIBlastOptions::nsg_compatibility_mode, and val.
Referenced by CBlastOptions::SetIgnoreMsaMaster().
◆ SetIgnoreUnsupportedOptions()
| void CBlastOptionsBuilder::SetIgnoreUnsupportedOptions | ( | bool | ignore | ) |
Set the 'ignore unsupported options' flag.
- Parameters
-
ignore True if the unsupported options should be ignored [in]
Definition at line 789 of file blast_options_builder.cpp.
References CBlastOptionsBuilder::m_IgnoreUnsupportedOptions.
◆ SetInclusionThreshold() [1/3]
|
inline |
Sets InclusionThreshold.
- Parameters
-
incthr InclusionThreshold [in]
Definition at line 69 of file psiblast_options.hpp.
Referenced by BOOST_FIXTURE_TEST_CASE().
◆ SetInclusionThreshold() [2/3]
|
inline |
Definition at line 1772 of file blast_options_local_priv.hpp.
References PSIBlastOptions::inclusion_ethresh, and CBlastOptionsLocal::m_PSIBlastOpts.
Referenced by CBlastOptions::SetInclusionThreshold().
◆ SetInclusionThreshold() [3/3]
| void CBlastOptions::SetInclusionThreshold | ( | double | u | ) |
Definition at line 2463 of file blast_options_cxx.cpp.
References eBlastOpt_InclusionThreshold, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetInclusionThreshold(), and CBlastOptionsRemote::SetValue().
Referenced by CPssmEngineArgs::ExtractAlgorithmOptions(), CDeltaBlastOptionsHandle::SetDeltaBlastDefaults(), CPSIBlastOptionsHandle::SetPSIBlastDefaults(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetInitialWordOptionsDefaults() [1/5]
|
protectedvirtual |
Overrides InitialWordOptionsDefaults for nucleotide options.
Implements CBlastOptionsHandle.
Definition at line 163 of file blast_nucl_options.cpp.
References BLAST_SCAN_RANGE_NUCL, BLAST_UNGAPPED_X_DROPOFF_NUCL, BLAST_WINDOW_SIZE_NUCL, CBlastOptionsHandle::SetOffDiagonalRange(), CBlastOptionsHandle::SetWindowSize(), and CBlastNucleotideOptionsHandle::SetXDropoff().
Referenced by CBlastNucleotideOptionsHandle::SetTraditionalBlastnDefaults().
◆ SetInitialWordOptionsDefaults() [2/5]
|
protectedvirtual |
Overrides InitialWordOptionsDefaults for protein options.
Implements CBlastOptionsHandle.
Definition at line 101 of file blast_prot_options.cpp.
References BLAST_UNGAPPED_X_DROPOFF_PROT, BLAST_WINDOW_SIZE_PROT, CBlastOptionsHandle::SetWindowSize(), and CBlastProteinOptionsHandle::SetXDropoff().
◆ SetInitialWordOptionsDefaults() [3/5]
|
protectedvirtual |
Overrides InitialWordOptionsDefaults for RPS-BLAST options.
Implements CBlastOptionsHandle.
Definition at line 77 of file blast_rps_options.cpp.
References BLAST_UNGAPPED_X_DROPOFF_PROT, BLAST_WINDOW_SIZE_PROT, CBlastOptionsHandle::SetWindowSize(), and CBlastRPSOptionsHandle::SetXDropoff().
◆ SetInitialWordOptionsDefaults() [4/5]
|
protectedvirtual |
Overrides InitialWordOptionsDefaults for nucleotide options.
Implements CBlastOptionsHandle.
Definition at line 163 of file magicblast_options.cpp.
Referenced by CMagicBlastOptionsHandle::SetGenomeToGenomeDefaults(), CMagicBlastOptionsHandle::SetRNAToGenomeDefaults(), and CMagicBlastOptionsHandle::SetRNAToRNADefaults().
◆ SetInitialWordOptionsDefaults() [5/5]
|
protectedpure virtual |
Sets InitialWordOptionsDefaults.
Implemented in CMagicBlastOptionsHandle, CBlastRPSOptionsHandle, CBlastProteinOptionsHandle, and CBlastNucleotideOptionsHandle.
Referenced by CBlastOptionsHandle::SetDefaults().
◆ SetInterruptCallback() [1/3]
|
inline |
Set a function callback to be invoked by the CORE of BLAST to allow interrupting a BLAST search in progress.
- Parameters
-
fnptr pointer to callback function [in] user_data user data to be attached to SBlastProgress structure [in]
- Returns
- the previously set TInterruptFnPtr (NULL if none was provided before)
Definition at line 302 of file bl2seq.hpp.
References CBl2Seq::m_InterruptFnx, CBl2Seq::m_InterruptUserData, and tmp.
Referenced by BOOST_AUTO_TEST_CASE(), CBLASTSeqToolJob::x_CreateProjectItems(), CSplignJob::x_CreateProjectItems(), and CProSplignJob::x_SetupAndRuntBlastn().
◆ SetInterruptCallback() [2/3]
|
inline |
Set a function callback to be invoked by the CORE of BLAST to allow interrupting a BLAST search in progress.
- Parameters
-
fnptr pointer to callback function [in] user_data user data to be attached to SBlastProgress structure [in]
- Returns
- the previously set TInterruptFnPtr (NULL if none was provided before)
Definition at line 100 of file local_blast.hpp.
References _ASSERT, CLocalBlast::m_PrelimSearch, and CBlastPrelimSearch::SetInterruptCallback().
Referenced by CBlastAligner::GenerateAlignments(), and CBl2Seq::x_InitCLocalBlast().
◆ SetInterruptCallback() [3/3]
|
inline |
Set a function callback to be invoked by the CORE of BLAST to allow interrupting a BLAST search in progress.
Definition at line 192 of file prelim_stage.hpp.
References SInternalData::m_FnInterrupt, CBlastPrelimSearch::m_InternalData, SInternalData::m_ProgressMonitor, CRef< C, Locker >::Reset(), SBlastProgressNew(), and swap().
Referenced by CLocalBlast::SetInterruptCallback().
◆ SetLengthAdjustment()
|
inline |
Set the length adjustment for boundary conditions.
Definition at line 126 of file blast_results.hpp.
Referenced by CRemoteBlast::GetResultSet().
◆ SetLongestIntronLength() [1/5]
| void CBlastOptions::SetLongestIntronLength | ( | int | l | ) |
for linking HSPs with uneven gaps
Definition at line 2063 of file blast_options_cxx.cpp.
References eBlastOpt_LongestIntronLength, l(), CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetLongestIntronLength(), and CBlastOptionsRemote::SetValue().
Referenced by CLargestIntronSizeArgs::ExtractAlgorithmOptions(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetLongestIntronLength() [2/5]
|
inline |
Sets LongestIntronLength.
- Parameters
-
l LongestIntronLength [in]
Definition at line 97 of file blastx_options.hpp.
References l().
◆ SetLongestIntronLength() [3/5]
|
inline |
Sets LongestIntronLength.
- Parameters
-
l LongestIntronLength [in]
Definition at line 80 of file tblastn_options.hpp.
References l().
◆ SetLongestIntronLength() [4/5]
|
inline |
Definition at line 1538 of file blast_options_local_priv.hpp.
References l(), BlastHitSavingOptions::longest_intron, and CBlastOptionsLocal::m_HitSaveOpts.
Referenced by CBlastOptions::SetLongestIntronLength().
◆ SetLongestIntronLength() [5/5]
|
inline |
Set max intron length.
- Parameters
-
len Max inrton length
Definition at line 220 of file magicblast_options.hpp.
References len.
Referenced by CMagicBlastOptionsHandle::SetHitSavingOptionsDefaults().
◆ SetLookupDbFilter() [1/3]
|
inline |
Set db filtering option for the lookup table.
The filtering removes from lookup table words that are frequent in the database.
- Parameters
-
b If true, words that are frequent in the dabase will be removed from the lookup table
Definition at line 87 of file magicblast_options.hpp.
References b.
Referenced by CMagicBlastOptionsHandle::SetGenomeToGenomeDefaults(), CMagicBlastOptionsHandle::SetQueryOptionDefaults(), and CMagicBlastOptionsHandle::SetRNAToRNADefaults().
◆ SetLookupDbFilter() [2/3]
| void CBlastOptions::SetLookupDbFilter | ( | bool | val | ) |
Definition at line 955 of file blast_options_cxx.cpp.
References CBlastOptions::m_Local, CBlastOptionsLocal::SetLookupDbFilter(), val, and CBlastOptions::x_Throwx().
Referenced by CMappingArgs::ExtractAlgorithmOptions().
◆ SetLookupDbFilter() [3/3]
|
inline |
Definition at line 664 of file blast_options_local_priv.hpp.
References LookupTableOptions::db_filter, CBlastOptionsLocal::m_LutOpts, and val.
Referenced by CBlastOptions::SetLookupDbFilter().
◆ SetLookupTableDefaults() [1/8]
|
protectedvirtual |
Overrides LookupTableDefaults for nucleotide options.
Implements CBlastOptionsHandle.
Definition at line 137 of file blast_nucl_options.cpp.
References BLAST_WORD_THRESHOLD_BLASTN, BLAST_WORDSIZE_NUCL, eNaLookupTable, CBlastOptionsHandle::m_Opts, CBlastOptions::SetLookupTableStride(), CBlastNucleotideOptionsHandle::SetLookupTableType(), CBlastNucleotideOptionsHandle::SetWordSize(), and CBlastOptions::SetWordThreshold().
Referenced by CBlastNucleotideOptionsHandle::SetTraditionalBlastnDefaults().
◆ SetLookupTableDefaults() [2/8]
|
protectedvirtual |
Overrides LookupTableDefaults for protein options.
Implements CBlastOptionsHandle.
Reimplemented in CTBlastxOptionsHandle, CTBlastnOptionsHandle, and CBlastxOptionsHandle.
Definition at line 86 of file blast_prot_options.cpp.
References BLAST_WORD_THRESHOLD_BLASTP, BLAST_WORDSIZE_PROT, eAaLookupTable, CBlastOptionsHandle::m_Opts, CBlastOptions::SetLookupTableType(), CBlastProteinOptionsHandle::SetWordSize(), and CBlastProteinOptionsHandle::SetWordThreshold().
Referenced by CBlastxOptionsHandle::SetLookupTableDefaults(), CTBlastnOptionsHandle::SetLookupTableDefaults(), and CTBlastxOptionsHandle::SetLookupTableDefaults().
◆ SetLookupTableDefaults() [3/8]
|
protectedvirtual |
Overrides LookupTableDefaults for RPS-BLAST options.
Implements CBlastOptionsHandle.
Definition at line 61 of file blast_rps_options.cpp.
References eRPSLookupTable, CBlastOptionsHandle::m_Opts, and CBlastOptions::SetLookupTableType().
◆ SetLookupTableDefaults() [4/8]
|
protectedvirtual |
Overrides LookupTableDefaults for blastx options.
Reimplemented from CBlastProteinOptionsHandle.
Definition at line 55 of file blastx_options.cpp.
References BLAST_WORD_THRESHOLD_BLASTX, CBlastOptionsHandle::m_Opts, CBlastProteinOptionsHandle::SetLookupTableDefaults(), and CBlastOptions::SetWordThreshold().
◆ SetLookupTableDefaults() [5/8]
|
protectedvirtual |
Overrides LookupTableDefaults for nucleotide options.
Implements CBlastOptionsHandle.
Definition at line 133 of file magicblast_options.cpp.
References BLAST_WORD_THRESHOLD_BLASTN, BLAST_WORDSIZE_MAPPER, eMBLookupTable, eNaHashLookupTable, CBlastOptionsHandle::m_Opts, MAX_DB_WORD_COUNT_MAPPER, CMagicBlastOptionsHandle::SetLookupTableStride(), CBlastOptions::SetLookupTableType(), CMagicBlastOptionsHandle::SetMaxDbWordCount(), CMagicBlastOptionsHandle::SetWordSize(), and CBlastOptions::SetWordThreshold().
Referenced by CMagicBlastOptionsHandle::SetGenomeToGenomeDefaults(), CMagicBlastOptionsHandle::SetRNAToGenomeDefaults(), and CMagicBlastOptionsHandle::SetRNAToRNADefaults().
◆ SetLookupTableDefaults() [6/8]
|
protectedvirtual |
Sets LookupTableDefaults for tblastn options.
Reimplemented from CBlastProteinOptionsHandle.
Definition at line 54 of file tblastn_options.cpp.
References BLAST_WORD_THRESHOLD_TBLASTN, CBlastProteinOptionsHandle::SetLookupTableDefaults(), and CBlastProteinOptionsHandle::SetWordThreshold().
◆ SetLookupTableDefaults() [7/8]
|
protectedvirtual |
Overrides LookupTableDefaults for tblastx options.
Reimplemented from CBlastProteinOptionsHandle.
Definition at line 55 of file tblastx_options.cpp.
References BLAST_WORD_THRESHOLD_TBLASTX, CBlastOptionsHandle::m_Opts, CBlastProteinOptionsHandle::SetLookupTableDefaults(), and CBlastOptions::SetWordThreshold().
◆ SetLookupTableDefaults() [8/8]
|
protectedpure virtual |
Sets LookupTableDefaults.
Implemented in CTBlastxOptionsHandle, CTBlastnOptionsHandle, CMagicBlastOptionsHandle, CBlastxOptionsHandle, CBlastRPSOptionsHandle, CBlastProteinOptionsHandle, and CBlastNucleotideOptionsHandle.
Referenced by CBlastOptionsHandle::SetDefaults().
◆ SetLookupTableStride() [1/3]
|
inline |
Set lookup table stride: number of words skipped between collected ones when creating a lookup table.
- Parameters
-
s lookup table stride [in]
Definition at line 104 of file magicblast_options.hpp.
Referenced by CMagicBlastOptionsHandle::SetLookupTableDefaults().
◆ SetLookupTableStride() [2/3]
| void CBlastOptions::SetLookupTableStride | ( | Uint4 | val | ) |
Definition at line 939 of file blast_options_cxx.cpp.
References CBlastOptions::m_Local, CBlastOptionsLocal::SetLookupTableStride(), val, and CBlastOptions::x_Throwx().
Referenced by CMappingArgs::ExtractAlgorithmOptions(), CBlastNucleotideOptionsHandle::SetLookupTableDefaults(), and CBlastNucleotideOptionsHandle::SetMBLookupTableDefaults().
◆ SetLookupTableStride() [3/3]
|
inline |
Definition at line 628 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_LutOpts, LookupTableOptions::stride, and val.
Referenced by CBlastOptions::SetLookupTableStride().
◆ SetLookupTableType() [1/3]
|
inline |
Sets LookupTableType.
- Parameters
-
type LookupTableType [in]
Definition at line 77 of file blast_nucl_options.hpp.
Referenced by BOOST_FIXTURE_TEST_CASE(), CBlastNucleotideOptionsHandle::SetLookupTableDefaults(), and CBlastNucleotideOptionsHandle::SetMBLookupTableDefaults().
◆ SetLookupTableType() [2/3]
| void CBlastOptions::SetLookupTableType | ( | ELookupTableType | type | ) |
Definition at line 903 of file blast_options_cxx.cpp.
References eBlastOpt_LookupTableType, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetLookupTableType(), and CBlastOptionsRemote::SetValue().
Referenced by BOOST_AUTO_TEST_CASE(), CBlastOptionsFactory::CreateTask(), CGenericSearchArgs::ExtractAlgorithmOptions(), CSetupFactory::InitializeMegablastDbIndex(), CBlastProteinOptionsHandle::SetLookupTableDefaults(), CBlastRPSOptionsHandle::SetLookupTableDefaults(), CMagicBlastOptionsHandle::SetLookupTableDefaults(), CBlastProteinOptionsHandle::SetWordSize(), CTblastnAppArgs::x_CreateOptionsHandle(), and CPsiBlastApp::x_RunLocalPsiBlastIterations().
◆ SetLookupTableType() [3/3]
|
inline |
Definition at line 597 of file blast_options_local_priv.hpp.
References BLAST_WORDSIZE_MEGABLAST, eMBLookupTable, LookupTableOptions::lut_type, CBlastOptionsLocal::m_LutOpts, type, and LookupTableOptions::word_size.
Referenced by CBlastOptions::SetLookupTableType().
◆ SetLowScorePerc() [1/3]
|
inline |
Sets low score percentage for ungapped alignments.
Definition at line 302 of file blast_options_handle.hpp.
References CBlastOptionsHandle::m_Opts, and CBlastOptions::SetLowScorePerc().
Referenced by CBlastNucleotideOptionsHandle::SetHitSavingOptionsDefaults(), and CBlastNucleotideOptionsHandle::SetMBHitSavingOptionsDefaults().
◆ SetLowScorePerc() [2/3]
| void CBlastOptions::SetLowScorePerc | ( | double | p = 0.0 | ) |
Definition at line 2147 of file blast_options_cxx.cpp.
References CBlastOptions::m_Local, and CBlastOptionsLocal::SetLowScorePerc().
Referenced by CMagicBlastOptionsHandle::SetHitSavingOptionsDefaults(), and CBlastOptionsHandle::SetLowScorePerc().
◆ SetLowScorePerc() [3/3]
|
inline |
Definition at line 1576 of file blast_options_local_priv.hpp.
References BlastHitSavingOptions::low_score_perc, and CBlastOptionsLocal::m_HitSaveOpts.
Referenced by CBlastOptions::SetLowScorePerc().
◆ SetMaskAtHash() [1/3]
Sets MaskAtHash.
- Parameters
-
m whether masking should only be done for lookup table [in]
Definition at line 201 of file blast_options_handle.hpp.
References CBlastOptionsHandle::m_Opts, and CBlastOptions::SetMaskAtHash().
Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), and CBlastNucleotideOptionsHandle::SetQueryOptionDefaults().
◆ SetMaskAtHash() [2/3]
Definition at line 1142 of file blast_options_cxx.cpp.
References eBlastOpt_MaskAtHash, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetMaskAtHash(), CBlastOptionsRemote::SetValue(), and val.
Referenced by BOOST_AUTO_TEST_CASE(), CBlastOptions::ClearFilterOptions(), CFilteringArgs::ExtractAlgorithmOptions(), CBlastOptionsHandle::SetMaskAtHash(), CMagicBlastOptionsHandle::SetQueryOptionDefaults(), CBlastNucleotideOptionsHandle::SetVecScreenDefaults(), CBlastOptionsBuilder::x_ProcessOneOption(), and CSplignApp::x_SetupBlastOptions().
◆ SetMaskAtHash() [3/3]
Definition at line 742 of file blast_options_local_priv.hpp.
References QuerySetUpOptions::filtering_options, CBlastOptionsLocal::m_QueryOpts, SBlastFilterOptions::mask_at_hash, and val.
Referenced by CBlastOptions::SetMaskAtHash().
◆ SetMaskedQueryRegions()
| void CSearchResults::SetMaskedQueryRegions | ( | const TMaskedQueryRegions & | flt_query_regions | ) |
Mutator for the masked query regions, intended to be used by internal BLAST APIs to populate this object.
- Parameters
-
flt_query_regions the input value [in]
Definition at line 235 of file blast_results.cpp.
References copy(), and CSearchResults::m_Masks.
Referenced by CSearchResults::CSearchResults().
◆ SetMaskLevel() [1/3]
|
inline |
Sets MaskLevel -RMH-.
- Parameters
-
ml MaskLevel [in]
Definition at line 291 of file blast_options_handle.hpp.
References CBlastOptionsHandle::m_Opts, and CBlastOptions::SetMaskLevel().
Referenced by CBlastNucleotideOptionsHandle::SetHitSavingOptionsDefaults(), and CBlastNucleotideOptionsHandle::SetMBHitSavingOptionsDefaults().
◆ SetMaskLevel() [2/3]
| void CBlastOptions::SetMaskLevel | ( | int | s | ) |
Definition at line 2105 of file blast_options_cxx.cpp.
References eBlastOpt_MaskLevel, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetMaskLevel(), and CBlastOptionsRemote::SetValue().
Referenced by CRMBlastNArg::ExtractAlgorithmOptions(), and CBlastOptionsHandle::SetMaskLevel().
◆ SetMaskLevel() [3/3]
|
inline |
Definition at line 1564 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_HitSaveOpts, and BlastHitSavingOptions::mask_level.
Referenced by CBlastOptions::SetMaskLevel().
◆ SetMatchReward() [1/3]
|
inline |
Sets MatchReward.
- Parameters
-
r MatchReward [in]
Definition at line 186 of file blast_nucl_options.hpp.
References r().
Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), CBlastOptionsFactory::CreateTask(), s_CreateRepeatsSearchOptions(), CBlastNucleotideOptionsHandle::SetMBScoringOptionsDefaults(), and CBlastNucleotideOptionsHandle::SetScoringOptionsDefaults().
◆ SetMatchReward() [2/3]
| void CBlastOptions::SetMatchReward | ( | int | r | ) |
Definition at line 2225 of file blast_options_cxx.cpp.
References eBlastOpt_MatchReward, CBlastOptions::m_Local, CBlastOptions::m_Remote, r(), CBlastOptionsLocal::SetMatchReward(), and CBlastOptionsRemote::SetValue().
Referenced by CNuclArgs::ExtractAlgorithmOptions(), CMagicBlastOptionsHandle::SetScoringOptionsDefaults(), CBlastNucleotideOptionsHandle::SetVecScreenDefaults(), CIgBlastnAppArgs::x_CreateOptionsHandle(), CBlastOptionsBuilder::x_ProcessOneOption(), CIgBlast::x_SetupCRegionSearch(), CIgBlast::x_SetupDJSearch(), CIgBlast::x_SetupNoOverlapDSearch(), and CIgBlast::x_SetupVSearch().
◆ SetMatchReward() [3/3]
|
inline |
Definition at line 1628 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_ScoringOpts, r(), and BlastScoringOptions::reward.
Referenced by CBlastOptions::SetMatchReward().
◆ SetMatrixName() [1/4]
|
inline |
Sets MatrixName.
- Parameters
-
matrix MatrixName [in]
Definition at line 198 of file blast_nucl_options.hpp.
Referenced by BOOST_FIXTURE_TEST_CASE(), CBlastNucleotideOptionsHandle::SetMBScoringOptionsDefaults(), and CBlastNucleotideOptionsHandle::SetScoringOptionsDefaults().
◆ SetMatrixName() [2/4]
| void CBlastOptions::SetMatrixName | ( | const char * | matrix | ) |
Definition at line 2206 of file blast_options_cxx.cpp.
References eBlastOpt_MatrixName, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetMatrixName(), and CBlastOptionsRemote::SetValue().
Referenced by BOOST_AUTO_TEST_CASE(), CSetupFactory::CreateRpsStructures(), CRMBlastNArg::ExtractAlgorithmOptions(), CMatrixNameArg::ExtractAlgorithmOptions(), CMagicBlastOptionsHandle::SetScoringOptionsDefaults(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetMatrixName() [3/4]
|
inline |
Sets MatrixName.
- Parameters
-
matrix MatrixName [in]
Definition at line 115 of file blast_prot_options.hpp.
Referenced by CdBlaster::blast(), BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), CBlastOptionsFactory::CreateTask(), CSimpleB2SWrapper::InitializeToDefaults(), CdBlaster::psiBlast(), CSimpleB2SWrapper::SetMatrixName(), and CBlastProteinOptionsHandle::SetScoringOptionsDefaults().
◆ SetMatrixName() [4/4]
|
inline |
Definition at line 569 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_ScoringOpts, BlastScoringOptions::matrix, sfree, and strdup.
Referenced by CBlastOptions::SetMatrixName().
◆ SetMaxDbWordCount() [1/3]
| void CBlastOptions::SetMaxDbWordCount | ( | Uint1 | num | ) |
Set maximum word count for lookup table word masking by database frequency.
Definition at line 971 of file blast_options_cxx.cpp.
References CBlastOptions::m_Local, CBlastOptionsLocal::SetMaxDbWordCount(), and CBlastOptions::x_Throwx().
Referenced by CMappingArgs::ExtractAlgorithmOptions().
◆ SetMaxDbWordCount() [2/3]
|
inline |
Set maximum word count for lookup table word masking by database frequency.
Definition at line 95 of file magicblast_options.hpp.
Referenced by CMagicBlastOptionsHandle::SetLookupTableDefaults().
◆ SetMaxDbWordCount() [3/3]
|
inline |
Definition at line 676 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_LutOpts, LookupTableOptions::max_db_word_count, and val.
Referenced by CBlastOptions::SetMaxDbWordCount().
◆ SetMaxEditDistance() [1/3]
| void CBlastOptions::SetMaxEditDistance | ( | int | e | ) |
Definition at line 1988 of file blast_options_cxx.cpp.
References CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetMaxEditDistance(), and CBlastOptions::x_Throwx().
Referenced by CMappingArgs::ExtractAlgorithmOptions().
◆ SetMaxEditDistance() [2/3]
|
inline |
Definition at line 192 of file magicblast_options.hpp.
Referenced by CMagicBlastOptionsHandle::SetHitSavingOptionsDefaults().
◆ SetMaxEditDistance() [3/3]
|
inline |
Definition at line 1490 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_HitSaveOpts, and BlastHitSavingOptions::max_edit_distance.
Referenced by CBlastOptions::SetMaxEditDistance().
◆ SetMaxFractionAmbiguous()
|
inline |
Get maximum fraction of ambiguous bases for query quality filtering.
Definition at line 122 of file magicblast_options.hpp.
References val.
◆ SetMaxHspsPerSubject() [1/3]
| void CBlastOptions::SetMaxHspsPerSubject | ( | int | m | ) |
Definition at line 1818 of file blast_options_cxx.cpp.
References eBlastOpt_MaxHspsPerSubject, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetMaxHspsPerSubject(), and CBlastOptionsRemote::SetValue().
Referenced by CGenericSearchArgs::ExtractAlgorithmOptions(), CMagicBlastOptionsHandle::SetHitSavingOptionsDefaults(), CBlastOptionsHandle::SetMaxHspsPerSubject(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetMaxHspsPerSubject() [2/3]
|
inline |
Sets MaxHspPerSubjectQueryPair.
- Parameters
-
m MaxNumHspPerSequence [in]
Definition at line 244 of file blast_options_handle.hpp.
References CBlastOptionsHandle::m_Opts, and CBlastOptions::SetMaxHspsPerSubject().
Referenced by BOOST_AUTO_TEST_CASE(), CBlastNucleotideOptionsHandle::SetHitSavingOptionsDefaults(), CBlastProteinOptionsHandle::SetHitSavingOptionsDefaults(), CBlastRPSOptionsHandle::SetHitSavingOptionsDefaults(), and CBlastNucleotideOptionsHandle::SetMBHitSavingOptionsDefaults().
◆ SetMaxHspsPerSubject() [3/3]
|
inline |
Definition at line 1287 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_HitSaveOpts, and BlastHitSavingOptions::max_hsps_per_subject.
Referenced by CBlastOptions::SetMaxHspsPerSubject().
◆ SetMaxLength()
|
inline |
Sets maximal length.
Definition at line 85 of file seqsrc_multiseq.cpp.
References CMultiSeqInfo::m_iMaxLength.
◆ SetMaxMismatches() [1/2]
| void CBlastOptions::SetMaxMismatches | ( | int | m | ) |
Definition at line 1716 of file blast_options_cxx.cpp.
References CBlastOptions::m_Local, CBlastOptionsLocal::SetMaxMismatches(), and CBlastOptions::x_Throwx().
Referenced by CMagicBlastOptionsHandle::SetGappedExtensionDefaults().
◆ SetMaxMismatches() [2/2]
|
inline |
Definition at line 1238 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_ExtnOpts, and BlastExtensionOptions::max_mismatches.
Referenced by CBlastOptions::SetMaxMismatches().
◆ SetMaxNumHspPerSequence() [1/3]
| void CBlastOptions::SetMaxNumHspPerSequence | ( | int | m | ) |
Definition at line 1799 of file blast_options_cxx.cpp.
References eBlastOpt_MaxNumHspPerSequence, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetMaxNumHspPerSequence(), and CBlastOptionsRemote::SetValue().
Referenced by CMagicBlastOptionsHandle::SetHitSavingOptionsDefaults(), and CBlastOptionsHandle::SetMaxNumHspPerSequence().
◆ SetMaxNumHspPerSequence() [2/3]
|
inline |
Sets MaxNumHspPerSequence.
- Parameters
-
m MaxNumHspPerSequence [in]
Definition at line 236 of file blast_options_handle.hpp.
References CBlastOptionsHandle::m_Opts, and CBlastOptions::SetMaxNumHspPerSequence().
Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), CBlastNucleotideOptionsHandle::SetHitSavingOptionsDefaults(), CBlastProteinOptionsHandle::SetHitSavingOptionsDefaults(), CBlastRPSOptionsHandle::SetHitSavingOptionsDefaults(), and CBlastNucleotideOptionsHandle::SetMBHitSavingOptionsDefaults().
◆ SetMaxNumHspPerSequence() [3/3]
|
inline |
Definition at line 1299 of file blast_options_local_priv.hpp.
References BlastHitSavingOptions::hsp_num_max, and CBlastOptionsLocal::m_HitSaveOpts.
Referenced by CBlastOptions::SetMaxNumHspPerSequence().
◆ SetMBGappedExtensionDefaults() [1/2]
|
protectedvirtual |
Overrides MBGappedExtensionDefaults for nucleotide options.
Reimplemented in CDiscNucleotideOptionsHandle.
Definition at line 187 of file blast_nucl_options.cpp.
References BLAST_GAP_TRIGGER_NUCL, BLAST_GAP_X_DROPOFF_FINAL_NUCL, BLAST_GAP_X_DROPOFF_GREEDY, eGreedyScoreOnly, eGreedyTbck, CBlastNucleotideOptionsHandle::SetGapExtnAlgorithm(), CBlastNucleotideOptionsHandle::SetGapTracebackAlgorithm(), CBlastOptionsHandle::SetGapTrigger(), CBlastOptionsHandle::SetGapXDropoff(), and CBlastOptionsHandle::SetGapXDropoffFinal().
Referenced by CBlastNucleotideOptionsHandle::SetTraditionalMegablastDefaults().
◆ SetMBGappedExtensionDefaults() [2/2]
|
protectedvirtual |
Sets MBGappedExtensionDefaults.
Reimplemented from CBlastNucleotideOptionsHandle.
Definition at line 77 of file disc_nucl_options.cpp.
References BLAST_GAP_TRIGGER_NUCL, BLAST_GAP_X_DROPOFF_FINAL_NUCL, BLAST_GAP_X_DROPOFF_NUCL, eDynProgScoreOnly, eDynProgTbck, CBlastNucleotideOptionsHandle::SetGapExtnAlgorithm(), CBlastNucleotideOptionsHandle::SetGapTracebackAlgorithm(), CBlastOptionsHandle::SetGapTrigger(), CBlastOptionsHandle::SetGapXDropoff(), and CBlastOptionsHandle::SetGapXDropoffFinal().
◆ SetMBHitSavingOptionsDefaults()
|
protectedvirtual |
Overrides MBHitSavingOptionsDefaults for nucleotide options.
Definition at line 251 of file blast_nucl_options.cpp.
References BLAST_EXPECT_VALUE, CBlastOptionsHandle::SetCutoffScore(), CBlastOptionsHandle::SetEvalueThreshold(), CBlastOptionsHandle::SetHitlistSize(), CBlastOptionsHandle::SetLowScorePerc(), CBlastOptionsHandle::SetMaskLevel(), CBlastOptionsHandle::SetMaxHspsPerSubject(), CBlastOptionsHandle::SetMaxNumHspPerSequence(), CBlastOptionsHandle::SetMinDiagSeparation(), CBlastOptionsHandle::SetPercentIdentity(), and CBlastOptionsHandle::SetQueryCovHspPerc().
Referenced by CBlastNucleotideOptionsHandle::SetTraditionalMegablastDefaults().
◆ SetMBIndexLoaded() [1/2]
Definition at line 2636 of file blast_options_cxx.cpp.
References CBlastOptions::m_Local, CBlastOptionsLocal::SetMBIndexLoaded(), and CBlastOptions::x_Throwx().
Referenced by CSetupFactory::InitializeMegablastDbIndex().
◆ SetMBIndexLoaded() [2/2]
Definition at line 1849 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_MBIndexLoaded.
Referenced by CBlastOptions::SetMBIndexLoaded().
◆ SetMBInitialWordOptionsDefaults() [1/2]
|
protectedvirtual |
Overrides MBInitialWordOptionsDefaults for nucleotide options.
Reimplemented in CDiscNucleotideOptionsHandle.
Definition at line 171 of file blast_nucl_options.cpp.
References BLAST_WINDOW_SIZE_NUCL, and CBlastOptionsHandle::SetWindowSize().
Referenced by CBlastNucleotideOptionsHandle::SetTraditionalMegablastDefaults().
◆ SetMBInitialWordOptionsDefaults() [2/2]
|
protectedvirtual |
Sets MBInitialWordOptionsDefaults.
Reimplemented from CBlastNucleotideOptionsHandle.
Definition at line 67 of file disc_nucl_options.cpp.
References BLAST_UNGAPPED_X_DROPOFF_NUCL, BLAST_WINDOW_SIZE_DISC, CBlastOptions::GetDefaultsMode(), CBlastOptionsHandle::m_Opts, CBlastOptions::SetDefaultsMode(), CBlastOptionsHandle::SetWindowSize(), and CBlastNucleotideOptionsHandle::SetXDropoff().
◆ SetMBLookupTableDefaults() [1/2]
|
protectedvirtual |
Overrides MBLookupTableDefaults for nucleotide options.
Reimplemented in CDiscNucleotideOptionsHandle.
Definition at line 146 of file blast_nucl_options.cpp.
References BLAST_WORD_THRESHOLD_MEGABLAST, BLAST_WORDSIZE_MEGABLAST, eMBLookupTable, CBlastOptionsHandle::m_Opts, CBlastOptions::SetLookupTableStride(), CBlastNucleotideOptionsHandle::SetLookupTableType(), CBlastNucleotideOptionsHandle::SetWordSize(), and CBlastOptions::SetWordThreshold().
Referenced by CDiscNucleotideOptionsHandle::SetMBLookupTableDefaults(), and CBlastNucleotideOptionsHandle::SetTraditionalMegablastDefaults().
◆ SetMBLookupTableDefaults() [2/2]
|
protectedvirtual |
Sets MBLookupTableDefaults.
Reimplemented from CBlastNucleotideOptionsHandle.
Definition at line 55 of file disc_nucl_options.cpp.
References BLAST_WORDSIZE_NUCL, CBlastOptions::GetDefaultsMode(), CBlastOptionsHandle::m_Opts, CBlastOptions::SetDefaultsMode(), CBlastNucleotideOptionsHandle::SetMBLookupTableDefaults(), CDiscNucleotideOptionsHandle::SetTemplateLength(), CDiscNucleotideOptionsHandle::SetTemplateType(), and CDiscNucleotideOptionsHandle::SetWordSize().
◆ SetMBScoringOptionsDefaults() [1/2]
|
protectedvirtual |
Overrides MBScoringOptionsDefaults for nucleotide options.
Reimplemented in CDiscNucleotideOptionsHandle.
Definition at line 215 of file blast_nucl_options.cpp.
References BLAST_GAP_EXTN_MEGABLAST, BLAST_GAP_OPEN_MEGABLAST, INT2_MAX, CBlastOptionsHandle::m_Opts, NULL, CBlastOptionsHandle::SetComplexityAdjMode(), CBlastOptions::SetFrameShiftPenalty(), CBlastNucleotideOptionsHandle::SetGapExtensionCost(), CBlastNucleotideOptionsHandle::SetGapOpeningCost(), CBlastOptionsHandle::SetGappedMode(), CBlastNucleotideOptionsHandle::SetMatchReward(), CBlastNucleotideOptionsHandle::SetMatrixName(), CBlastNucleotideOptionsHandle::SetMismatchPenalty(), and CBlastOptions::SetOutOfFrameMode().
Referenced by CBlastNucleotideOptionsHandle::SetTraditionalMegablastDefaults().
◆ SetMBScoringOptionsDefaults() [2/2]
|
protectedvirtual |
Sets MBScoringOptionsDefaults.
Reimplemented from CBlastNucleotideOptionsHandle.
Definition at line 87 of file disc_nucl_options.cpp.
References CBlastNucleotideOptionsHandle::SetScoringOptionsDefaults().
◆ SetMBTemplateLength() [1/2]
| void CBlastOptions::SetMBTemplateLength | ( | unsigned char | len | ) |
Definition at line 990 of file blast_options_cxx.cpp.
References eBlastOpt_MBTemplateLength, len, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetMBTemplateLength(), and CBlastOptionsRemote::SetValue().
Referenced by CDiscontiguousMegablastArgs::ExtractAlgorithmOptions(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetMBTemplateLength() [2/2]
|
inline |
Definition at line 640 of file blast_options_local_priv.hpp.
References len, CBlastOptionsLocal::m_LutOpts, and LookupTableOptions::mb_template_length.
Referenced by CBlastOptions::SetMBTemplateLength().
◆ SetMBTemplateType() [1/2]
| void CBlastOptions::SetMBTemplateType | ( | unsigned char | type | ) |
Definition at line 1009 of file blast_options_cxx.cpp.
References eBlastOpt_MBTemplateType, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetMBTemplateType(), and CBlastOptionsRemote::SetValue().
Referenced by CDiscontiguousMegablastArgs::ExtractAlgorithmOptions(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetMBTemplateType() [2/2]
|
inline |
Definition at line 652 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_LutOpts, LookupTableOptions::mb_template_type, and type.
Referenced by CBlastOptions::SetMBTemplateType().
◆ SetMinCddEvalue()
|
inline |
Set minimum e-value threshold for inclusion of CDs in PSSM computation.
The minimum e-value is used only for experimental purposes hence it does not appear in CddOptions
- Parameters
-
val Minimum e-value threshold [in]
Definition at line 179 of file cdd_pssm_input.hpp.
References CCddInputData::m_MinEvalue, and val.
◆ SetMinDiagSeparation() [1/3]
| void CBlastOptions::SetMinDiagSeparation | ( | int | d | ) |
Definition at line 2027 of file blast_options_cxx.cpp.
References CBlastOptions::m_Local, CBlastOptionsLocal::SetMinDiagSeparation(), and CBlastOptions::x_Throwx().
Referenced by CBlastOptionsHandle::SetMinDiagSeparation().
◆ SetMinDiagSeparation() [2/3]
|
inline |
Sets MinDiagSeparation.
- Parameters
-
d MinDiagSeparation [in]
Definition at line 273 of file blast_options_handle.hpp.
References CBlastOptionsHandle::m_Opts, and CBlastOptions::SetMinDiagSeparation().
Referenced by CBlastNucleotideOptionsHandle::SetHitSavingOptionsDefaults(), CBlastProteinOptionsHandle::SetHitSavingOptionsDefaults(), CBlastRPSOptionsHandle::SetHitSavingOptionsDefaults(), and CBlastNucleotideOptionsHandle::SetMBHitSavingOptionsDefaults().
◆ SetMinDiagSeparation() [3/3]
|
inline |
Definition at line 1514 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_HitSaveOpts, and BlastHitSavingOptions::min_diag_separation.
Referenced by CBlastOptions::SetMinDiagSeparation().
◆ SetMinDimerEntropy()
|
inline |
Set minimum dimer entropy for query quality filtering.
Definition at line 129 of file magicblast_options.hpp.
References val.
◆ SetMinHits()
|
inline |
Sets the number of hits ot initiate calculation of Jaccard distance.
- Parameters
-
hits Minimum number of LSH hits to proceed with subject [in]
Definition at line 78 of file blastp_kmer_options.hpp.
Referenced by CBlastKmerThread::Main(), and CBlastKmerApplication::Run().
◆ SetMinusStrand()
|
inline |
For nucleotide sequences this instructs the implementation to convert its representation to be that of the minus strand.
Definition at line 228 of file blast_setup.hpp.
References eNa_strand_minus, IBlastSeqVector::m_Strand, and IBlastSeqVector::x_SetMinusStrand().
◆ SetMismatchPenalty() [1/4]
|
inline |
Sets MismatchPenalty.
- Parameters
-
p MismatchPenalty [in]
Definition at line 192 of file blast_nucl_options.hpp.
Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), CBlastOptionsFactory::CreateTask(), s_CreateRepeatsSearchOptions(), CBlastNucleotideOptionsHandle::SetMBScoringOptionsDefaults(), and CBlastNucleotideOptionsHandle::SetScoringOptionsDefaults().
◆ SetMismatchPenalty() [2/4]
| void CBlastOptions::SetMismatchPenalty | ( | int | p | ) |
Definition at line 2244 of file blast_options_cxx.cpp.
References eBlastOpt_MismatchPenalty, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetMismatchPenalty(), and CBlastOptionsRemote::SetValue().
Referenced by CNuclArgs::ExtractAlgorithmOptions(), CIgBlast::Run(), CIgBlastnApp::Run(), CBlastNucleotideOptionsHandle::SetVecScreenDefaults(), CIgBlastnAppArgs::x_CreateOptionsHandle(), CBlastOptionsBuilder::x_ProcessOneOption(), CIgBlast::x_SetupCRegionSearch(), CIgBlast::x_SetupDJSearch(), CIgBlast::x_SetupNoOverlapDSearch(), and CIgBlast::x_SetupVSearch().
◆ SetMismatchPenalty() [3/4]
|
inline |
Sets mismatch penalty.
- Parameters
-
p mismatch penalty [in]
Definition at line 157 of file magicblast_options.hpp.
Referenced by CMagicBlastOptionsHandle::SetGenomeToGenomeDefaults(), CMagicBlastOptionsHandle::SetRNAToRNADefaults(), and CMagicBlastOptionsHandle::SetScoringOptionsDefaults().
◆ SetMismatchPenalty() [4/4]
|
inline |
Definition at line 1640 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_ScoringOpts, and BlastScoringOptions::penalty.
Referenced by CBlastOptions::SetMismatchPenalty().
◆ SetMismatchWindow() [1/2]
| void CBlastOptions::SetMismatchWindow | ( | int | w | ) |
Definition at line 1738 of file blast_options_cxx.cpp.
References CBlastOptions::m_Local, CBlastOptionsLocal::SetMismatchWindow(), and CBlastOptions::x_Throwx().
Referenced by CMagicBlastOptionsHandle::SetGappedExtensionDefaults().
◆ SetMismatchWindow() [2/2]
|
inline |
Definition at line 1250 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_ExtnOpts, and BlastExtensionOptions::mismatch_window.
Referenced by CBlastOptions::SetMismatchWindow().
◆ SetMoleculeType()
| void CSearchDatabase::SetMoleculeType | ( | EMoleculeType | mol_type | ) |
Mutator for the molecule type.
- Parameters
-
mol_type molecule type [in]
Definition at line 76 of file uniform_search.cpp.
References CSearchDatabase::m_MolType.
◆ SetMultipleThreads()
|
inline |
Set the concurrency status.
- Parameters
-
multiple_threads 'true' if concurrent search is being performed; 'false' otherwise
Definition at line 549 of file blast_dbindex.cpp.
References IDX_TRACE, CIndexedDb_New::multiple_threads_, and CIndexedDb_New::n_threads_.
Referenced by IndexedDbSetUsingThreads().
◆ SetNegativeGIList()
This excludes the provided GIs from the subject database (this is not supported yet on the server end).
- Parameters
-
gi_list list of GIs to exclude [in]
Definition at line 1513 of file remote_blast.cpp.
References copy(), eBlastOpt_GiList, eBlastOpt_NegativeGiList, CBlast4Field::Get(), GI_TO, ITERATE, CRemoteBlast::m_NegativeGiList, NCBI_THROW, and CRemoteBlast::x_SetOneParam().
Referenced by CRemoteBlast::x_Init().
◆ SetNegativeGiList()
| void CSearchDatabase::SetNegativeGiList | ( | CSeqDBGiList * | gilist | ) |
Mutator for the negative gi list.
- Parameters
-
gilist list of gis [in]
Definition at line 125 of file uniform_search.cpp.
References CSearchDatabase::m_GiListSet, CSearchDatabase::m_NegativeGiList, NCBI_THROW, and CRef< C, Locker >::Reset().
Referenced by BOOST_AUTO_TEST_CASE(), CBlastDbSet::CreateLocalDbAdapter(), CBlastDatabaseArgs::ExtractAlgorithmOptions(), CMagicBlastThread::Main(), CBlastFormatterApp::PrintFormattedOutput(), s_GetTaxIDList(), and s_ImportDatabase().
◆ SetNucleotideBlastDbDataLoader()
Definition at line 88 of file blast_input_unit_test_aux.hpp.
References CAutoNcbiConfigFile::kNuclBlastDbDataLoader, CAutoNcbiConfigFile::kSection, CAutoNcbiConfigFile::m_Registry, and IRWRegistry::Set().
Referenced by s_RetrieveSequenceLength().
◆ SetNumberOfThreads() [1/3]
|
virtual |
@inheritDoc
Reimplemented from CThreadable.
Definition at line 103 of file prelim_stage.cpp.
References Blast_CMT_LOCKInit(), Blast_DiagnosticsFree(), BlastHSPStreamRegisterMTLock(), CSetupFactory::CreateDiagnosticsStructure(), CSetupFactory::CreateDiagnosticsStructureMT(), CBlastOptions::CreateSnapshot(), CThreadable::IsMultiThreaded(), SInternalData::m_Diagnostics, SInternalData::m_HspStream, CBlastPrelimSearch::m_InternalData, CBlastPrelimSearch::m_Options, CBlastPrelimSearch::m_QueryFactory, IQueryFactory::MakeLocalQueryData(), and CThreadable::SetNumberOfThreads().
Referenced by BOOST_AUTO_TEST_CASE(), CBlastPrelimSearch::CBlastPrelimSearch(), CLocalBlast::Run(), CPsiBlastImpl::Run(), and CMagicBlast::x_Run().
◆ SetNumberOfThreads() [2/3]
|
inlinevirtual |
Mutator for the number of threads.
- Parameters
-
nthreads number of threads to use
Reimplemented in CBlastPrelimSearch.
Definition at line 367 of file setup_factory.hpp.
References CThreadable::kMinNumThreads, and CThreadable::m_NumThreads.
Referenced by CDeltaBlastApp::DoPsiBlastIterations(), CBlastnNode::Main(), CBlastpNode::Main(), CBlastxNode::Main(), CTblastnNode::Main(), CDeltaBlast::Run(), CLocalBlast::Run(), CPsiBlast::Run(), CIgBlast::Run(), CPsiBlastImpl::Run(), CTblastxApp::Run(), CRMBlastnApp::Run(), s_RunLocalVDBSearch(), s_RunPsiVDBSearch(), CBlastPrelimSearch::SetNumberOfThreads(), CPsiBlastApp::x_RunLocalPsiBlastIterations(), CBlastnApp::x_RunMTBySplitDB(), CBlastpApp::x_RunMTBySplitDB(), CBlastxApp::x_RunMTBySplitDB(), and CTblastnApp::x_RunMTBySplitDB().
◆ SetNumberOfThreads() [3/3]
|
inline |
Set MT mode.
Definition at line 289 of file igblast.hpp.
References CIgBlast::m_NumThreads.
Referenced by CIgBlastnApp::CIgWorker::Main(), and CIgBlastpApp::Run().
◆ SetNumThreads()
|
inline |
Set the number of threads used for concurrent search.
- Parameters
-
n_threads number of search threads.
Definition at line 561 of file blast_dbindex.cpp.
References ASSERT, IDX_TRACE, and CIndexedDb_New::n_threads_.
Referenced by IndexedDbSetNumThreads().
◆ SetOffDiagonalRange() [1/3]
| void CBlastOptions::SetOffDiagonalRange | ( | int | r | ) |
Definition at line 1518 of file blast_options_cxx.cpp.
References CBlastOptions::m_Local, and CBlastOptionsLocal::SetOffDiagonalRange().
Referenced by COffDiagonalRangeArg::ExtractAlgorithmOptions(), and CBlastOptionsHandle::SetOffDiagonalRange().
◆ SetOffDiagonalRange() [2/3]
|
inline |
Definition at line 186 of file blast_options_handle.hpp.
References CBlastOptionsHandle::m_Opts, r(), and CBlastOptions::SetOffDiagonalRange().
Referenced by CBlastNucleotideOptionsHandle::SetInitialWordOptionsDefaults().
◆ SetOffDiagonalRange() [3/3]
|
inline |
Definition at line 1111 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_InitWordOpts, r(), and BlastInitialWordOptions::scan_range.
Referenced by CBlastOptions::SetOffDiagonalRange().
◆ SetOptions() [1/6]
|
inline |
Returns a reference to the internal options class which this object is a handle for.
Please note that using objects of type CBlastOptions directly allows one to set inconsistent combinations of options.
- Note
- Assumes user knows exactly how to set the individual options correctly. Calling CBlastOptions::Validate on this object is STRONGLY recommended.
Definition at line 169 of file blast_options_handle.hpp.
References CBlastOptionsHandle::m_Opts.
Referenced by BOOST_AUTO_TEST_CASE(), CheckForFreqRatioFile(), CBlastOptionsFactory::CreateTask(), CBlastnNode::Main(), CBlastFormatterApp::PrintFormattedOutput(), CBlastFormatterVdbApp::PrintFormattedOutput(), CSplitQueryTestFixture::QuerySplitter_BlastnMultiQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastnSingleQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastxMultiQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastxSingleQueryMultiChunk(), CIgBlast::Run(), CLocalVDBBlast::Run(), CPsiBlastApp::Run(), CIgBlastnApp::Run(), CRMBlastnApp::Run(), CLocalVDBBlast::RunThreadedSearch(), CBlastArgs::s_ExtractBlastArgs(), CBlastAppArgs::SetOptions(), CBlastAppArgs::SetOptionsForSavedStrategy(), CLocalVDBBlast::x_AdjustDbSize(), CBlastOptionsBuilder::x_ApplyInteractions(), CIgBlastnAppArgs::x_CreateOptionsHandle(), CIgBlastpAppArgs::x_CreateOptionsHandle(), CTblastnAppArgs::x_CreateOptionsHandle(), CRemoteBlast::x_Init(), CExportStrategy::x_Process_BlastOptions(), CBlastOptionsBuilder::x_ProcessOneOption(), CPsiBlastApp::x_RunLocalPsiBlastIterations(), CBlastnApp::x_RunMTBySplitDB(), CSplignApp::x_SetupBlastOptions(), CIgBlast::x_SetupCRegionSearch(), CIgBlast::x_SetupDJSearch(), CIgBlast::x_SetupNoOverlapDSearch(), CIgBlast::x_SetupVSearch(), and CSplitQueryTestFixture::x_TestCContextTranslator().
◆ SetOptions() [2/6]
|
virtual |
Configure the search.
Implements ISearch.
Definition at line 115 of file local_search.cpp.
References CLocalSeqSearch::m_SearchOpts.
◆ SetOptions() [3/6]
|
virtual |
Configure this search.
Implements ISearch.
Definition at line 137 of file local_search.cpp.
References CLocalPssmSearch::m_SearchOpts.
◆ SetOptions() [4/6]
|
virtual |
Configure the search.
Implements ISearch.
Definition at line 159 of file remote_search.cpp.
References CRemoteSeqSearch::m_SearchOpts.
◆ SetOptions() [5/6]
|
virtual |
Configure the search.
Implements ISearch.
Definition at line 290 of file remote_search.cpp.
References CRemotePssmSearch::m_RemoteBlast, CRemotePssmSearch::m_SearchOpts, and CRef< C, Locker >::Reset().
◆ SetOptions() [6/6]
|
pure virtual |
Configure the search.
- Parameters
-
options The search will be configured with these options.
Implemented in CRemotePssmSearch, CRemoteSeqSearch, CLocalPssmSearch, and CLocalSeqSearch.
◆ SetOptionsHandle()
|
inline |
Set the options handle.
Definition at line 278 of file bl2seq.hpp.
References CBl2Seq::m_OptsHandle, and CBl2Seq::x_ResetInternalDs().
Referenced by BOOST_AUTO_TEST_CASE(), and CSplignApp::x_GetBl2SeqHits().
◆ SetOutOfFrameMode() [1/4]
Definition at line 2320 of file blast_options_cxx.cpp.
References eBlastOpt_OutOfFrameMode, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetOutOfFrameMode(), and CBlastOptionsRemote::SetValue().
Referenced by CFrameShiftArgs::ExtractAlgorithmOptions(), CBlastNucleotideOptionsHandle::SetMBScoringOptionsDefaults(), CBlastNucleotideOptionsHandle::SetScoringOptionsDefaults(), CBlastProteinOptionsHandle::SetScoringOptionsDefaults(), CBlastRPSOptionsHandle::SetScoringOptionsDefaults(), CMagicBlastOptionsHandle::SetScoringOptionsDefaults(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetOutOfFrameMode() [2/4]
Sets OutOfFrameMode.
- Parameters
-
m OutOfFrameMode [in]
Definition at line 85 of file blastx_options.hpp.
◆ SetOutOfFrameMode() [3/4]
Sets OutOfFrameMode.
- Parameters
-
m OutOfFrameMode [in]
Definition at line 68 of file tblastn_options.hpp.
◆ SetOutOfFrameMode() [4/4]
Definition at line 1688 of file blast_options_local_priv.hpp.
References BlastScoringOptions::is_ooframe, and CBlastOptionsLocal::m_ScoringOpts.
Referenced by CBlastOptions::SetOutOfFrameMode().
◆ SetPaired() [1/3]
| void CBlastOptions::SetPaired | ( | bool | p | ) |
Definition at line 2164 of file blast_options_cxx.cpp.
References CBlastOptions::m_Local, CBlastOptionsLocal::SetPaired(), and CBlastOptions::x_Throwx().
Referenced by CMapperQueryOptionsArgs::ExtractAlgorithmOptions().
◆ SetPaired() [2/3]
|
inline |
Set input reads as paired/not paired.
- Parameters
-
p If true, the input sequences are paired [in]
Definition at line 203 of file magicblast_options.hpp.
Referenced by CMagicBlastOptionsHandle::SetQueryOptionDefaults().
◆ SetPaired() [3/3]
|
inline |
Definition at line 1588 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_HitSaveOpts, and BlastHitSavingOptions::paired.
Referenced by CBlastOptions::SetPaired().
◆ SetPercentIdentity() [1/3]
| void CBlastOptions::SetPercentIdentity | ( | double | p | ) |
Definition at line 1969 of file blast_options_cxx.cpp.
References eBlastOpt_PercentIdentity, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetPercentIdentity(), and CBlastOptionsRemote::SetValue().
Referenced by CGenericSearchArgs::ExtractAlgorithmOptions(), CMagicBlastOptionsHandle::SetHitSavingOptionsDefaults(), and CBlastOptionsHandle::SetPercentIdentity().
◆ SetPercentIdentity() [2/3]
|
inline |
Sets PercentIdentity.
- Parameters
-
p PercentIdentity [in]
Definition at line 261 of file blast_options_handle.hpp.
References CBlastOptionsHandle::m_Opts, and CBlastOptions::SetPercentIdentity().
Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), CBlastNucleotideOptionsHandle::SetHitSavingOptionsDefaults(), CBlastProteinOptionsHandle::SetHitSavingOptionsDefaults(), CBlastRPSOptionsHandle::SetHitSavingOptionsDefaults(), CBlastNucleotideOptionsHandle::SetMBHitSavingOptionsDefaults(), CSimpleB2SWrapper::SetPercIdThreshold(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetPercentIdentity() [3/3]
|
inline |
Definition at line 1478 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_HitSaveOpts, and BlastHitSavingOptions::percent_identity.
Referenced by CBlastOptions::SetPercentIdentity().
◆ SetPHIPattern() [1/4]
|
inline |
Sets the pattern string option.
- Parameters
-
pattern The pattern string satisfying PROSITE rules.
Definition at line 81 of file phiblast_nucl_options.hpp.
References CBlastOptionsHandle::m_Opts, and CBlastOptions::SetPHIPattern().
◆ SetPHIPattern() [2/4]
|
inline |
Sets the pattern string option.
- Parameters
-
pattern The pattern string satisfying PROSITE rules.
Definition at line 82 of file phiblast_prot_options.hpp.
References CBlastOptionsHandle::m_Opts, and CBlastOptions::SetPHIPattern().
◆ SetPHIPattern() [3/4]
Definition at line 2431 of file blast_options_cxx.cpp.
References eBlastOpt_PHIPattern, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetPHIPattern(), and CBlastOptionsRemote::SetValue().
Referenced by BOOST_AUTO_TEST_CASE(), CPhiBlastArgs::ExtractAlgorithmOptions(), CPHIBlastNuclOptionsHandle::SetPHIPattern(), CPHIBlastProtOptionsHandle::SetPHIPattern(), CBlastOptionsBuilder::x_ProcessOneOption(), and CPsiBlastApp::x_RunLocalPsiBlastIterations().
◆ SetPHIPattern() [4/4]
Definition at line 1802 of file blast_options_local_priv.hpp.
References ePhiLookupTable, ePhiNaLookupTable, LookupTableOptions::lut_type, CBlastOptionsLocal::m_LutOpts, LookupTableOptions::phi_pattern, sfree, and strdup.
Referenced by CBlastOptions::SetPHIPattern().
◆ SetPlusStrand()
|
inline |
For nucleotide sequences this instructs the implementation to convert its representation to be that of the plus strand.
Definition at line 222 of file blast_setup.hpp.
References eNa_strand_plus, IBlastSeqVector::m_Strand, and IBlastSeqVector::x_SetPlusStrand().
◆ SetProgram() [1/2]
| void CBlastOptions::SetProgram | ( | EProgram | p | ) |
Sets the task this object is best suited for.
Definition at line 851 of file blast_options_cxx.cpp.
References eBlastOpt_Program, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetProgram(), and CBlastOptionsRemote::SetValue().
Referenced by BOOST_AUTO_TEST_CASE(), CMagicBlastOptionsHandle::SetGenomeToGenomeDefaults(), CPSIBlastOptionsHandle::SetPSITblastnDefaults(), CMagicBlastOptionsHandle::SetRNAToGenomeDefaults(), CMagicBlastOptionsHandle::SetRNAToRNADefaults(), CBlastNucleotideOptionsHandle::SetTraditionalBlastnDefaults(), CBlastNucleotideOptionsHandle::SetTraditionalMegablastDefaults(), LinkHspTestFixture::setupCutoffScores(), LinkHspTestFixture::setupLinkHspInputTblastn(), and CBlastNucleotideOptionsHandle::SetVecScreenDefaults().
◆ SetProgram() [2/2]
|
inline |
Definition at line 542 of file blast_options_local_priv.hpp.
References _ASSERT, Blast_SubjectIsTranslated(), eBlastn, eBlastProgramMax, eBlastTypeUndefined, EProgramToEBlastProgramType(), BlastDatabaseOptions::genetic_code, CBlastOptionsLocal::GetDbOpts(), CBlastOptionsLocal::GetExtnOpts(), CBlastOptionsLocal::GetHitSaveOpts(), CBlastOptionsLocal::GetInitWordOpts(), CBlastOptionsLocal::GetLutOpts(), CBlastOptionsLocal::GetScoringOpts(), CBlastOptionsLocal::m_Program, LookupTableOptions::program_number, BlastInitialWordOptions::program_number, BlastExtensionOptions::program_number, BlastHitSavingOptions::program_number, and BlastScoringOptions::program_number.
Referenced by CBlastOptions::SetProgram().
◆ SetProteinBlastDbDataLoader()
Definition at line 84 of file blast_input_unit_test_aux.hpp.
References CAutoNcbiConfigFile::kProtBlastDbDataLoader, CAutoNcbiConfigFile::kSection, CAutoNcbiConfigFile::m_Registry, and IRWRegistry::Set().
Referenced by BOOST_AUTO_TEST_CASE(), and s_RetrieveSequenceLength().
◆ SetPseudoCount() [1/3]
|
inline |
Sets PseudoCount.
- Parameters
-
p PseudoCount [in]
Definition at line 75 of file psiblast_options.hpp.
Referenced by CDUpdater::blast(), and CdBlaster::psiBlast().
◆ SetPseudoCount() [2/3]
|
inline |
Definition at line 1784 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_PSIBlastOpts, and PSIBlastOptions::pseudo_count.
Referenced by CBlastOptions::SetPseudoCount().
◆ SetPseudoCount() [3/3]
| void CBlastOptions::SetPseudoCount | ( | int | u | ) |
Definition at line 2482 of file blast_options_cxx.cpp.
References eBlastOpt_PseudoCount, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetPseudoCount(), and CBlastOptionsRemote::SetValue().
Referenced by CPssmEngineArgs::ExtractAlgorithmOptions(), CDeltaBlastOptionsHandle::SetDeltaBlastDefaults(), CPSIBlastOptionsHandle::SetPSIBlastDefaults(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetPSIBlastDefaults()
|
protected |
Sets PSIBlastDefaults.
Definition at line 63 of file psiblast_options.cpp.
References CBlastOptionsHandle::m_Opts, PSI_INCLUSION_ETHRESH, PSI_PSEUDO_COUNT_CONST, CBlastOptions::SetInclusionThreshold(), and CBlastOptions::SetPseudoCount().
◆ SetPSIInclusionThreshold()
|
inline |
Set e-value threshold for including sequences in Pssm calculation.
- Parameters
-
th E-value cutoff for sequences [in]
Same as SetInclusionThreshold().It was added for clear distinction between Psi and Delta Blast inclusion thresholds
Definition at line 86 of file deltablast_options.hpp.
References th.
◆ SetPSITblastnDefaults()
| void CPSIBlastOptionsHandle::SetPSITblastnDefaults | ( | void | ) |
Sets default options for psi tblastn search.
Definition at line 69 of file psiblast_options.cpp.
References BLAST_GENETIC_CODE, BLAST_WORD_THRESHOLD_TBLASTN, ePSITblastn, CBlastOptionsHandle::m_Opts, CBlastOptions::SetDbGeneticCode(), CBlastOptions::SetProgram(), CBlastOptions::SetSmithWatermanMode(), and CBlastOptions::SetWordThreshold().
Referenced by CTblastnAppArgs::x_CreateOptionsHandle(), and CTblastnVdbAppArgs::x_CreateOptionsHandle().
◆ SetPssm() [1/2]
| void CPsiBlast::SetPssm | ( | CConstRef< objects::CPssmWithParameters > | pssm | ) |
This method allows the same object to be reused when performing multiple iterations.
Iteration state is kept in the CPsiBlastIterationState object
Definition at line 83 of file psiblast.cpp.
References CPsiBlast::m_Impl, and CPsiBlastImpl::SetPssm().
Referenced by BOOST_AUTO_TEST_CASE(), CDeltaBlastApp::DoPsiBlastIterations(), and CPsiBlastApp::x_RunLocalPsiBlastIterations().
◆ SetPssm() [2/2]
| void CPsiBlastImpl::SetPssm | ( | CConstRef< objects::CPssmWithParameters > | pssm | ) |
This method allows the same object to be reused when performing multiple iterations.
Iteration state is kept in the CPsiBlastIterationState object
- Parameters
-
pssm PSSM [in]
Definition at line 173 of file psiblast_impl.cpp.
References CConstRef< C, Locker >::Empty(), CPsiBlastImpl::m_Pssm, NCBI_THROW, CPsiBlastValidate::Pssm(), and CRef< C, Locker >::Reset().
Referenced by CPsiBlast::SetPssm().
◆ SetQueries() [1/6]
|
inline |
Set a vector of query sequences for a concatenated search.
Definition at line 236 of file bl2seq.hpp.
References CBl2Seq::m_tQueries, and CBl2Seq::x_ResetInternalDs().
◆ SetQueries() [2/6]
| void CRemoteBlast::SetQueries | ( | CRef< objects::CBioseq_set > | bioseqs | ) |
Set the query as a Bioseq_set.
Definition at line 986 of file remote_blast.cpp.
References CRef< C, Locker >::Empty(), CRemoteBlast::eQueries, CRemoteBlast::m_NeedConfig, CRemoteBlast::m_QSR, CRemoteBlast::m_Queries, NCBI_THROW, and CRef< C, Locker >::Reset().
Referenced by BOOST_AUTO_TEST_CASE(), CRemoteBlast::CRemoteBlast(), CRemoteBlast::SetQueries(), CRemoteBlast::x_InitQueries(), CRemoteSeqSearch::x_RemoteBlast(), and CRemotePssmSearch::x_RemoteBlast().
◆ SetQueries() [3/6]
| void CRemoteBlast::SetQueries | ( | CRef< objects::CBioseq_set > | bioseqs, |
| const TSeqLocInfoVector & | masking_locations | ||
| ) |
Set the query as a Bioseq_set along with the corresponding masking locations.
- Parameters
-
bioseqs Query sequence data [in] masking_locations Masked regions for the queries above [in]
Definition at line 1000 of file remote_blast.cpp.
References CRemoteBlast::SetQueries(), and CRemoteBlast::x_SetMaskingLocationsForQueries().
◆ SetQueries() [4/6]
| void CRemoteBlast::SetQueries | ( | CRef< objects::CPssmWithParameters > | pssm | ) |
Set a PSSM query (as for PSI blast), which must include a bioseq set.
Definition at line 1162 of file remote_blast.cpp.
References CRef< C, Locker >::Empty(), CRemoteBlast::eQueries, CRemoteBlast::m_NeedConfig, CRemoteBlast::m_QSR, NCBI_THROW, CPsiBlastValidate::Pssm(), and CBlast4_queries_Base::SetPssm().
◆ SetQueries() [5/6]
| void CRemoteBlast::SetQueries | ( | TSeqLocList & | seqlocs | ) |
Set the query as a list of Seq_locs.
- Parameters
-
seqlocs One interval Seq_loc or a list of whole Seq_locs.
◆ SetQueries() [6/6]
| void CRemoteBlast::SetQueries | ( | TSeqLocList & | seqlocs, |
| const TSeqLocInfoVector & | masking_locations | ||
| ) |
Set the query as a list of Seq_locs.
- Parameters
-
seqlocs One interval Seq_loc or a list of whole Seq_locs. masking_locations Masked regions for the queries above [in]
◆ SetQuery() [1/4]
Set the query.
Definition at line 222 of file bl2seq.hpp.
References CBl2Seq::m_tQueries, query, and CBl2Seq::x_ResetInternalDs().
Referenced by BOOST_AUTO_TEST_CASE().
◆ SetQuery() [2/4]
|
virtual |
Set the PSSM with which to search the database.
Implements IPssmSearch.
Definition at line 149 of file local_search.cpp.
References CLocalPssmSearch::m_Pssm, and CPsiBlastValidate::Pssm().
◆ SetQuery() [3/4]
|
pure virtual |
Set the queries to search.
- Parameters
-
pssm PSSM [in]
Implemented in CRemotePssmSearch, and CLocalPssmSearch.
◆ SetQuery() [4/4]
|
virtual |
Set the query to search with.
Implements IPssmSearch.
Definition at line 356 of file remote_search.cpp.
References CRef< C, Locker >::Empty(), CRemotePssmSearch::m_Pssm, and NCBI_THROW.
◆ SetQueryCovHspPerc() [1/3]
| void CBlastOptions::SetQueryCovHspPerc | ( | double | p | ) |
Definition at line 2007 of file blast_options_cxx.cpp.
References eBlastOpt_QueryCovHspPerc, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetQueryCovHspPerc(), and CBlastOptionsRemote::SetValue().
Referenced by BOOST_AUTO_TEST_CASE(), CGenericSearchArgs::ExtractAlgorithmOptions(), CMagicBlastOptionsHandle::SetHitSavingOptionsDefaults(), and CBlastOptionsHandle::SetQueryCovHspPerc().
◆ SetQueryCovHspPerc() [2/3]
|
inline |
Sets QueryCovHspPerc.
- Parameters
-
p QueryCovHspPerc [in]
Definition at line 267 of file blast_options_handle.hpp.
References CBlastOptionsHandle::m_Opts, and CBlastOptions::SetQueryCovHspPerc().
Referenced by BOOST_AUTO_TEST_CASE(), CBlastNucleotideOptionsHandle::SetHitSavingOptionsDefaults(), CBlastProteinOptionsHandle::SetHitSavingOptionsDefaults(), CBlastRPSOptionsHandle::SetHitSavingOptionsDefaults(), CBlastNucleotideOptionsHandle::SetMBHitSavingOptionsDefaults(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetQueryCovHspPerc() [3/3]
|
inline |
Definition at line 1502 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_HitSaveOpts, and BlastHitSavingOptions::query_cov_hsp_perc.
Referenced by CBlastOptions::SetQueryCovHspPerc().
◆ SetQueryFactory() [1/3]
|
virtual |
Set the factory which will return the queries to search for.
Implements ISeqSearch.
Definition at line 127 of file local_search.cpp.
References CLocalSeqSearch::m_QueryFactory.
◆ SetQueryFactory() [2/3]
|
virtual |
Set the factory which will return the queries to search for.
Implements ISeqSearch.
Definition at line 169 of file remote_search.cpp.
References CRef< C, Locker >::Empty(), CRemoteSeqSearch::m_Queries, IQueryFactory::MakeRemoteQueryData(), NCBI_THROW, and CRef< C, Locker >::Reset().
◆ SetQueryFactory() [3/3]
|
pure virtual |
Set the queries to search.
- Parameters
-
query_factory This supplies the queries for which to search.
Implemented in CRemoteSeqSearch, and CLocalSeqSearch.
◆ SetQueryGeneticCode() [1/4]
| void CBlastOptions::SetQueryGeneticCode | ( | int | gc | ) |
Definition at line 1478 of file blast_options_cxx.cpp.
References CAutomaticGenCodeSingleton::AddGeneticCode(), eBlastOpt_QueryGeneticCode, CBlastOptions::m_GenCodeSingletonVar, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetQueryGeneticCode(), and CBlastOptionsRemote::SetValue().
Referenced by CGeneticCodeArgs::ExtractAlgorithmOptions(), CBlastxOptionsHandle::SetQueryOptionDefaults(), CRPSTBlastnOptionsHandle::SetQueryOptionDefaults(), CTBlastxOptionsHandle::SetQueryOptionDefaults(), LinkHspTestFixture::setupCutoffScores(), LinkHspTestFixture::setupLinkHspInputTblastn(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetQueryGeneticCode() [2/4]
|
inline |
Sets QueryGeneticCode.
- Parameters
-
gc QueryGeneticCode [in]
Definition at line 77 of file blastx_options.hpp.
◆ SetQueryGeneticCode() [3/4]
|
inline |
Sets QueryGeneticCode.
- Parameters
-
gc QueryGeneticCode [in]
Definition at line 92 of file tblastx_options.hpp.
◆ SetQueryGeneticCode() [4/4]
|
inline |
Definition at line 1019 of file blast_options_local_priv.hpp.
References QuerySetUpOptions::genetic_code, and CBlastOptionsLocal::m_QueryOpts.
Referenced by CBlastOptions::SetQueryGeneticCode().
◆ SetQueryId()
Set the query id as a string.
- Parameters
-
id The query id.
Definition at line 966 of file blast_aux.cpp.
References TQueryMessages::m_IdString.
Referenced by CBlastKmerResults::GetErrors(), and MakeEmptyResults().
◆ SetQueryInfo()
|
inline |
Set the current set of unmasked query segments.
- Parameters
-
locs_wrap unmasked query segments
Definition at line 187 of file blast_dbindex.cpp.
References CIndexedDb::locs_wrap_.
Referenced by IndexedDbSetQueryInfo().
◆ SetQueryMasks()
| void CRemoteBlast::SetQueryMasks | ( | const TSeqLocInfoVector & | masking_locations | ) |
Set the masking locations for queries.
- Parameters
-
masking_locations Masked regions for the queries above [in]
Definition at line 1007 of file remote_blast.cpp.
References CRemoteBlast::m_QSR, NCBI_THROW, and CRemoteBlast::x_SetMaskingLocationsForQueries().
◆ SetQueryOptionDefaults() [1/11]
|
protectedvirtual |
Overrides SetQueryOptionDefaults for advanced blastp options to disable filtering.
Reimplemented from CBlastProteinOptionsHandle.
Reimplemented in CPSIBlastOptionsHandle, and CDeltaBlastOptionsHandle.
Definition at line 63 of file blast_advprot_options.cpp.
References CBlastProteinOptionsHandle::SetQueryOptionDefaults(), and CBlastProteinOptionsHandle::SetSegFiltering().
◆ SetQueryOptionDefaults() [2/11]
|
protectedvirtual |
Overrides QueryOptionDefaults for nucleotide options.
Implements CBlastOptionsHandle.
Definition at line 155 of file blast_nucl_options.cpp.
References eNa_strand_both, CBlastNucleotideOptionsHandle::SetDustFiltering(), CBlastOptionsHandle::SetMaskAtHash(), and CBlastNucleotideOptionsHandle::SetStrandOption().
Referenced by CBlastNucleotideOptionsHandle::SetTraditionalBlastnDefaults(), and CBlastNucleotideOptionsHandle::SetTraditionalMegablastDefaults().
◆ SetQueryOptionDefaults() [3/11]
|
protectedvirtual |
Overrides QueryOptionDefaults for protein options.
Implements CBlastOptionsHandle.
Reimplemented in CTBlastxOptionsHandle, CPSIBlastOptionsHandle, CDeltaBlastOptionsHandle, CBlastxOptionsHandle, and CBlastAdvancedProteinOptionsHandle.
Definition at line 94 of file blast_prot_options.cpp.
References eNa_strand_unknown, CBlastOptionsHandle::m_Opts, CBlastProteinOptionsHandle::SetSegFiltering(), and CBlastOptions::SetStrandOption().
Referenced by CBlastAdvancedProteinOptionsHandle::SetQueryOptionDefaults(), CBlastxOptionsHandle::SetQueryOptionDefaults(), and CTBlastxOptionsHandle::SetQueryOptionDefaults().
◆ SetQueryOptionDefaults() [4/11]
|
protectedvirtual |
Overrides QueryOptionDefaults for RPS-BLAST options.
Implements CBlastOptionsHandle.
Reimplemented in CRPSTBlastnOptionsHandle.
Definition at line 70 of file blast_rps_options.cpp.
References eNa_strand_unknown, CBlastOptionsHandle::m_Opts, CBlastRPSOptionsHandle::SetSegFiltering(), and CBlastOptions::SetStrandOption().
◆ SetQueryOptionDefaults() [5/11]
|
protectedvirtual |
Overrides QueryOptionDefaults for blastx options.
Reimplemented from CBlastProteinOptionsHandle.
Definition at line 62 of file blastx_options.cpp.
References BLAST_GENETIC_CODE, eNa_strand_both, CBlastOptionsHandle::m_Opts, CBlastOptions::SetQueryGeneticCode(), CBlastProteinOptionsHandle::SetQueryOptionDefaults(), CBlastProteinOptionsHandle::SetSegFiltering(), and CBlastOptions::SetStrandOption().
◆ SetQueryOptionDefaults() [6/11]
|
protectedvirtual |
Override the parent class' default for filtering query sequence (i.e.
: no filtering applied to the query by default)
Reimplemented from CPSIBlastOptionsHandle.
Definition at line 58 of file deltablast_options.cpp.
References CBlastOptions::ClearFilterOptions(), and CBlastOptionsHandle::m_Opts.
◆ SetQueryOptionDefaults() [7/11]
|
protectedvirtual |
Overrides QueryOptionDefaults for nucleotide options.
Implements CBlastOptionsHandle.
Definition at line 149 of file magicblast_options.cpp.
References eNa_strand_both, CBlastOptionsHandle::m_Opts, CBlastOptions::SetDustFiltering(), CMagicBlastOptionsHandle::SetLookupDbFilter(), CBlastOptions::SetMaskAtHash(), CMagicBlastOptionsHandle::SetPaired(), CMagicBlastOptionsHandle::SetReadQualityFiltering(), and CBlastOptions::SetStrandOption().
Referenced by CMagicBlastOptionsHandle::SetGenomeToGenomeDefaults(), CMagicBlastOptionsHandle::SetRNAToGenomeDefaults(), and CMagicBlastOptionsHandle::SetRNAToRNADefaults().
◆ SetQueryOptionDefaults() [8/11]
|
protectedvirtual |
Override the parent class' default for filtering query sequence (i.e.
: no filtering applied to the query by default)
Reimplemented from CBlastAdvancedProteinOptionsHandle.
Reimplemented in CDeltaBlastOptionsHandle.
Definition at line 58 of file psiblast_options.cpp.
References CBlastOptions::ClearFilterOptions(), and CBlastOptionsHandle::m_Opts.
◆ SetQueryOptionDefaults() [9/11]
|
protectedvirtual |
Overrides SubjectSequenceOptionsDefaults for RPS-TBLASTN options.
Reimplemented from CBlastRPSOptionsHandle.
Definition at line 61 of file rpstblastn_options.cpp.
References BLAST_GENETIC_CODE, CBlastOptionsHandle::m_Opts, and CBlastOptions::SetQueryGeneticCode().
◆ SetQueryOptionDefaults() [10/11]
|
protectedvirtual |
Overrides QueryOptionDefaults for tblastx options.
Reimplemented from CBlastProteinOptionsHandle.
Definition at line 62 of file tblastx_options.cpp.
References BLAST_GENETIC_CODE, eNa_strand_both, CBlastOptionsHandle::m_Opts, CBlastOptions::SetQueryGeneticCode(), CBlastProteinOptionsHandle::SetQueryOptionDefaults(), and CBlastOptions::SetStrandOption().
◆ SetQueryOptionDefaults() [11/11]
|
protectedpure virtual |
Sets QueryOptionDefaults.
Implemented in CTBlastxOptionsHandle, CRPSTBlastnOptionsHandle, CPSIBlastOptionsHandle, CMagicBlastOptionsHandle, CDeltaBlastOptionsHandle, CBlastxOptionsHandle, CBlastRPSOptionsHandle, CBlastProteinOptionsHandle, CBlastNucleotideOptionsHandle, and CBlastAdvancedProteinOptionsHandle.
Referenced by CBlastOptionsHandle::SetDefaults().
◆ SetReadMaxFractionAmbiguous() [1/2]
| void CBlastOptions::SetReadMaxFractionAmbiguous | ( | double | val | ) |
Set maximum fraction of ambiguous bases for next-generation read quality filtering.
Definition at line 1421 of file blast_options_cxx.cpp.
References CBlastOptions::m_Local, CBlastOptionsLocal::SetReadMaxFractionAmbiguous(), val, and CBlastOptions::x_Throwx().
◆ SetReadMaxFractionAmbiguous() [2/2]
|
inline |
Definition at line 1059 of file blast_options_local_priv.hpp.
References QuerySetUpOptions::filtering_options, SReadQualityOptions::frac_ambig, CBlastOptionsLocal::m_QueryOpts, NULL, SBlastFilterOptions::readQualityOptions, SReadQualityOptionsNew(), and val.
Referenced by CBlastOptions::SetReadMaxFractionAmbiguous().
◆ SetReadMinDimerEntropy() [1/2]
| void CBlastOptions::SetReadMinDimerEntropy | ( | int | val | ) |
Set minimum dimer entropy for next-generation read quality filtering.
Definition at line 1441 of file blast_options_cxx.cpp.
References CBlastOptions::m_Local, CBlastOptionsLocal::SetReadMinDimerEntropy(), val, and CBlastOptions::x_Throwx().
◆ SetReadMinDimerEntropy() [2/2]
|
inline |
Definition at line 1080 of file blast_options_local_priv.hpp.
References SReadQualityOptions::entropy, QuerySetUpOptions::filtering_options, CBlastOptionsLocal::m_QueryOpts, NULL, SBlastFilterOptions::readQualityOptions, SReadQualityOptionsNew(), and val.
Referenced by CBlastOptions::SetReadMinDimerEntropy().
◆ SetReadQualityFiltering() [1/3]
Turn on/off next-generation read quality filtering with deafult parameters.
Definition at line 1401 of file blast_options_cxx.cpp.
References CBlastOptions::m_Local, CBlastOptionsLocal::SetReadQualityFiltering(), val, and CBlastOptions::x_Throwx().
Referenced by CMapperQueryOptionsArgs::ExtractAlgorithmOptions().
◆ SetReadQualityFiltering() [2/3]
Turn on/off query quaility filtering with default parameters.
Definition at line 114 of file magicblast_options.hpp.
References val.
Referenced by CMagicBlastOptionsHandle::SetQueryOptionDefaults().
◆ SetReadQualityFiltering() [3/3]
Definition at line 1036 of file blast_options_local_priv.hpp.
References QuerySetUpOptions::filtering_options, CBlastOptionsLocal::m_QueryOpts, SBlastFilterOptions::readQualityOptions, SReadQualityOptionsFree(), SReadQualityOptionsNew(), and val.
Referenced by CBlastOptions::SetReadQualityFiltering().
◆ SetRemoteProgramAndService_Blast3() [1/13]
|
inlineprotectedvirtual |
Set the program and service name for remote blast.
Implements CBlastOptionsHandle.
Reimplemented in CDiscNucleotideOptionsHandle.
Definition at line 221 of file blast_nucl_options.hpp.
◆ SetRemoteProgramAndService_Blast3() [2/13]
|
inlineprotectedvirtual |
Set the program and service name for remote blast.
Implements CBlastOptionsHandle.
Reimplemented in CTBlastxOptionsHandle, CTBlastnOptionsHandle, CPSIBlastOptionsHandle, CDeltaBlastOptionsHandle, CBlastxOptionsHandle, and CBlastpKmerOptionsHandle.
Definition at line 138 of file blast_prot_options.hpp.
◆ SetRemoteProgramAndService_Blast3() [3/13]
|
inlineprotectedvirtual |
Set the program and service name for remote blast.
Implements CBlastOptionsHandle.
Reimplemented in CRPSTBlastnOptionsHandle.
Definition at line 122 of file blast_rps_options.hpp.
◆ SetRemoteProgramAndService_Blast3() [4/13]
|
inlineprotectedvirtual |
Set the program and service name for remote blast.
Reimplemented from CBlastProteinOptionsHandle.
Definition at line 93 of file blastp_kmer_options.hpp.
◆ SetRemoteProgramAndService_Blast3() [5/13]
|
inlineprotectedvirtual |
Set the program and service name for remote blast.
Reimplemented from CBlastProteinOptionsHandle.
Definition at line 127 of file blastx_options.hpp.
◆ SetRemoteProgramAndService_Blast3() [6/13]
|
inlineprotectedvirtual |
Set the program and service name for remote blast.
Reimplemented from CPSIBlastOptionsHandle.
Definition at line 92 of file deltablast_options.hpp.
◆ SetRemoteProgramAndService_Blast3() [7/13]
|
inlineprotectedvirtual |
Set the program and service name for remote blast.
Reimplemented from CBlastNucleotideOptionsHandle.
Definition at line 102 of file disc_nucl_options.hpp.
◆ SetRemoteProgramAndService_Blast3() [8/13]
|
inlineprotectedvirtual |
Set the program and service name for remote blast.
Implements CBlastOptionsHandle.
Definition at line 225 of file magicblast_options.hpp.
◆ SetRemoteProgramAndService_Blast3() [9/13]
|
inlineprotectedvirtual |
Set the program and service name for remote blast.
Reimplemented from CBlastProteinOptionsHandle.
Reimplemented in CDeltaBlastOptionsHandle.
Definition at line 82 of file psiblast_options.hpp.
◆ SetRemoteProgramAndService_Blast3() [10/13]
|
inlineprotectedvirtual |
Set the program and service name for remote blast.
Reimplemented from CBlastRPSOptionsHandle.
Definition at line 74 of file rpstblastn_options.hpp.
◆ SetRemoteProgramAndService_Blast3() [11/13]
|
inlineprotectedvirtual |
Set the program and service name for remote blast.
Reimplemented from CBlastProteinOptionsHandle.
Definition at line 95 of file tblastn_options.hpp.
◆ SetRemoteProgramAndService_Blast3() [12/13]
|
inlineprotectedvirtual |
Set the program and service name for remote blast.
Reimplemented from CBlastProteinOptionsHandle.
Definition at line 98 of file tblastx_options.hpp.
◆ SetRemoteProgramAndService_Blast3() [13/13]
|
protectedpure virtual |
Set the program and service name for remote blast.
Implemented in CTBlastxOptionsHandle, CTBlastnOptionsHandle, CRPSTBlastnOptionsHandle, CPSIBlastOptionsHandle, CMagicBlastOptionsHandle, CDiscNucleotideOptionsHandle, CDeltaBlastOptionsHandle, CBlastxOptionsHandle, CBlastpKmerOptionsHandle, CBlastRPSOptionsHandle, CBlastProteinOptionsHandle, and CBlastNucleotideOptionsHandle.
Referenced by CBlastOptionsHandle::SetDefaults().
◆ SetRepeatFiltering() [1/3]
|
inline |
Enable repeat filtering.
- Parameters
-
val enable repeat filtering [in]
Definition at line 130 of file blast_nucl_options.hpp.
References val.
Referenced by BOOST_AUTO_TEST_CASE(), and BOOST_FIXTURE_TEST_CASE().
◆ SetRepeatFiltering() [2/3]
Turns on repeat filtering using the default repeat database, namely kDefaultRepeatFilterDb.
- Note
- Either SetRepeatFiltering or SetRepeatFilteringDB should be called, if both are called, only the last one called will take effect
Definition at line 1313 of file blast_options_cxx.cpp.
References eBlastOpt_RepeatFiltering, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetRepeatFiltering(), CBlastOptionsRemote::SetValue(), and val.
Referenced by BOOST_AUTO_TEST_CASE(), CBlastOptions::ClearFilterOptions(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetRepeatFiltering() [3/3]
Definition at line 926 of file blast_options_local_priv.hpp.
References QuerySetUpOptions::filtering_options, CBlastOptionsLocal::m_QueryOpts, SBlastFilterOptions::repeatFilterOptions, SRepeatFilterOptionsFree(), SRepeatFilterOptionsNew(), and val.
Referenced by CBlastOptions::SetRepeatFiltering().
◆ SetRepeatFilteringDB() [1/3]
|
inline |
Enable repeat filtering.
- Parameters
-
db repeat filtering database [in]
Definition at line 136 of file blast_nucl_options.hpp.
Referenced by BOOST_AUTO_TEST_CASE(), and BOOST_FIXTURE_TEST_CASE().
◆ SetRepeatFilteringDB() [2/3]
| void CBlastOptions::SetRepeatFilteringDB | ( | const char * | db | ) |
Sets the repeat filtering database to use.
- Note
- Either SetRepeatFiltering or SetRepeatFilteringDB should be called, if both are called, only the last one called will take effect
Definition at line 1332 of file blast_options_cxx.cpp.
References eBlastOpt_RepeatFilteringDB, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetRepeatFilteringDB(), and CBlastOptionsRemote::SetValue().
Referenced by BOOST_AUTO_TEST_CASE(), CFilteringArgs::ExtractAlgorithmOptions(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetRepeatFilteringDB() [3/3]
|
inline |
Definition at line 951 of file blast_options_local_priv.hpp.
References QuerySetUpOptions::filtering_options, CBlastOptionsLocal::m_QueryOpts, SBlastFilterOptions::repeatFilterOptions, and SRepeatFilterOptionsResetDB().
Referenced by CBlastOptions::SetRepeatFilteringDB().
◆ SetResultType() [1/2]
| void CBlastTracebackSearch::SetResultType | ( | EResultType | type | ) |
Specifies how the Seq-align-set returned as part of the results is formatted.
Definition at line 114 of file traceback_stage.cpp.
References CBlastTracebackSearch::m_ResultType, and type.
Referenced by CLocalBlast::Run(), and CPsiBlastImpl::Run().
◆ SetResultType() [2/2]
| void CPsiBlastImpl::SetResultType | ( | EResultType | type | ) |
Set the desired result type.
- Parameters
-
type of result requested [in]
Definition at line 184 of file psiblast_impl.cpp.
References CPsiBlastImpl::m_ResultType, and type.
Referenced by CPsiBl2Seq::Run().
◆ SetRID() [1/2]
Sets the RID for these results.
- Parameters
-
rid RID to set [in]
Definition at line 186 of file blast_results.hpp.
References CSearchResults::m_RID.
◆ SetRID() [2/2]
Sets the RID for these results.
- Parameters
-
rid RID to set [in]
Definition at line 616 of file blast_results.cpp.
References CSearchResultSet::m_Results, and NON_CONST_ITERATE.
Referenced by CRemoteBlast::GetResultSet().
◆ SetRNAToGenomeDefaults()
|
virtual |
Definition at line 70 of file magicblast_options.cpp.
References eMapper, CBlastOptionsHandle::m_Opts, CBlastOptions::SetDefaultsMode(), CMagicBlastOptionsHandle::SetEffectiveLengthsOptionsDefaults(), CMagicBlastOptionsHandle::SetGappedExtensionDefaults(), CMagicBlastOptionsHandle::SetHitSavingOptionsDefaults(), CMagicBlastOptionsHandle::SetInitialWordOptionsDefaults(), CMagicBlastOptionsHandle::SetLookupTableDefaults(), CBlastOptions::SetProgram(), CMagicBlastOptionsHandle::SetQueryOptionDefaults(), CMagicBlastOptionsHandle::SetScoringOptionsDefaults(), and CMagicBlastOptionsHandle::SetSubjectSequenceOptionsDefaults().
Referenced by CBlastOptionsFactory::CreateTask(), and CMagicBlastOptionsHandle::SetDefaults().
◆ SetRNAToRNADefaults()
|
virtual |
Definition at line 86 of file magicblast_options.cpp.
References eMapper, CBlastOptionsHandle::m_Opts, CBlastOptions::SetDefaultsMode(), CMagicBlastOptionsHandle::SetEffectiveLengthsOptionsDefaults(), CMagicBlastOptionsHandle::SetGapExtensionCost(), CMagicBlastOptionsHandle::SetGappedExtensionDefaults(), CMagicBlastOptionsHandle::SetHitSavingOptionsDefaults(), CMagicBlastOptionsHandle::SetInitialWordOptionsDefaults(), CMagicBlastOptionsHandle::SetLookupDbFilter(), CMagicBlastOptionsHandle::SetLookupTableDefaults(), CMagicBlastOptionsHandle::SetMismatchPenalty(), CBlastOptions::SetProgram(), CMagicBlastOptionsHandle::SetQueryOptionDefaults(), CMagicBlastOptionsHandle::SetScoringOptionsDefaults(), CMagicBlastOptionsHandle::SetSpliceAlignments(), CMagicBlastOptionsHandle::SetSubjectSequenceOptionsDefaults(), and CMagicBlastOptionsHandle::SetWordSize().
Referenced by CBlastOptionsFactory::CreateTask().
◆ SetScoringOptionsDefaults() [1/8]
|
protectedvirtual |
Overrides ScoringOptionsDefaults for nucleotide options.
Implements CBlastOptionsHandle.
Definition at line 198 of file blast_nucl_options.cpp.
References BLAST_GAP_EXTN_NUCL, BLAST_GAP_OPEN_NUCL, INT2_MAX, CBlastOptionsHandle::m_Opts, NULL, CBlastOptionsHandle::SetComplexityAdjMode(), CBlastOptions::SetFrameShiftPenalty(), CBlastNucleotideOptionsHandle::SetGapExtensionCost(), CBlastNucleotideOptionsHandle::SetGapOpeningCost(), CBlastOptionsHandle::SetGappedMode(), CBlastNucleotideOptionsHandle::SetMatchReward(), CBlastNucleotideOptionsHandle::SetMatrixName(), CBlastNucleotideOptionsHandle::SetMismatchPenalty(), and CBlastOptions::SetOutOfFrameMode().
Referenced by CDiscNucleotideOptionsHandle::SetMBScoringOptionsDefaults(), and CBlastNucleotideOptionsHandle::SetTraditionalBlastnDefaults().
◆ SetScoringOptionsDefaults() [2/8]
|
protectedvirtual |
Overrides ScoringOptionsDefaults for protein options.
Implements CBlastOptionsHandle.
Reimplemented in CTBlastxOptionsHandle, CTBlastnOptionsHandle, and CBlastxOptionsHandle.
Definition at line 119 of file blast_prot_options.cpp.
References BLAST_DEFAULT_MATRIX, BLAST_GAP_EXTN_PROT, BLAST_GAP_OPEN_PROT, INT2_MAX, CBlastOptionsHandle::m_Opts, CBlastOptions::SetFrameShiftPenalty(), CBlastProteinOptionsHandle::SetGapExtensionCost(), CBlastProteinOptionsHandle::SetGapOpeningCost(), CBlastOptionsHandle::SetGappedMode(), CBlastProteinOptionsHandle::SetMatrixName(), and CBlastOptions::SetOutOfFrameMode().
Referenced by CBlastxOptionsHandle::SetScoringOptionsDefaults(), CTBlastnOptionsHandle::SetScoringOptionsDefaults(), and CTBlastxOptionsHandle::SetScoringOptionsDefaults().
◆ SetScoringOptionsDefaults() [3/8]
|
protectedvirtual |
Overrides ScoringOptionsDefaults for RPS-BLAST options.
Implements CBlastOptionsHandle.
Definition at line 97 of file blast_rps_options.cpp.
References INT2_MAX, CBlastOptionsHandle::m_Opts, CBlastOptions::SetFrameShiftPenalty(), CBlastOptionsHandle::SetGappedMode(), and CBlastOptions::SetOutOfFrameMode().
◆ SetScoringOptionsDefaults() [4/8]
|
protectedvirtual |
Overrides ScoringOptionsDefaults for blastx options.
Reimplemented from CBlastProteinOptionsHandle.
Definition at line 80 of file blastx_options.cpp.
References CBlastProteinOptionsHandle::SetScoringOptionsDefaults().
◆ SetScoringOptionsDefaults() [5/8]
|
protectedvirtual |
Overrides ScoringOptionsDefaults for nucleotide options.
Implements CBlastOptionsHandle.
Definition at line 181 of file magicblast_options.cpp.
References BLAST_GAP_EXTN_MAPPER, BLAST_GAP_OPEN_MAPPER, BLAST_PENALTY_MAPPER, BLAST_REWARD_MAPPER, INT2_MAX, CBlastOptionsHandle::m_Opts, NULL, CBlastOptions::SetComplexityAdjMode(), CBlastOptions::SetFrameShiftPenalty(), CMagicBlastOptionsHandle::SetGapExtensionCost(), CMagicBlastOptionsHandle::SetGapOpeningCost(), CBlastOptions::SetGappedMode(), CBlastOptions::SetMatchReward(), CBlastOptions::SetMatrixName(), CMagicBlastOptionsHandle::SetMismatchPenalty(), and CBlastOptions::SetOutOfFrameMode().
Referenced by CMagicBlastOptionsHandle::SetGenomeToGenomeDefaults(), CMagicBlastOptionsHandle::SetRNAToGenomeDefaults(), and CMagicBlastOptionsHandle::SetRNAToRNADefaults().
◆ SetScoringOptionsDefaults() [6/8]
|
protectedvirtual |
Sets ScoringOptionsDefaults for tblastn options.
Reimplemented from CBlastProteinOptionsHandle.
Definition at line 61 of file tblastn_options.cpp.
References CBlastProteinOptionsHandle::SetScoringOptionsDefaults().
◆ SetScoringOptionsDefaults() [7/8]
|
protectedvirtual |
Overrides ScoringOptionsDefaults for tblastx options.
Reimplemented from CBlastProteinOptionsHandle.
Definition at line 70 of file tblastx_options.cpp.
References CBlastOptionsHandle::m_Opts, CBlastOptions::SetGappedMode(), and CBlastProteinOptionsHandle::SetScoringOptionsDefaults().
◆ SetScoringOptionsDefaults() [8/8]
|
protectedpure virtual |
Sets ScoringOptionsDefaults.
Implemented in CTBlastxOptionsHandle, CTBlastnOptionsHandle, CMagicBlastOptionsHandle, CBlastxOptionsHandle, CBlastRPSOptionsHandle, CBlastProteinOptionsHandle, and CBlastNucleotideOptionsHandle.
Referenced by CBlastOptionsHandle::SetDefaults().
◆ SetSegFiltering() [1/4]
|
inline |
Enable SEG filtering.
- Parameters
-
val enable SEG filtering [in]
Definition at line 89 of file blast_prot_options.hpp.
References val.
Referenced by CDUpdater::blast(), CdBlaster::blast(), BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), CSimpleB2SWrapper::InitializeToDefaults(), CdBlaster::psiBlast(), CBlastAdvancedProteinOptionsHandle::SetQueryOptionDefaults(), CBlastProteinOptionsHandle::SetQueryOptionDefaults(), and CBlastxOptionsHandle::SetQueryOptionDefaults().
◆ SetSegFiltering() [2/4]
|
inline |
Enable SEG filtering.
- Parameters
-
val enable SEG filtering [in]
Definition at line 82 of file blast_rps_options.hpp.
References val.
Referenced by CBlastRPSOptionsHandle::SetQueryOptionDefaults().
◆ SetSegFiltering() [3/4]
Definition at line 1237 of file blast_options_cxx.cpp.
References eBlastOpt_SegFiltering, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetSegFiltering(), CBlastOptionsRemote::SetValue(), and val.
Referenced by BOOST_AUTO_TEST_CASE(), CBlastOptions::ClearFilterOptions(), CFilteringArgs::ExtractAlgorithmOptions(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetSegFiltering() [4/4]
Definition at line 841 of file blast_options_local_priv.hpp.
References QuerySetUpOptions::filtering_options, CBlastOptionsLocal::m_QueryOpts, SBlastFilterOptions::segOptions, SSegOptionsFree(), SSegOptionsNew(), and val.
Referenced by CBlastOptions::SetSegFiltering().
◆ SetSegFilteringHicut() [1/4]
|
inline |
Set hicut parameter for seg.
Acceptable values are greater than Locut (see SetSegFilteringLocut).
- Parameters
-
hicut seg filtering parameter hicut [in]
Definition at line 108 of file blast_prot_options.hpp.
Referenced by BOOST_FIXTURE_TEST_CASE().
◆ SetSegFilteringHicut() [2/4]
|
inline |
Set hicut parameter for seg.
Acceptable values are greater than Locut
- Parameters
-
hicut seg filtering parameter hicut [in]
Definition at line 100 of file blast_rps_options.hpp.
◆ SetSegFilteringHicut() [3/4]
| void CBlastOptions::SetSegFilteringHicut | ( | double | m | ) |
Definition at line 1294 of file blast_options_cxx.cpp.
References eBlastOpt_SegFilteringHicut, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetSegFilteringHicut(), and CBlastOptionsRemote::SetValue().
Referenced by CFilteringArgs::ExtractAlgorithmOptions(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetSegFilteringHicut() [4/4]
|
inline |
Definition at line 906 of file blast_options_local_priv.hpp.
References QuerySetUpOptions::filtering_options, SSegOptions::hicut, CBlastOptionsLocal::m_QueryOpts, NULL, SBlastFilterOptions::segOptions, and SSegOptionsNew().
Referenced by CBlastOptions::SetSegFilteringHicut().
◆ SetSegFilteringLocut() [1/4]
|
inline |
Set locut parameter for seg.
Acceptable values are greater than 0.
- Parameters
-
locut seg filtering parameter locut [in]
Definition at line 101 of file blast_prot_options.hpp.
Referenced by BOOST_FIXTURE_TEST_CASE().
◆ SetSegFilteringLocut() [2/4]
|
inline |
Set locut parameter for seg.
Acceptable values are greater than 0.
- Parameters
-
locut seg filtering parameter locut [in]
Definition at line 94 of file blast_rps_options.hpp.
◆ SetSegFilteringLocut() [3/4]
| void CBlastOptions::SetSegFilteringLocut | ( | double | m | ) |
Definition at line 1275 of file blast_options_cxx.cpp.
References eBlastOpt_SegFilteringLocut, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetSegFilteringLocut(), and CBlastOptionsRemote::SetValue().
Referenced by CFilteringArgs::ExtractAlgorithmOptions(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetSegFilteringLocut() [4/4]
|
inline |
Definition at line 886 of file blast_options_local_priv.hpp.
References QuerySetUpOptions::filtering_options, SSegOptions::locut, CBlastOptionsLocal::m_QueryOpts, NULL, SBlastFilterOptions::segOptions, and SSegOptionsNew().
Referenced by CBlastOptions::SetSegFilteringLocut().
◆ SetSegFilteringWindow() [1/4]
| void CBlastOptions::SetSegFilteringWindow | ( | int | m | ) |
Definition at line 1256 of file blast_options_cxx.cpp.
References eBlastOpt_SegFilteringWindow, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetSegFilteringWindow(), and CBlastOptionsRemote::SetValue().
Referenced by CFilteringArgs::ExtractAlgorithmOptions(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetSegFilteringWindow() [2/4]
|
inline |
Definition at line 866 of file blast_options_local_priv.hpp.
References QuerySetUpOptions::filtering_options, CBlastOptionsLocal::m_QueryOpts, NULL, SBlastFilterOptions::segOptions, SSegOptionsNew(), and SSegOptions::window.
Referenced by CBlastOptions::SetSegFilteringWindow().
◆ SetSegFilteringWindow() [3/4]
|
inline |
Set window parameter for seg.
Acceptable value are > 0.
- Parameters
-
window seg filtering parameter window [in]
Definition at line 95 of file blast_prot_options.hpp.
Referenced by BOOST_FIXTURE_TEST_CASE().
◆ SetSegFilteringWindow() [4/4]
|
inline |
Set window parameter for seg.
Acceptable value are > 0.
- Parameters
-
window seg filtering parameter window [in]
Definition at line 88 of file blast_rps_options.hpp.
◆ SetSeqAlign() [1/3]
|
inline |
Only intended to be used if you need to edit the seqlign.
Otherwise use GetSeqAlign()
Definition at line 200 of file blast_results.hpp.
References CSearchResults::m_Alignment.
Referenced by CIgBlast::x_ProcessDGeneResult().
◆ SetSeqAlign() [2/3]
|
inline |
Definition at line 214 of file igblast.hpp.
References CSearchResults::m_Alignment.
Referenced by CIgBlast::s_AppendResults().
◆ SetSeqAlign() [3/3]
|
inline |
Get non-const alignments.
Definition at line 177 of file magicblast.hpp.
References CMagicBlastResults::m_Aligns.
◆ SetSeqDb()
Mutator for the seqdb.
- Parameters
-
seqdb reference to an initialized db [in]
Definition at line 235 of file uniform_search.cpp.
References CSearchDatabase::m_DbInitialized, CSearchDatabase::m_SeqDb, and CRef< C, Locker >::Reset().
◆ SetSmithWatermanMode() [1/4]
Sets this mode, specifying that smith waterman rather than the normal blast heuristic should be used for final extensions.
- Parameters
-
m use smith-waterman if true [in]
Definition at line 89 of file blast_advprot_options.hpp.
Referenced by BOOST_FIXTURE_TEST_CASE().
◆ SetSmithWatermanMode() [2/4]
Sets this mode, specifying that smith waterman rather than the normal blast heuristic should be used for final extensions.
- Parameters
-
m use smith-waterman if true [in]
Definition at line 123 of file blastx_options.hpp.
◆ SetSmithWatermanMode() [3/4]
Definition at line 1674 of file blast_options_cxx.cpp.
References eBlastOpt_SmithWatermanMode, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetSmithWatermanMode(), and CBlastOptionsRemote::SetValue().
Referenced by s_SetCompositionBasedStats(), CBlastAdvancedProteinOptionsHandle::SetGappedExtensionDefaults(), CBlastxOptionsHandle::SetGappedExtensionDefaults(), CTBlastnOptionsHandle::SetGappedExtensionDefaults(), CPSIBlastOptionsHandle::SetPSITblastnDefaults(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetSmithWatermanMode() [4/4]
Definition at line 1211 of file blast_options_local_priv.hpp.
References eDynProgTbck, eSmithWatermanTbck, BlastExtensionOptions::eTbackExt, and CBlastOptionsLocal::m_ExtnOpts.
Referenced by CBlastOptions::SetSmithWatermanMode().
◆ SetSplice()
|
inline |
Definition at line 1600 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_HitSaveOpts, and BlastHitSavingOptions::splice.
Referenced by CBlastOptions::SetSpliceAlignments().
◆ SetSpliceAlignments() [1/2]
| void CBlastOptions::SetSpliceAlignments | ( | bool | s | ) |
Definition at line 2185 of file blast_options_cxx.cpp.
References CBlastOptions::m_Local, CBlastOptionsLocal::SetSplice(), and CBlastOptions::x_Throwx().
Referenced by CMappingArgs::ExtractAlgorithmOptions().
◆ SetSpliceAlignments() [2/2]
|
inline |
Set splicing alignments.
- Parameters
-
s if true alignments will be spliced [in]
Definition at line 211 of file magicblast_options.hpp.
Referenced by CMagicBlastOptionsHandle::SetGappedExtensionDefaults(), CMagicBlastOptionsHandle::SetGenomeToGenomeDefaults(), and CMagicBlastOptionsHandle::SetRNAToRNADefaults().
◆ SetStrandOption() [1/5]
| void CBlastOptions::SetStrandOption | ( | objects::ENa_strand | s | ) |
Definition at line 1459 of file blast_options_cxx.cpp.
References eBlastOpt_StrandOption, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetStrandOption(), and CBlastOptionsRemote::SetValue().
Referenced by CSplitQueryTestFixture::QuerySplitter_BlastnMultiQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastnSingleQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastxMultiQueryMultiChunk(), CBlastProteinOptionsHandle::SetQueryOptionDefaults(), CBlastRPSOptionsHandle::SetQueryOptionDefaults(), CBlastxOptionsHandle::SetQueryOptionDefaults(), CMagicBlastOptionsHandle::SetQueryOptionDefaults(), CTBlastxOptionsHandle::SetQueryOptionDefaults(), LinkHspTestFixture::setupCutoffScores(), LinkHspTestFixture::setupLinkHspInputTblastn(), CBlastOptionsBuilder::x_ProcessOneOption(), and CSplitQueryTestFixture::x_TestCContextTranslator().
◆ SetStrandOption() [2/5]
|
inline |
Definition at line 1007 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_QueryOpts, and QuerySetUpOptions::strand_option.
Referenced by CBlastOptions::SetStrandOption().
◆ SetStrandOption() [3/5]
|
inline |
Sets StrandOption.
- Parameters
-
strand StrandOption [in]
Definition at line 98 of file blast_nucl_options.hpp.
Referenced by CBlastNucleotideOptionsHandle::SetQueryOptionDefaults().
◆ SetStrandOption() [4/5]
|
inline |
Sets StrandOption.
- Parameters
-
strand StrandOption [in]
Definition at line 69 of file blastx_options.hpp.
◆ SetStrandOption() [5/5]
|
inline |
Sets StrandOption.
- Parameters
-
strand StrandOption [in]
Definition at line 71 of file tblastx_options.hpp.
◆ SetSubject() [1/6]
|
virtual |
Set the databases to search.
Implements ISearch.
Definition at line 121 of file local_search.cpp.
References CLocalSeqSearch::m_Database, and subject.
◆ SetSubject() [2/6]
|
virtual |
Set the databases to search.
Implements ISearch.
Definition at line 143 of file local_search.cpp.
References CLocalPssmSearch::m_Subject, and subject.
◆ SetSubject() [3/6]
|
virtual |
Set the databases to search.
Implements ISearch.
Definition at line 164 of file remote_search.cpp.
References CRemoteSeqSearch::m_Subject, and subject.
◆ SetSubject() [4/6]
|
virtual |
Set the databases to search.
Implements ISearch.
Definition at line 296 of file remote_search.cpp.
References CRemotePssmSearch::m_Subject, and subject.
◆ SetSubject() [5/6]
|
pure virtual |
Set the subject database(s) to search.
Implemented in CRemotePssmSearch, CRemoteSeqSearch, CLocalPssmSearch, and CLocalSeqSearch.
◆ SetSubject() [6/6]
Set the subject sequence.
Definition at line 250 of file bl2seq.hpp.
References CBl2Seq::m_tSubjects, subject, and CBl2Seq::x_ResetInternalDs().
Referenced by BOOST_AUTO_TEST_CASE().
◆ SetSubjectBestHit() [1/2]
| void CBlastOptions::SetSubjectBestHit | ( | ) |
Definition at line 1856 of file blast_options_cxx.cpp.
References eBlastOpt_SubjectBestHit, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetSubjectBestHit(), and CBlastOptionsRemote::SetValue().
Referenced by CHspFilteringArgs::ExtractAlgorithmOptions(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetSubjectBestHit() [2/2]
|
inline |
Definition at line 1404 of file blast_options_local_priv.hpp.
References _ASSERT, Blast_ProgramIsNucleotide(), BlastHSPFilteringOptions_AddSubjectBestHit(), BlastHSPFilteringOptionsNew(), BlastHSPSubjectBestHitOptionsNew(), EProgramToEBlastProgramType(), BlastHitSavingOptions::hsp_filt_opt, CBlastOptionsLocal::m_HitSaveOpts, CBlastOptionsLocal::m_Program, NULL, and BlastHSPFilteringOptions::subject_besthit_opts.
Referenced by CBlastOptions::SetSubjectBestHit().
◆ SetSubjectMasks()
| void CSearchResults::SetSubjectMasks | ( | const TSeqLocInfoVector & | subj_masks | ) |
Set the masked locations for the subject sequences in the contained alignment.
- Parameters
-
subj_masks masked locations [in]
Definition at line 341 of file blast_results.cpp.
References copy(), and CSearchResults::m_SubjectMasks.
◆ SetSubjects()
|
inline |
Set a vector of subject sequences.
Definition at line 264 of file bl2seq.hpp.
References CBl2Seq::m_tSubjects, and CBl2Seq::x_ResetInternalDs().
◆ SetSubjectSequenceOptionsDefaults() [1/7]
|
protectedvirtual |
Overrides SubjectSequenceOptionsDefaults for nucleotide options.
Implements CBlastOptionsHandle.
Definition at line 281 of file blast_nucl_options.cpp.
◆ SetSubjectSequenceOptionsDefaults() [2/7]
|
protectedvirtual |
Overrides SubjectSequenceOptionsDefaults for protein options.
Implements CBlastOptionsHandle.
Reimplemented in CTBlastxOptionsHandle, and CTBlastnOptionsHandle.
Definition at line 159 of file blast_prot_options.cpp.
◆ SetSubjectSequenceOptionsDefaults() [3/7]
|
protectedvirtual |
Overrides SubjectSequenceOptionsDefaults for RPS-BLAST options.
Implements CBlastOptionsHandle.
Definition at line 133 of file blast_rps_options.cpp.
◆ SetSubjectSequenceOptionsDefaults() [4/7]
|
protectedvirtual |
Overrides SubjectSequenceOptionsDefaults for nucleotide options.
Implements CBlastOptionsHandle.
Definition at line 228 of file magicblast_options.cpp.
Referenced by CMagicBlastOptionsHandle::SetGenomeToGenomeDefaults(), CMagicBlastOptionsHandle::SetRNAToGenomeDefaults(), and CMagicBlastOptionsHandle::SetRNAToRNADefaults().
◆ SetSubjectSequenceOptionsDefaults() [5/7]
|
protectedvirtual |
Sets SubjectSequenceOptionsDefaults for tblastn options.
Reimplemented from CBlastProteinOptionsHandle.
Definition at line 82 of file tblastn_options.cpp.
References BLAST_GENETIC_CODE, and CTBlastnOptionsHandle::SetDbGeneticCode().
◆ SetSubjectSequenceOptionsDefaults() [6/7]
|
protectedvirtual |
Overrides SubjectSequenceOptionsDefaults for tblastx options.
Reimplemented from CBlastProteinOptionsHandle.
Definition at line 92 of file tblastx_options.cpp.
References BLAST_GENETIC_CODE, CBlastOptionsHandle::m_Opts, and CBlastOptions::SetDbGeneticCode().
◆ SetSubjectSequenceOptionsDefaults() [7/7]
|
protectedpure virtual |
Sets SubjectSequenceOptionsDefaults.
Implemented in CTBlastxOptionsHandle, CTBlastnOptionsHandle, CMagicBlastOptionsHandle, CBlastRPSOptionsHandle, CBlastProteinOptionsHandle, and CBlastNucleotideOptionsHandle.
Referenced by CBlastOptionsHandle::SetDefaults().
◆ SetSubjectSequences() [1/2]
Set a list of subject sequences to search against.
Definition at line 1588 of file remote_blast.cpp.
References CRemoteBlast::eSubject, CRemoteBlast::m_NeedConfig, CRemoteBlast::m_QSR, CBlast4_subject_Base::SetSequences(), and CRemoteBlast::x_SetSubjectSequences().
◆ SetSubjectSequences() [2/2]
| void CRemoteBlast::SetSubjectSequences | ( | CRef< IQueryFactory > | subj | ) |
Set a list of subject sequences to search against.
Definition at line 1570 of file remote_blast.cpp.
References CRef< C, Locker >::Empty(), FlattenBioseqSet(), IRemoteQueryData::GetBioseqSet(), IQueryFactory::MakeRemoteQueryData(), and NCBI_THROW.
Referenced by CRemoteBlast::CRemoteBlast().
◆ SetSumStatisticsMode() [1/2]
Definition at line 2044 of file blast_options_cxx.cpp.
References eBlastOpt_SumStatisticsMode, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetSumStatisticsMode(), and CBlastOptionsRemote::SetValue().
Referenced by CGenericSearchArgs::ExtractAlgorithmOptions(), CBlastRPSOptionsHandle::SetHitSavingOptionsDefaults(), CBlastxOptionsHandle::SetHitSavingOptionsDefaults(), CTBlastnOptionsHandle::SetHitSavingOptionsDefaults(), CTBlastxOptionsHandle::SetHitSavingOptionsDefaults(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetSumStatisticsMode() [2/2]
Definition at line 1526 of file blast_options_local_priv.hpp.
References BlastHitSavingOptions::do_sum_stats, and CBlastOptionsLocal::m_HitSaveOpts.
Referenced by CBlastOptions::SetSumStatisticsMode().
◆ SetTemplateLength()
|
inline |
Sets TemplateLength.
- Parameters
-
length TemplateLength [in]
Definition at line 69 of file disc_nucl_options.hpp.
Referenced by BOOST_FIXTURE_TEST_CASE(), and CDiscNucleotideOptionsHandle::SetMBLookupTableDefaults().
◆ SetTemplateType()
|
inline |
Sets TemplateType.
- Parameters
-
type TemplateType [in]
Definition at line 80 of file disc_nucl_options.hpp.
Referenced by BOOST_FIXTURE_TEST_CASE(), and CDiscNucleotideOptionsHandle::SetMBLookupTableDefaults().
◆ SetThresh()
|
inline |
Sets Threshold for Jaccard distance.
- Parameters
-
thresh Jaccard threshold [in]
Definition at line 69 of file blastp_kmer_options.hpp.
Referenced by CBlastKmerThread::Main(), and CBlastKmerApplication::Run().
◆ SetTraditionalBlastnDefaults() [1/2]
| void CBlastNucleotideOptionsHandle::SetTraditionalBlastnDefaults | ( | ) |
Sets TraditionalBlastnDefaults.
Definition at line 70 of file blast_nucl_options.cpp.
References eBlastn, CBlastOptions::eRemote, CBlastOptions::GetLocality(), CBlastOptionsHandle::m_Opts, CBlastOptions::SetDefaultsMode(), CBlastNucleotideOptionsHandle::SetEffectiveLengthsOptionsDefaults(), CBlastNucleotideOptionsHandle::SetGappedExtensionDefaults(), CBlastNucleotideOptionsHandle::SetHitSavingOptionsDefaults(), CBlastNucleotideOptionsHandle::SetInitialWordOptionsDefaults(), CBlastNucleotideOptionsHandle::SetLookupTableDefaults(), CBlastOptions::SetProgram(), CBlastNucleotideOptionsHandle::SetQueryOptionDefaults(), CBlastOptions::SetRemoteProgramAndService_Blast3(), and CBlastNucleotideOptionsHandle::SetScoringOptionsDefaults().
Referenced by BOOST_AUTO_TEST_CASE(), CBlastOptionsFactory::Create(), and s_CreateRepeatsSearchOptions().
◆ SetTraditionalBlastnDefaults() [2/2]
| void CDiscNucleotideOptionsHandle::SetTraditionalBlastnDefaults | ( | ) |
NOTE: Unavailable for discontiguous megablast.
- Exceptions
-
CBlastException if this is called on an object configured for discontiguous megablast
Definition at line 93 of file disc_nucl_options.cpp.
References NCBI_THROW.
Referenced by BOOST_AUTO_TEST_CASE().
◆ SetTraditionalMegablastDefaults()
| void CBlastNucleotideOptionsHandle::SetTraditionalMegablastDefaults | ( | ) |
Sets TraditionalMegablastDefaults.
Definition at line 115 of file blast_nucl_options.cpp.
References eMegablast, CBlastOptions::eRemote, CBlastOptions::GetLocality(), CBlastOptionsHandle::m_Opts, CBlastOptions::SetDefaultsMode(), CBlastNucleotideOptionsHandle::SetEffectiveLengthsOptionsDefaults(), CBlastNucleotideOptionsHandle::SetMBGappedExtensionDefaults(), CBlastNucleotideOptionsHandle::SetMBHitSavingOptionsDefaults(), CBlastNucleotideOptionsHandle::SetMBInitialWordOptionsDefaults(), CBlastNucleotideOptionsHandle::SetMBLookupTableDefaults(), CBlastNucleotideOptionsHandle::SetMBScoringOptionsDefaults(), CBlastOptions::SetProgram(), CBlastNucleotideOptionsHandle::SetQueryOptionDefaults(), and CBlastOptions::SetRemoteProgramAndService_Blast3().
Referenced by BOOST_AUTO_TEST_CASE(), CBlastOptionsFactory::Create(), and CBlastNucleotideOptionsHandle::SetDefaults().
◆ SetUngappedStatisticalParams()
| void CPssmEngine::SetUngappedStatisticalParams | ( | CConstRef< CBlastAncillaryData > | ancillary_data | ) |
Sets the Karlin & Altschul parameters in the BlastScoreBlk to be used in PSSM generation.
This should be used when performing PSI-BLAST iterations, but it's not necessary for a single PSSM construction
- Parameters
-
ancillary_data BLAST ancillary data from a previous iteration
Definition at line 483 of file pssm_engine.cpp.
References _ASSERT, CBlastScoreBlk::Get(), CBlastAncillaryData::GetPsiGappedKarlinBlk(), CBlastAncillaryData::GetPsiUngappedKarlinBlk(), Blast_KarlinBlk::H, Blast_KarlinBlk::K, BlastScoreBlk::kbp_gap_psi, BlastScoreBlk::kbp_psi, Blast_KarlinBlk::Lambda, log, Blast_KarlinBlk::logK, CPssmEngine::m_ScoreBlk, CConstRef< C, Locker >::NotEmpty(), and NULL.
Referenced by PsiBlastComputePssmFromAlignment().
◆ SetUnifiedP() [1/2]
| void CBlastOptions::SetUnifiedP | ( | int | u = 0 | ) |
Definition at line 1695 of file blast_options_cxx.cpp.
References eBlastOpt_UnifiedP, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetUnifiedP(), and CBlastOptionsRemote::SetValue().
Referenced by BOOST_AUTO_TEST_CASE(), s_SetCompositionBasedStats(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetUnifiedP() [2/2]
|
inline |
Definition at line 1226 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_ExtnOpts, and BlastExtensionOptions::unifiedP.
Referenced by CBlastOptions::SetUnifiedP().
◆ SetUpDbIndexCallbacks()
| void SetUpDbIndexCallbacks | ( | void | ) |
Definition at line 1174 of file blast_dbindex.cpp.
References IndexedDbRunSearch(), IndexedDbSetNumThreads(), IndexedDbSetQueryInfo(), IndexedDbSetUsingThreads(), RunSearchFn, SetNumThreadsFn, SetQueryInfoFn, and SetUsingThreadsFn.
Referenced by BlastSetupPreliminarySearchEx().
◆ SetupQueries()
| void SetupQueries | ( | TSeqLocVector & | queries, |
| BlastQueryInfo * | qinfo, | ||
| BLAST_SequenceBlk ** | seqblk, | ||
| EBlastProgramType | prog, | ||
| objects::ENa_strand | strand_opt, | ||
| TSearchMessages & | messages | ||
| ) |
Populates BLAST_SequenceBlk with sequence data for use in CORE BLAST.
- Parameters
-
queries vector of blast::SSeqLoc structures [in] qinfo BlastQueryInfo structure to obtain context information [in] seqblk Structure to save sequence data, allocated in this function [out] messages object to save warnings/errors for all queries [out] prog program type from the CORE's point of view [in] strand_opt Unless the strand option is set to single strand, the actual CSeq_locs in the TSeqLocVector dictate which strand to use during the search [in]
Definition at line 401 of file blast_objmgr_tools.cpp.
References prog, and SetupQueries_OMF().
Referenced by BOOST_AUTO_TEST_CASE(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), LinkHspTestFixture::setupCutoffScores(), LinkHspTestFixture::setupLinkHspInputTblastn(), setupQueryStructures(), and CSplitQueryTestFixture::x_PrepareBlastQueryStructures().
◆ SetupQueries_OMF()
| void SetupQueries_OMF | ( | IBlastQuerySource & | queries, |
| BlastQueryInfo * | qinfo, | ||
| BLAST_SequenceBlk ** | seqblk, | ||
| EBlastProgramType | prog, | ||
| objects::ENa_strand | strand_opt, | ||
| TSearchMessages & | messages | ||
| ) |
ObjMgr Free version of SetupQueries.
- Parameters
-
queries vector of blast::SSeqLoc structures [in] qinfo BlastQueryInfo structure to obtain context information [in] seqblk Structure to save sequence data, allocated in this function [out] messages object to save warnings/errors for all queries [out] prog program type from the CORE's point of view [in] strand_opt Unless the strand option is set to single strand, the actual CSeq_locs in the TSeqLocVector dictacte which strand to use during the search [in]
Definition at line 485 of file blast_setup_cxx.cpp.
References _ASSERT, BLAST_GetTranslation(), Blast_QueryIsTranslated(), BlastMaskLocNew(), BlastQueryInfoGetQueryLength(), BlastSeqBlkNew(), BlastSeqBlkSetSequence(), BlastSetup_Validate(), buf, calloc(), BlastQueryInfo::contexts, SBlastSequence::data, eBlastSevWarning, eBlastTypeBlastn, eBlastTypeMapping, IBlastQuerySource::Empty(), eNa_strand_both, eNa_strand_minus, eNa_strand_plus, eNa_strand_unknown, eSentinels, FindGeneticCode(), BlastContextInfo::frame, GenCodeSingletonAdd(), GenCodeSingletonFind(), AutoPtr< X, Del >::get(), IBlastQuerySource::GetBlastSequence(), IBlastQuerySource::GetGeneticCodeId(), IBlastQuerySource::GetLength(), CException::GetMsg(), GetNumberOfContexts(), GetQueryEncoding(), IBlastQuerySource::GetSeqId(), IBlastQuerySource::GetStrand(), IBlastQuerySource::GetTitle(), TSearchMessages::HasMessages(), i, kEmptyStr, kTitle, SBlastSequence::length, mask, NCBI_THROW, NULL, BlastQueryInfo::num_queries, offset, prog, BlastContextInfo::query_length, BlastContextInfo::query_offset, QueryInfo_GetSeqBufLen(), s_AddMask(), s_BlastSetup_GetStrand(), s_GetRestrictedBlastSeqLocs(), s_InvalidateQueryContexts(), IBlastQuerySource::Size(), TSearchMessages::ToString(), TRUE, and true.
Referenced by SafeSetupQueries(), and SetupQueries().
◆ SetupQueryInfo() [1/2]
| void SetupQueryInfo | ( | const CBlastQueryVector & | queries, |
| EBlastProgramType | prog, | ||
| objects::ENa_strand | strand_opt, | ||
| BlastQueryInfo ** | qinfo | ||
| ) |
Allocates the query information structure and fills the context offsets, in case of multiple queries, frames or strands.
If query seqids cannot be resolved, they will be ignored as warnings will be issued in blast::SetupQueries. This version takes a CBlastQueryVector. NB: effective length will be assigned inside the engine.
- Parameters
-
queries Vector of query locations [in] prog program type from the CORE's point of view [in] strand_opt Unless the strand option is set to single strand, the actual CSeq_locs in the CBlastQueryVector dictate which strand to use during the search [in] qinfo Allocated query info structure [out]
◆ SetupQueryInfo() [2/2]
| void SetupQueryInfo | ( | TSeqLocVector & | queries, |
| EBlastProgramType | prog, | ||
| objects::ENa_strand | strand_opt, | ||
| BlastQueryInfo ** | qinfo | ||
| ) |
Allocates the query information structure and fills the context offsets, in case of multiple queries, frames or strands.
If query seqids cannot be resolved, they will be ignored as warnings will be issued in blast::SetupQueries. This version takes a TSeqLocVector. NB: effective length will be assigned inside the engine.
- Parameters
-
queries Vector of query locations [in] prog program type from the CORE's point of view [in] strand_opt Unless the strand option is set to single strand, the actual CSeq_locs in the TSeqLocVector dictate which strand to use during the search [in] qinfo Allocated query info structure [out]
Definition at line 392 of file blast_objmgr_tools.cpp.
References prog, and SetupQueryInfo_OMF().
Referenced by BOOST_AUTO_TEST_CASE(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), LinkHspTestFixture::setupCutoffScores(), LinkHspTestFixture::setupLinkHspInputTblastn(), setupQueryInfoForOffsetTranslation(), setupQueryStructures(), and CSplitQueryTestFixture::x_PrepareBlastQueryStructures().
◆ SetupQueryInfo_OMF()
| void SetupQueryInfo_OMF | ( | const IBlastQuerySource & | queries, |
| EBlastProgramType | prog, | ||
| objects::ENa_strand | strand_opt, | ||
| BlastQueryInfo ** | qinfo | ||
| ) |
ObjMgr Free version of SetupQueryInfo.
NB: effective length will be assigned inside the engine.
- Parameters
-
queries Vector of query locations [in] prog program type from the CORE's point of view [in] strand_opt Unless the strand option is set to single strand, the actual CSeq_locs in the TSeqLocVector dictacte which strand to use during the search [in] qinfo Allocated query info structure [out]
Definition at line 153 of file blast_setup_cxx.cpp.
References _ASSERT, abort(), BLAST_GetTranslatedProteinLength(), Blast_ProgramIsMapping(), Blast_QueryIsTranslated(), BlastQueryInfoNew(), BlastQueryInfo::contexts, eBlastTypeBlastn, eBlastTypeMapping, eNa_strand_both, eNa_strand_minus, eNa_strand_plus, eNa_strand_unknown, CBlastQueryInfo::Get(), IBlastQuerySource::GetLength(), GetNumberOfContexts(), IBlastQuerySource::GetSegmentInfo(), IBlastQuerySource::GetStrand(), i, INT4_MAX, MAX, BlastQueryInfo::max_length, MIN, BlastQueryInfo::min_length, NCBI_THROW, NULL, prog, CBlastQueryInfo::Release(), s_AdjustFirstContext(), s_BlastSetup_GetStrand(), s_QueryInfo_SetContext(), BlastContextInfo::segment_flags, IBlastQuerySource::Size(), and true.
Referenced by SafeSetupQueryInfo(), and SetupQueryInfo().
◆ SetupSubjects()
| void SetupSubjects | ( | TSeqLocVector & | subjects, |
| EBlastProgramType | program, | ||
| vector< BLAST_SequenceBlk * > * | seqblk_vec, | ||
| unsigned int * | max_subjlen | ||
| ) |
Sets up internal subject data structure for the BLAST search.
This uses the TSeqLocVector to create subject data structures.
- Parameters
-
subjects Vector of subject locations [in] program BLAST program [in] seqblk_vec Vector of subject sequence data structures [out] max_subjlen Maximal length of the subject sequences [out]
Definition at line 414 of file blast_objmgr_tools.cpp.
References prog, and SetupSubjects_OMF().
Referenced by BOOST_AUTO_TEST_CASE(), CMultiSeqInfo::CMultiSeqInfo(), and CQueryFactoryInfo::CQueryFactoryInfo().
◆ SetupSubjects_OMF()
| void SetupSubjects_OMF | ( | IBlastQuerySource & | subjects, |
| EBlastProgramType | program, | ||
| vector< BLAST_SequenceBlk * > * | seqblk_vec, | ||
| unsigned int * | max_subjlen | ||
| ) |
Object manager free version of SetupSubjects.
- Parameters
-
subjects Vector of subject locations [in] program BLAST program [in] seqblk_vec Vector of subject sequence data structures [out] max_subjlen Maximal length of the subject sequences [out]
Definition at line 733 of file blast_setup_cxx.cpp.
References _ASSERT, Blast_SubjectIsNucleotide(), Blast_SubjectIsTranslated(), BlastSeqBlkNew(), BlastSeqBlkSetCompressedSequence(), BlastSeqBlkSetSeqRanges(), BlastSeqBlkSetSequence(), BlastSequenceBlkFree(), SBlastSequence::data, eBlastEncodingNcbi2na, eBlastTypePsiTblastn, eBlastTypeTblastn, eBlastTypeTblastx, CBlastException::eInvalidArgument, CSeqDB::TSequenceRanges::empty(), IBlastQuerySource::Empty(), eNa_strand_plus, eNoSentinels, ERR_POST, eSentinels, eSoftSubjMasking, FALSE, FindGeneticCode(), BLAST_SequenceBlk::gen_code_string, GenCodeSingletonAdd(), GenCodeSingletonFind(), AutoPtr< X, Del >::get(), CSeqDB::TSequenceRanges::get_data(), IBlastQuerySource::GetBlastSequence(), CException::GetErrCode(), IBlastQuerySource::GetGeneticCodeId(), IBlastQuerySource::GetLength(), IBlastQuerySource::GetMask(), CException::GetMsg(), IBlastQuerySource::GetSeqId(), IBlastQuerySource::GetSeqLoc(), GetSubjectEncoding(), IBlastQuerySource::GetTitle(), i, kEmptyStr, BLAST_SequenceBlk::lcase_mask, BLAST_SequenceBlk::lcase_mask_allocated, BLAST_SequenceBlk::length, SBlastSequence::length, MAX, NCBI_RETHROW_SAME, NCBI_THROW, CConstRef< C, Locker >::NotEmpty(), NULL, BLAST_SequenceBlk::num_seq_ranges, prog, compile_time_bits::range(), AutoPtr< X, Del >::release(), s_SeqLoc2MaskedSubjRanges(), CSeqDB::TSequenceRanges::size(), IBlastQuerySource::Size(), true, and Warning().
Referenced by CQueryFactoryInfo::CQueryFactoryInfo(), and SetupSubjects().
◆ SetUseIndex() [1/2]
| void CBlastOptions::SetUseIndex | ( | bool | use_index = true, |
| const string & | index_name = "", |
||
| bool | force_index = false, |
||
| bool | old_style_index = false |
||
| ) |
Definition at line 2619 of file blast_options_cxx.cpp.
References eBlastOpt_ForceMbIndex, eBlastOpt_MbIndexName, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsLocal::SetUseIndex(), and CBlastOptionsRemote::SetValue().
Referenced by CMbIndexArgs::ExtractAlgorithmOptions(), CSetupFactory::InitializeMegablastDbIndex(), and CBlastOptionsBuilder::x_ApplyInteractions().
◆ SetUseIndex() [2/2]
|
inline |
Definition at line 1859 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_ForceMBIndex, CBlastOptionsLocal::m_MBIndexName, CBlastOptionsLocal::m_OldStyleMBIndex, and CBlastOptionsLocal::m_UseMBIndex.
Referenced by CBlastOptions::SetUseIndex().
◆ SetValue() [1/12]
| void CBlastOptionsRemote::SetValue | ( | EBlastOptIdx | opt, |
| const bool & | x | ||
| ) |
Definition at line 699 of file blast_options_cxx.cpp.
References eBlastOpt_ComplexityAdjMode, eBlastOpt_DustFiltering, eBlastOpt_ForceMbIndex, eBlastOpt_GappedMode, eBlastOpt_IgnoreMsaMaster, eBlastOpt_MaskAtHash, eBlastOpt_OutOfFrameMode, eBlastOpt_RepeatFiltering, eBlastOpt_SegFiltering, eBlastOpt_SmithWatermanMode, eBlastOpt_SubjectBestHit, eBlastOpt_SumStatisticsMode, CBlast4Field::Get(), CBlastOptionsRemote::m_DefaultsMode, CBlastOptionsRemote::x_SetParam(), and CBlastOptionsRemote::x_Throwx().
◆ SetValue() [2/12]
| void CBlastOptionsRemote::SetValue | ( | EBlastOptIdx | opt, |
| const char * | x | ||
| ) |
Definition at line 628 of file blast_options_cxx.cpp.
References eBlastOpt_FilterString, eBlastOpt_MatrixName, eBlastOpt_MbIndexName, eBlastOpt_PHIPattern, eBlastOpt_RepeatFilteringDB, eBlastOpt_WindowMaskerDatabase, CBlast4Field::Get(), CBlastOptionsRemote::m_DefaultsMode, CBlastOptionsRemote::x_SetParam(), and CBlastOptionsRemote::x_Throwx().
◆ SetValue() [3/12]
| void CBlastOptionsRemote::SetValue | ( | EBlastOptIdx | opt, |
| const double & | x | ||
| ) |
Definition at line 543 of file blast_options_cxx.cpp.
References eBlastOpt_BestHitOverhang, eBlastOpt_BestHitScoreEdge, eBlastOpt_DomainInclusionThreshold, eBlastOpt_EvalueThreshold, eBlastOpt_GapTrigger, eBlastOpt_GapXDropoff, eBlastOpt_GapXDropoffFinal, eBlastOpt_InclusionThreshold, eBlastOpt_PercentIdentity, eBlastOpt_QueryCovHspPerc, eBlastOpt_SegFilteringHicut, eBlastOpt_SegFilteringLocut, eBlastOpt_XDropoff, CBlast4Field::Get(), CBlastOptionsRemote::m_DefaultsMode, CBlastOptionsRemote::x_SetParam(), and CBlastOptionsRemote::x_Throwx().
◆ SetValue() [4/12]
| void CBlastOptionsRemote::SetValue | ( | EBlastOptIdx | opt, |
| const EProgram & | x | ||
| ) |
Definition at line 348 of file blast_options_cxx.cpp.
References eBlastOpt_Program, CBlastOptionsRemote::m_DefaultsMode, and CBlastOptionsRemote::x_Throwx().
Referenced by CBlastOptions::SetBestHitOverhang(), CBlastOptions::SetBestHitScoreEdge(), CBlastOptions::SetComplexityAdjMode(), CBlastOptions::SetCompositionBasedStats(), CBlastOptions::SetCullingLimit(), CBlastOptions::SetCutoffScore(), CBlastOptions::SetDbGeneticCode(), CBlastOptions::SetDbLength(), CBlastOptions::SetDbSeqNum(), CBlastOptions::SetDomainInclusionThreshold(), CBlastOptions::SetDustFiltering(), CBlastOptions::SetDustFilteringLevel(), CBlastOptions::SetDustFilteringLinker(), CBlastOptions::SetDustFilteringWindow(), CBlastOptions::SetEffectiveSearchSpace(), CBlastOptions::SetEvalueThreshold(), CBlastOptions::SetFilterString(), CBlastOptions::SetFrameShiftPenalty(), CBlastOptions::SetGapExtensionCost(), CBlastOptions::SetGapExtnAlgorithm(), CBlastOptions::SetGapOpeningCost(), CBlastOptions::SetGappedMode(), CBlastOptions::SetGapTracebackAlgorithm(), CBlastOptions::SetGapTrigger(), CBlastOptions::SetGapXDropoff(), CBlastOptions::SetGapXDropoffFinal(), CBlastOptions::SetHitlistSize(), CBlastOptions::SetIgnoreMsaMaster(), CBlastOptions::SetInclusionThreshold(), CBlastOptions::SetLongestIntronLength(), CBlastOptions::SetLookupTableType(), CBlastOptions::SetMaskAtHash(), CBlastOptions::SetMaskLevel(), CBlastOptions::SetMatchReward(), CBlastOptions::SetMatrixName(), CBlastOptions::SetMaxHspsPerSubject(), CBlastOptions::SetMaxNumHspPerSequence(), CBlastOptions::SetMBTemplateLength(), CBlastOptions::SetMBTemplateType(), CBlastOptions::SetMismatchPenalty(), CBlastOptions::SetOutOfFrameMode(), CBlastOptions::SetPercentIdentity(), CBlastOptions::SetPHIPattern(), CBlastOptions::SetProgram(), CBlastOptions::SetPseudoCount(), CBlastOptions::SetQueryCovHspPerc(), CBlastOptions::SetQueryGeneticCode(), CBlastOptions::SetRepeatFiltering(), CBlastOptions::SetRepeatFilteringDB(), CBlastOptions::SetSegFiltering(), CBlastOptions::SetSegFilteringHicut(), CBlastOptions::SetSegFilteringLocut(), CBlastOptions::SetSegFilteringWindow(), CBlastOptions::SetSmithWatermanMode(), CBlastOptions::SetStrandOption(), CBlastOptions::SetSubjectBestHit(), CBlastOptions::SetSumStatisticsMode(), CBlastOptions::SetUnifiedP(), CBlastOptions::SetUseIndex(), CBlastOptionsRemote::SetValue(), CBlastOptions::SetWindowMaskerDatabase(), CBlastOptions::SetWindowMaskerTaxId(), CBlastOptions::SetWindowSize(), CBlastOptions::SetWordSize(), CBlastOptions::SetWordThreshold(), and CBlastOptions::SetXDropoff().
◆ SetValue() [5/12]
| void CBlastOptionsRemote::SetValue | ( | EBlastOptIdx | opt, |
| const ESeedContainerType & | x | ||
| ) |
Definition at line 685 of file blast_options_cxx.cpp.
References CBlastOptionsRemote::m_DefaultsMode, and CBlastOptionsRemote::x_Throwx().
◆ SetValue() [6/12]
| void CBlastOptionsRemote::SetValue | ( | EBlastOptIdx | opt, |
| const int & | x | ||
| ) |
Definition at line 370 of file blast_options_cxx.cpp.
References eBlast4_strand_type_both_strands, eBlast4_strand_type_forward_strand, eBlast4_strand_type_reverse_strand, eBlastOpt_CompositionBasedStats, eBlastOpt_CullingLimit, eBlastOpt_CutoffScore, eBlastOpt_DbGeneticCode, eBlastOpt_DbLength, eBlastOpt_DbSeqNum, eBlastOpt_DustFilteringLevel, eBlastOpt_DustFilteringLinker, eBlastOpt_DustFilteringWindow, eBlastOpt_GapExtensionCost, eBlastOpt_GapExtnAlgorithm, eBlastOpt_GapOpeningCost, eBlastOpt_GapTracebackAlgorithm, eBlastOpt_HitlistSize, eBlastOpt_LongestIntronLength, eBlastOpt_LookupTableType, eBlastOpt_MaskLevel, eBlastOpt_MatchReward, eBlastOpt_MaxHspsPerSubject, eBlastOpt_MBTemplateLength, eBlastOpt_MBTemplateType, eBlastOpt_MismatchPenalty, eBlastOpt_PseudoCount, eBlastOpt_QueryGeneticCode, eBlastOpt_SegFilteringWindow, eBlastOpt_StrandOption, eBlastOpt_UnifiedP, eBlastOpt_WindowMaskerTaxId, eBlastOpt_WindowSize, eBlastOpt_WordSize, eBlastOpt_WordThreshold, eNumCompoAdjustModes, CBlast4Field::Get(), CBlastOptionsRemote::m_DefaultsMode, CBlastOptionsRemote::x_SetParam(), and CBlastOptionsRemote::x_Throwx().
◆ SetValue() [7/12]
| void CBlastOptionsRemote::SetValue | ( | EBlastOptIdx | opt, |
| const Int8 & | x | ||
| ) |
Definition at line 769 of file blast_options_cxx.cpp.
References eBlastOpt_DbLength, eBlastOpt_EffectiveSearchSpace, CBlast4Field::Get(), CBlastOptionsRemote::m_DefaultsMode, CBlastOptionsRemote::x_SetParam(), and CBlastOptionsRemote::x_Throwx().
◆ SetValue() [8/12]
|
inline |
Definition at line 122 of file blast_options_cxx.cpp.
References CBlastOptionsRemote::SetValue().
◆ SetValue() [9/12]
|
inline |
Definition at line 107 of file blast_options_cxx.cpp.
References CBlastOptionsRemote::SetValue().
◆ SetValue() [10/12]
| void CBlastOptionsRemote::SetValue | ( | EBlastOptIdx | opt, |
| const TSeqLocVector & | x | ||
| ) |
Definition at line 671 of file blast_options_cxx.cpp.
References CBlastOptionsRemote::m_DefaultsMode, and CBlastOptionsRemote::x_Throwx().
◆ SetValue() [11/12]
|
inline |
Definition at line 117 of file blast_options_cxx.cpp.
References CBlastOptionsRemote::SetValue().
◆ SetValue() [12/12]
|
inline |
Definition at line 112 of file blast_options_cxx.cpp.
References CBlastOptionsRemote::SetValue().
◆ SetVecScreenDefaults()
| void CBlastNucleotideOptionsHandle::SetVecScreenDefaults | ( | ) |
Sets default options for VecScreen.
Definition at line 93 of file blast_nucl_options.cpp.
References CBlastOptions::eRemote, eVecScreen, CBlastOptions::GetLocality(), CBlastOptionsHandle::m_Opts, CBlastOptions::SetDefaultsMode(), CBlastOptions::SetDustFiltering(), CBlastOptions::SetEffectiveSearchSpace(), CBlastOptions::SetEvalueThreshold(), CBlastOptions::SetGapExtensionCost(), CBlastOptions::SetGapOpeningCost(), CBlastOptions::SetMaskAtHash(), CBlastOptions::SetMatchReward(), CBlastOptions::SetMismatchPenalty(), CBlastOptions::SetProgram(), and CBlastOptions::SetRemoteProgramAndService_Blast3().
Referenced by CBlastOptionsFactory::Create(), and CBlastOptionsFactory::CreateTask().
◆ SetVerbose() [1/2]
Analogous to CRemoteBlast::SetVerbose.
Definition at line 113 of file blast_services.hpp.
References rapidjson::value.
◆ SetVerbose() [2/2]
| void CRemoteBlast::SetVerbose | ( | EDebugMode | verb = eDebug | ) |
Adjust the debugging level.
This causes debugging trace data to be dumped to standard output, along with ASN.1 objects used during the search and other text. It produces a great deal of output, none of which is expected to be useful to the end-user.
Definition at line 1629 of file remote_blast.cpp.
References CRemoteBlast::m_Verbose.
Referenced by InitializeRemoteBlast(), CBlastFormatterApp::Run(), and CBlastFormatterVdbApp::Run().
◆ SetWindowMaskerDatabase() [1/3]
|
inline |
Enable window masker and select a database (or NULL to disable).
- Parameters
-
taxid Select Window Masker filtering database by filename [in]
Definition at line 153 of file blast_nucl_options.hpp.
Referenced by BOOST_AUTO_TEST_CASE().
◆ SetWindowMaskerDatabase() [2/3]
| void CBlastOptions::SetWindowMaskerDatabase | ( | const char * | db | ) |
Sets the windowmasker database to use.
This must be the name of a subdirectory of WINDOW_MASKER_PATH
- Note
- this only runs on machines that have the WINDOW_MASKER_PATH configuration value set and have the the correct endianness. If windowmasker databases are not available, the filtering will fail silently
Definition at line 1376 of file blast_options_cxx.cpp.
References eBlastOpt_WindowMaskerDatabase, CBlast4Field::Get(), CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsRemote::ResetValue(), CBlastOptionsRemote::SetValue(), CBlastOptionsLocal::SetWindowMaskerDatabase(), and rapidjson::value.
Referenced by CBlastOptions::ClearFilterOptions(), and CFilteringArgs::ExtractAlgorithmOptions().
◆ SetWindowMaskerDatabase() [3/3]
|
inline |
Definition at line 990 of file blast_options_local_priv.hpp.
References QuerySetUpOptions::filtering_options, CBlastOptionsLocal::m_QueryOpts, NULL, SWindowMaskerOptionsNew(), SWindowMaskerOptionsResetDB(), and SBlastFilterOptions::windowMaskerOptions.
Referenced by CBlastOptions::SetWindowMaskerDatabase().
◆ SetWindowMaskerTaxId() [1/3]
|
inline |
Enable window masker and select a taxid (or 0 to disable).
- Parameters
-
taxid Select Window Masker filtering database for this taxid [in]
Definition at line 143 of file blast_nucl_options.hpp.
Referenced by BOOST_AUTO_TEST_CASE().
◆ SetWindowMaskerTaxId() [2/3]
| void CBlastOptions::SetWindowMaskerTaxId | ( | int | taxid | ) |
Sets the tax id to select an appropriate windowmasker database Conversion algorithm from tax id to database name is specific to NCBI, will not work outside NCBI.
- Note
- this only runs on machines that have the WINDOW_MASKER_PATH configuration value set and have the the correct endianness. If windowmasker databases are not available, the filtering will fail silently
Definition at line 1352 of file blast_options_cxx.cpp.
References eBlastOpt_WindowMaskerTaxId, CBlast4Field::Get(), CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsRemote::ResetValue(), CBlastOptionsRemote::SetValue(), CBlastOptionsLocal::SetWindowMaskerTaxId(), and rapidjson::value.
Referenced by CBlastOptions::ClearFilterOptions(), CFilteringArgs::ExtractAlgorithmOptions(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetWindowMaskerTaxId() [3/3]
|
inline |
Definition at line 971 of file blast_options_local_priv.hpp.
References QuerySetUpOptions::filtering_options, CBlastOptionsLocal::m_QueryOpts, NULL, SWindowMaskerOptionsNew(), SWindowMaskerOptions::taxid, and SBlastFilterOptions::windowMaskerOptions.
Referenced by CBlastOptions::SetWindowMaskerTaxId().
◆ SetWindowSize() [1/3]
| void CBlastOptions::SetWindowSize | ( | int | w | ) |
Definition at line 1499 of file blast_options_cxx.cpp.
References eBlastOpt_WindowSize, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsRemote::SetValue(), and CBlastOptionsLocal::SetWindowSize().
Referenced by BOOST_AUTO_TEST_CASE(), CWindowSizeArg::ExtractAlgorithmOptions(), and CBlastOptionsHandle::SetWindowSize().
◆ SetWindowSize() [2/3]
|
inline |
Definition at line 1099 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_InitWordOpts, and BlastInitialWordOptions::window_size.
Referenced by CBlastOptions::SetWindowSize().
◆ SetWindowSize() [3/3]
|
inline |
Sets WindowSize.
- Parameters
-
ws WindowSize [in]
Definition at line 184 of file blast_options_handle.hpp.
References CBlastOptionsHandle::m_Opts, and CBlastOptions::SetWindowSize().
Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), CBlastNucleotideOptionsHandle::SetInitialWordOptionsDefaults(), CBlastProteinOptionsHandle::SetInitialWordOptionsDefaults(), CBlastRPSOptionsHandle::SetInitialWordOptionsDefaults(), CBlastNucleotideOptionsHandle::SetMBInitialWordOptionsDefaults(), CDiscNucleotideOptionsHandle::SetMBInitialWordOptionsDefaults(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetWordSize() [1/6]
|
inline |
Set word size.
- Parameters
-
w word size [in]
Definition at line 139 of file magicblast_options.hpp.
Referenced by CMagicBlastOptionsHandle::SetGenomeToGenomeDefaults(), CMagicBlastOptionsHandle::SetLookupTableDefaults(), and CMagicBlastOptionsHandle::SetRNAToRNADefaults().
◆ SetWordSize() [2/6]
|
inline |
Sets WordSize.
- Parameters
-
ws WordSize [in]
Definition at line 86 of file blast_nucl_options.hpp.
Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), CBlastOptionsFactory::CreateTask(), s_CreateRepeatsSearchOptions(), CBlastNucleotideOptionsHandle::SetLookupTableDefaults(), and CBlastNucleotideOptionsHandle::SetMBLookupTableDefaults().
◆ SetWordSize() [3/6]
| void CBlastOptions::SetWordSize | ( | int | ws | ) |
Definition at line 922 of file blast_options_cxx.cpp.
References eBlastOpt_WordSize, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsRemote::SetValue(), and CBlastOptionsLocal::SetWordSize().
Referenced by BOOST_AUTO_TEST_CASE(), CGenericSearchArgs::ExtractAlgorithmOptions(), CIgBlast::Run(), CBlastProteinOptionsHandle::SetWordSize(), CIgBlastnAppArgs::x_CreateOptionsHandle(), CBlastOptionsBuilder::x_ProcessOneOption(), CSplignApp::x_SetupBlastOptions(), CIgBlast::x_SetupCRegionSearch(), CIgBlast::x_SetupDJSearch(), CIgBlast::x_SetupNoOverlapDSearch(), and CIgBlast::x_SetupVSearch().
◆ SetWordSize() [4/6]
| void CBlastProteinOptionsHandle::SetWordSize | ( | int | ws | ) |
Sets WordSize.
- Parameters
-
ws WordSize [in]
Definition at line 56 of file blast_prot_options.cpp.
References BLAST_WORD_THRESHOLD_BLASTP, BLAST_WORD_THRESHOLD_BLASTP_FAST, BLAST_WORD_THRESHOLD_BLASTP_WD_SZ_6, BLAST_WORD_THRESHOLD_BLASTP_WD_SZ_7, eAaLookupTable, eCompressedAaLookupTable, CBlastOptionsHandle::m_Opts, CBlastOptions::SetLookupTableType(), CBlastOptions::SetWordSize(), and CBlastOptions::SetWordThreshold().
Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), CBlastOptionsFactory::CreateTask(), CBlastProteinOptionsHandle::SetLookupTableDefaults(), and CTblastnAppArgs::x_CreateOptionsHandle().
◆ SetWordSize() [5/6]
|
inline |
Sets WordSize.
- Parameters
-
ws WordSize [in]
Definition at line 86 of file disc_nucl_options.hpp.
References NCBI_THROW.
Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), and CDiscNucleotideOptionsHandle::SetMBLookupTableDefaults().
◆ SetWordSize() [6/6]
|
inline |
Definition at line 612 of file blast_options_local_priv.hpp.
References eAaLookupTable, eCompressedAaLookupTable, LookupTableOptions::lut_type, CBlastOptionsLocal::m_LutOpts, and LookupTableOptions::word_size.
Referenced by CBlastOptions::SetWordSize().
◆ SetWordThreshold() [1/3]
| void CBlastOptions::SetWordThreshold | ( | double | w | ) |
Sets WordThreshold.
- Parameters
-
w WordThreshold [in]
Definition at line 884 of file blast_options_cxx.cpp.
References eBlastOpt_WordThreshold, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsRemote::SetValue(), and CBlastOptionsLocal::SetWordThreshold().
Referenced by BOOST_AUTO_TEST_CASE(), CWordThresholdArg::ExtractAlgorithmOptions(), CGenericSearchArgs::ExtractAlgorithmOptions(), CBlastNucleotideOptionsHandle::SetLookupTableDefaults(), CBlastxOptionsHandle::SetLookupTableDefaults(), CMagicBlastOptionsHandle::SetLookupTableDefaults(), CTBlastxOptionsHandle::SetLookupTableDefaults(), CBlastNucleotideOptionsHandle::SetMBLookupTableDefaults(), CPSIBlastOptionsHandle::SetPSITblastnDefaults(), CBlastProteinOptionsHandle::SetWordSize(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ SetWordThreshold() [2/3]
|
inline |
Definition at line 585 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_LutOpts, and LookupTableOptions::threshold.
Referenced by CBlastOptions::SetWordThreshold().
◆ SetWordThreshold() [3/3]
|
inline |
Sets WordThreshold.
- Parameters
-
wt WordThreshold [in]
Definition at line 69 of file blast_prot_options.hpp.
Referenced by BOOST_FIXTURE_TEST_CASE(), CBlastOptionsFactory::CreateTask(), CBlastProteinOptionsHandle::SetLookupTableDefaults(), CTBlastnOptionsHandle::SetLookupTableDefaults(), and CTblastnAppArgs::x_CreateOptionsHandle().
◆ SetXDropoff() [1/5]
|
inline |
Sets XDropoff.
- Parameters
-
x XDropoff [in]
Definition at line 164 of file blast_nucl_options.hpp.
Referenced by BOOST_FIXTURE_TEST_CASE(), s_CreateRepeatsSearchOptions(), CBlastNucleotideOptionsHandle::SetInitialWordOptionsDefaults(), and CDiscNucleotideOptionsHandle::SetMBInitialWordOptionsDefaults().
◆ SetXDropoff() [2/5]
| void CBlastOptions::SetXDropoff | ( | double | x | ) |
Definition at line 1537 of file blast_options_cxx.cpp.
References eBlastOpt_XDropoff, CBlastOptions::m_Local, CBlastOptions::m_Remote, CBlastOptionsRemote::SetValue(), and CBlastOptionsLocal::SetXDropoff().
Referenced by CGenericSearchArgs::ExtractAlgorithmOptions().
◆ SetXDropoff() [3/5]
|
inline |
Sets XDropoff.
- Parameters
-
x XDropoff [in]
Definition at line 82 of file blast_prot_options.hpp.
Referenced by BOOST_FIXTURE_TEST_CASE(), and CBlastProteinOptionsHandle::SetInitialWordOptionsDefaults().
◆ SetXDropoff() [4/5]
|
inline |
Sets XDropoff.
- Parameters
-
x XDropoff [in]
Definition at line 75 of file blast_rps_options.hpp.
Referenced by CBlastRPSOptionsHandle::SetInitialWordOptionsDefaults().
◆ SetXDropoff() [5/5]
|
inline |
Definition at line 1123 of file blast_options_local_priv.hpp.
References CBlastOptionsLocal::m_InitWordOpts, and BlastInitialWordOptions::x_dropoff.
Referenced by CBlastOptions::SetXDropoff().
◆ SInternalData()
| SInternalData::SInternalData | ( | ) |
Default ctor.
Definition at line 465 of file setup_factory.cpp.
References SInternalData::m_Queries, and SInternalData::m_QueryInfo.
◆ size() [1/3]
|
inline |
Identical to GetNumResults, provided to facilitate STL-style iteration.
- See also
- note in GetNumResults
Definition at line 424 of file blast_results.hpp.
References CSearchResultSet::GetNumResults().
Referenced by BlastBuildSearchResultSet(), BOOST_AUTO_TEST_CASE(), CSearchResultSet::empty(), CVecscreenRun::CFormatter::FormatResults(), CDeltaBlast::Run(), s_TrimResults(), and CBl2Seq::x_BuildAncillaryData().
◆ size() [2/3]
|
inline |
Get number of results, provided to facilitate STL-style iteration.
Definition at line 264 of file magicblast.hpp.
References CMagicBlastResultSet::m_Results.
Referenced by CMagicBlastResultSet::empty().
◆ Size() [1/7]
|
virtual |
Returns the size of the underlying container of sequences.
Implements IBlastSeqInfoSrc.
Definition at line 82 of file seqinfosrc_seqdb.cpp.
References CSeqDB::GetNumOIDs(), and CSeqDbSeqInfoSrc::m_iSeqDb.
◆ Size() [2/7]
|
virtual |
Returns the size of the underlying container of sequences.
Implements IBlastSeqInfoSrc.
Definition at line 99 of file seqinfosrc_seqvec.cpp.
References CSeqVecSeqInfoSrc::m_SeqVec.
◆ Size() [3/7]
|
virtual |
Return the number of elements in the sequence container.
Implements IBlastQuerySource.
Definition at line 260 of file bioseq_extract_data_priv.cpp.
References CBlastQuerySourceBioseqSet::m_Bioseqs.
Referenced by s_ConstBioseqSetToSeqLocs(), and CBioseqSeqInfoSrc::Size().
◆ Size() [4/7]
|
virtual |
Return the number of elements in the sequence container.
Implements IBlastQuerySource.
Definition at line 382 of file blast_objmgr_tools.cpp.
References CBlastQuerySourceOM::m_QueryVector, CBlastQuerySourceOM::m_TSeqLocVector, CRef< C, Locker >::NotEmpty(), and CBlastQueryVector::Size().
◆ size() [3/3]
|
inline |
Returns the length of the sequence data (in the case of nucleotides, only one strand)
- Exceptions
-
CBlastException if the size returned is 0
Definition at line 192 of file blast_setup.hpp.
References NCBI_THROW, and IBlastSeqVector::x_Size().
Referenced by CBlastSeqVectorFromCSeq_data::GetCompressedPlusStrand(), CBlastSeqVectorOM::GetCompressedPlusStrand(), GetSequenceNucleotideBothStrands(), GetSequenceProtein(), GetSequenceSingleNucleotideStrand(), IBlastSeqVector::GetStrandData(), CBlastSeqVectorFromCSeq_data::SetCoding(), and CBlastSeqVectorFromCSeq_data::x_ComplementData().
◆ Size() [5/7]
|
virtual |
Returns the size of the underlying container of sequences.
Implements IBlastSeqInfoSrc.
Definition at line 84 of file seqinfosrc_bioseq.cpp.
References CBioseqSeqInfoSrc::m_DataSource, and CBlastQuerySourceBioseqSet::Size().
◆ Size() [6/7]
|
pure virtual |
Returns the size of the underlying container of sequences.
Implemented in CBioseqSeqInfoSrc, CSeqVecSeqInfoSrc, and CSeqDbSeqInfoSrc.
Referenced by CLocalBlast::Run(), s_BlastResults2SeqAlignSequenceCmp_OMF(), s_MakeEmptyResults(), and CMagicBlast::x_Run().
◆ Size() [7/7]
|
pure virtual |
Return the number of elements in the sequence container.
Implemented in CBlastQuerySourceOM, and CBlastQuerySourceBioseqSet.
Referenced by CQueryFactoryInfo::CQueryFactoryInfo(), IBlastQuerySource::Empty(), CObjMgr_LocalQueryData::GetNumQueries(), CObjMgrFree_LocalQueryData::GetNumQueries(), SetupQueries_OMF(), SetupQueryInfo_OMF(), and SetupSubjects_OMF().
◆ SmithWatermanScoreWithTraceback()
| void SmithWatermanScoreWithTraceback | ( | EBlastProgramType | program_number, |
| const Uint1 * | A, | ||
| Int4 | a_size, | ||
| const Uint1 * | B, | ||
| Int4 | b_size, | ||
| BlastHSP * | template_hsp, | ||
| BlastHSPList * | hsp_list, | ||
| const BlastScoringParameters * | score_params, | ||
| const BlastHitSavingParameters * | hit_params, | ||
| BlastGapAlignStruct * | gap_align, | ||
| Int4 | start_shift, | ||
| Int4 | cutoff | ||
| ) |
Find all local alignments between two (unpacked) sequences, using the Smith-Waterman algorithm, then save the list of alignments found.
The algorithm to recover all high-scoring local alignments, and not just the best one, is described in
Geoffrey J. Barton, "An Efficient Algorithm to Locate All Locally Optimal Alignments Between Two Sequences Allowing for Gaps". Computer Applications in the Biosciences, (1993), 9, pp. 729-734
- Parameters
-
program_number Blast program requesting traceback [in] A The first sequence [in] a_size Length of the first sequence [in] B The second sequence [in] b_size Length of the second sequence [in] template_hsp Placeholder alignment, used only to determine contexts and frames [in] hsp_list Collection of alignments found so far [in][out] score_params Structure containing gap penalties [in] hit_params Structure used for percent identity calculation [in] gap_align Auxiliary data for gapped alignment (used for score matrix info) [in] start_shift Bias to be applied to subject offsets [in] cutoff Alignments are saved if their score exceeds this value [in]
Definition at line 414 of file blast_sw.c.
References A, B, BlastGapSW::best, BlastGapSW::best_gap, calloc(), SBlastScoreMatrix::data, EDIT_GAP_IN_A, EDIT_GAP_IN_B, EDIT_START_GAP_A, EDIT_START_GAP_B, EDIT_SUB, FALSE, free(), BlastScoringParameters::gap_extend, BlastScoringParameters::gap_open, i, malloc(), BlastScoreBlk::matrix, MAX, BlastHitSavingParameters::options, BlastScoringParameters::options, BlastGapSW::path_score, BlastGapSW::path_stop_i, BlastGapSW::path_stop_j, BlastGapAlignStruct::positionBased, BlastScoreBlk::psi_matrix, SPsiBlastScoreMatrix::pssm, s_GetTraceback(), BlastGapAlignStruct::sbp, SWAP_INT, SWAP_SEQS, and TRUE.
Referenced by Blast_TracebackFromHSPList().
◆ SMultiSeqSrcNewArgs()
|
inline |
Constructor.
Definition at line 467 of file seqsrc_multiseq.cpp.
◆ SNcbiMatrix2DoubleMatrix()
|
inline |
Constructor.
- Parameters
-
m standard c++ toolkit matrix
Definition at line 309 of file pssm_engine.cpp.
References CNcbiMatrix< T >::GetCols(), CNcbiMatrix< T >::GetRows(), SNcbiMatrix2DoubleMatrix::m_Data, and r().
◆ SOptional()
|
inline |
Constructor.
Definition at line 213 of file blast_options_builder.hpp.
◆ SortAlignments()
| void CMagicBlastResults::SortAlignments | ( | CMagicBlastResults::EOrdering | order | ) |
Sort alignments by selected criteria (pair configuration)
Definition at line 640 of file magicblast.cpp.
References CMagicBlastResults::eFwRevFirst, CMagicBlastResults::m_Aligns, and CSeq_align_set_Base::Set().
◆ SPatternUnit()
Definition at line 56 of file seedtop.hpp.
References NCBI_THROW, string, and NStr::StringToUInt().
◆ Split()
| CRef< CSplitQueryBlk > CQuerySplitter::Split | ( | ) |
Split the query sequence(s)
Definition at line 858 of file split_query_cxx.cpp.
References _TRACE, CBlastOptions::GetGappedMode(), CQuerySplitter::m_NumChunks, CQuerySplitter::m_Options, CQuerySplitter::m_QueryChunkFactories, CQuerySplitter::m_QueryFactory, CQuerySplitter::m_SplitBlk, CQuerySplitter::m_SplitQueriesInChunk, CRef< C, Locker >::NotEmpty(), CRef< C, Locker >::Reset(), CQuerySplitter::x_ComputeChunkRanges(), CQuerySplitter::x_ComputeContextOffsetsForChunks(), CQuerySplitter::x_ComputeQueryContextsForChunks(), and CQuerySplitter::x_ComputeQueryIndicesForChunks().
Referenced by BOOST_AUTO_TEST_CASE(), CQuerySplitter::GetQueryFactoryForChunk(), CSplitQueryTestFixture::QuerySplitter_BlastnMultiQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastnSingleQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastxMultiQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastxSingleQueryMultiChunk(), CBlastPrelimSearch::Run(), CSplitQueryTestFixture::x_TestCContextTranslator(), and CSplitQueryTestFixture::x_ValidateLocalQueryData().
◆ SplitQuery_CalculateNumChunks()
| Uint4 SplitQuery_CalculateNumChunks | ( | EBlastProgramType | program, |
| size_t * | chunk_size, | ||
| size_t | concatenated_query_length, | ||
| size_t | num_queries | ||
| ) |
Calculate the number of chunks that a query will be split into based upon query length, chunk_size and program.
- Parameters
-
program BLAST program type [in] chunk_size size of each of the query chunks, may be adjusted [in|out] concatenated_query_length length of the concatenated query [in] num_queries number of queries to split [in]
Definition at line 100 of file split_query_aux_priv.cpp.
References _ASSERT, _DEBUG_ARG, _TRACE, Blast_QueryIsTranslated(), chunk_size, CODON_LENGTH, SplitQuery_GetOverlapChunkSize(), and SplitQuery_ShouldSplit().
Referenced by BOOST_AUTO_TEST_CASE(), CQuerySplitter::CQuerySplitter(), and CSplitQueryTestFixture::x_TestCContextTranslator().
◆ SplitQuery_CreateChunkData()
| CRef< SInternalData > SplitQuery_CreateChunkData | ( | CRef< IQueryFactory > | qf, |
| CRef< CBlastOptions > | options, | ||
| CRef< SInternalData > | full_data, | ||
| size_t | num_threads | ||
| ) |
Function used by search class to retrieve a query factory for a given chunk.
Definition at line 185 of file split_query_aux_priv.cpp.
References _ASSERT, BlastSeqSrcCopy(), BlastSeqSrcFree(), BlastSeqSrcResetChunkIterator(), BlastSetupPreliminarySearchEx(), CSBlastProgress::Get(), SInternalData::m_FnInterrupt, SInternalData::m_ProgressMonitor, SInternalData::m_SeqSrc, CRef< C, Locker >::Reset(), SBlastProgressNew(), and SBlastProgress::user_data.
Referenced by CBlastPrelimSearch::Run().
◆ SplitQuery_GetChunkSize()
| size_t SplitQuery_GetChunkSize | ( | EProgram | program | ) |
Returns the optimal chunk size for a given task.
- Parameters
-
program BLAST task [in]
Definition at line 54 of file local_blast.cpp.
References _TRACE, Blast_QueryIsTranslated(), Blast_SubjectIsPssm(), CODON_LENGTH, eBlastn, eBlastp, eBlastx, eDiscMegablast, eMapper, eMegablast, EProgramToEBlastProgramType(), EProgramToTaskName(), eTblastn, eTblastx, eVecScreen, NStr::IsBlank(), NCBI_THROW, and NStr::StringToInt().
Referenced by BOOST_AUTO_TEST_CASE(), CQuerySplitter::CQuerySplitter(), CBlastnNode::Main(), CVDBBlastnApp::Run(), and CBlastnApp::x_RunMTBySplitDB().
◆ SplitQuery_GetOverlapChunkSize()
| size_t SplitQuery_GetOverlapChunkSize | ( | EBlastProgramType | program | ) |
Size of the region that overlaps in between each query chunk.
- Parameters
-
program BLAST program type [in]
Definition at line 51 of file split_query_aux_priv.cpp.
References _TRACE, Blast_QueryIsTranslated(), NStr::IsBlank(), and NStr::StringToInt().
Referenced by BOOST_AUTO_TEST_CASE(), SplitQuery_CalculateNumChunks(), CQuerySplitter::x_ComputeChunkRanges(), CQuerySplitter::x_ComputeContextOffsets_NonTranslatedQueries(), CQuerySplitter::x_ComputeContextOffsets_TranslatedQueries(), and CSplitQueryTestFixture::x_ValidateChunkBounds().
◆ SplitQuery_SetEffectiveSearchSpace()
| void SplitQuery_SetEffectiveSearchSpace | ( | CRef< CBlastOptions > | options, |
| CRef< IQueryFactory > | full_query_fact, | ||
| CRef< SInternalData > | full_data | ||
| ) |
this might supercede the function below...
Definition at line 150 of file split_query_aux_priv.cpp.
References _ASSERT, BlastSeqSrcGetNumSeqs(), BlastSeqSrcGetNumSeqsStats(), BlastSeqSrcGetTotLen(), BlastSeqSrcGetTotLenStats(), CBlastOptions::GetEffectiveSearchSpace(), CEffectiveSearchSpaceCalculator::GetEffSearchSpaceForContext(), BlastQueryInfo::last_context, SInternalData::m_QueryInfo, SInternalData::m_ScoreBlk, SInternalData::m_SeqSrc, and CBlastOptions::SetEffectiveSearchSpace().
Referenced by CBlastPrelimSearch::Run().
◆ SplitQuery_ShouldSplit()
| bool SplitQuery_ShouldSplit | ( | EBlastProgramType | program, |
| size_t | chunk_size, | ||
| size_t | concatenated_query_length, | ||
| size_t | num_queries | ||
| ) |
Determines if the input query sequence(s) should be split because it.
is supported by the current implementation. The splitting decision in this function is not based upon query length.
- Parameters
-
program BLAST program type [in] chunk_size size of each of the query chunks [in] concatenated_query_length length of the concatenated query [in] num_queries number of queries to split [in]
Definition at line 73 of file split_query_aux_priv.cpp.
References Blast_ProgramIsPhiBlast(), Blast_SubjectIsPssm(), eBlastTypeBlastx, and eBlastTypeMapping.
Referenced by SplitQuery_CalculateNumChunks().
◆ SQueryFactorySrcNewArgs()
|
inline |
Constructor.
Definition at line 445 of file seqsrc_query_factory.cpp.
◆ SSeqDB_SeqSrc_Data() [1/2]
|
inline |
Constructor.
Definition at line 55 of file seqsrc_seqdb.cpp.
Referenced by SSeqDB_SeqSrc_Data::clone().
◆ SSeqDB_SeqSrc_Data() [2/2]
|
inline |
Constructor.
Definition at line 61 of file seqsrc_seqdb.cpp.
◆ Submit()
| bool CRemoteBlast::Submit | ( | void | ) |
This submits the search (if necessary) and returns immediately.
If a new search is configured, and not already submitted, this will submit it. It then polls for results until either completion or error state is reached, or until the search times out. The polling is done at an increasing interval, which starts out at 10 seconds, increasing by 30% after each check to a maximum of 300 seconds per sleep.
- Returns
- true if the search was submitted, otherwise false.
Definition at line 297 of file remote_blast.cpp.
References CRemoteBlast::eStart, CRemoteBlast::m_Errs, CRemoteBlast::x_GetState(), and CRemoteBlast::x_SubmitSearch().
Referenced by BOOST_AUTO_TEST_CASE(), CRemoteBlast::CheckDone(), and CIgBlast::Run().
◆ SubmitSync() [1/2]
This submits the search (if necessary) and polls for results.
If a new search is configured, and not already submitted, this will submit it. It then polls for results until either completion or error state is reached, or until the search times out. The polling is done at an increasing interval, which starts out at 10 seconds, increasing by 30% after each check to a maximum of 300 seconds per sleep.
- Parameters
-
timeout Search timeout specified as a number of seconds.
- Returns
- true if the search was submitted, otherwise false.
Definition at line 264 of file remote_blast.cpp.
References CRemoteBlast::eDone, CRemoteBlast::ePollAsync, CRemoteBlast::ePollImmed, CRemoteBlast::eStart, CRemoteBlast::eWait, CRemoteBlast::m_Errs, CRemoteBlast::x_GetState(), CRemoteBlast::x_PollUntilDone(), and CRemoteBlast::x_SubmitSearch().
◆ SubmitSync() [2/2]
| bool CRemoteBlast::SubmitSync | ( | void | ) |
This submits the search (if necessary) and polls for results.
If a new search is configured, and not already submitted, this will submit it. It then polls for results until either completion or error state is reached, or until the search times out. The polling is done at an increasing interval, which starts out at 10 seconds, increasing by 30% after each check to a maximum of 300 seconds per sleep.
- Returns
- true if the search was submitted, otherwise false.
Definition at line 1619 of file remote_blast.cpp.
References CRemoteBlast::x_DefaultTimeout().
Referenced by CRemoteBlast::GetResultSet(), CRemoteSeqSearch::Run(), CRemotePssmSearch::Run(), and CRemoteBlast::x_GetGSRR().
◆ Subtract()
Subtract from another hit from this hit using query ranges.
- Parameters
-
hit Hit to subtract [in]
Definition at line 614 of file cdd_pssm_input.cpp.
References _ASSERT, CCddInputData::CHitSegment::AdjustRanges(), CRange_Base::GetFrom(), CCddInputData::CHit::GetSegments(), CCddInputData::CHit::IsEmpty(), CCddInputData::CHitSegment::m_QueryRange, and NULL.
◆ SVolResults()
|
inline |
Definition at line 381 of file blast_dbindex.cpp.
◆ test()
Definition at line 124 of file seedtop.hpp.
References letter().
◆ ThrowIfInvalidTask()
Validates that the task provided is indeed a valid task, otherwise throws a CBlastException.
- Parameters
-
task task name to validate [in]
Definition at line 662 of file blast_aux.cpp.
References set< Key, Compare >::empty(), set< Key, Compare >::end(), set< Key, Compare >::find(), CBlastOptionsFactory::GetTasks(), and NCBI_THROW.
Referenced by CBlastOptionsFactory::CreateTask(), EProgramToTaskName(), ProgramNameToEnum(), and CBlastAppArgs::SetTask().
◆ ToString()
| string TSearchMessages::ToString | ( | ) | const |
Converts messages to a string, which is returned.
- Returns
- A string containing all such messages.
Definition at line 1013 of file blast_aux.cpp.
References ITERATE, and msg().
Referenced by BOOST_AUTO_TEST_CASE(), CSetupFactory::CreateLookupTable(), CSetupFactory::CreateScoreBlock(), CRemoteBlast::GetResultSet(), and SetupQueries_OMF().
◆ TraceNames()
This is only used for debugging output.
Definition at line 407 of file blast_dbindex.cpp.
References i, IDX_TRACE, ITERATE, and names.
Referenced by CIndexedDb_New::CIndexedDb_New().
◆ TraceVolumes()
|
inlineprivate |
This is only used for debugging output.
Definition at line 415 of file blast_dbindex.cpp.
References i, IDX_TRACE, ITERATE, and CIndexedDb_New::volumes_.
Referenced by CIndexedDb_New::CIndexedDb_New().
◆ TrimSeqAlign()
| void CSearchResults::TrimSeqAlign | ( | objects::CSeq_align_set::Tdata::size_type | max_size | ) |
Trim align_set size @parm size max num of alignments to keep (0 will erase all)
Definition at line 347 of file blast_results.cpp.
References CSearchResults::HasAlignments(), CSearchResults::m_Alignment, CSeq_id::Match(), and CRef< C, Locker >::Reset().
◆ TSeqLocVector2Bioseqs()
| CRef<objects::CBioseq_set> TSeqLocVector2Bioseqs | ( | const TSeqLocVector & | input | ) |
Convert a TSeqLocVector to a CBioseq_set.
- Parameters
-
input TSeqLocVector to convert [in]
- Returns
- CBioseq_set with CBioseqs from the input, or NULL of input is empty
Definition at line 1070 of file blast_aux.cpp.
References CSeq_entry_Handle::GetCompleteSeq_entry(), CBioseq_Handle::GetTopLevelEntry(), input(), ITERATE, and CRef< C, Locker >::Reset().
Referenced by BOOST_AUTO_TEST_CASE().
◆ TSeqLocVector2Packed_seqint()
| CRef<objects::CPacked_seqint> TSeqLocVector2Packed_seqint | ( | const TSeqLocVector & | sequences | ) |
Converts a TSeqLocVector into a CPacked_seqint.
Note that a consequence of this is that the CSeq_loc-s specified in the TSeqLocVector cannot be of type mix or packed int
- Parameters
-
sequences data to convert from [in]
- Returns
- CPacked_seqint containing data from previous sequences
Definition at line 581 of file blast_objmgr_tools.cpp.
References GetId(), GetLength(), GetStart(), GetStop(), COpenRange< TSeqPos >::GetWhole(), ITERATE, NCBI_THROW, compile_time_bits::range(), and CRef< C, Locker >::Reset().
Referenced by BOOST_AUTO_TEST_CASE().
◆ UpdateIndex()
Update the seed sets, if necessary.
If oid belongs to the volume at vol_idx, then does nothing. Otherwise finds the index of the volume containing oid and saves it in *vol_idx. Updates the reference counts of all volumes between the old and new values of *vol_idx, releasing the result sets if necessary. If the results for new volume are not yet available, searches the new volume and stores the results.
- Parameters
-
oid ordinal id of the subject sequence vol_idx [in/out] index of the volume containing ordinal id of the sequence last accessed by this thread; updated to the index of the volume containing oid
Definition at line 812 of file blast_dbindex.cpp.
References ASSERT, CIndexedDb_New::FindVolume(), CBlastSeqLocWrap::getLocs(), IDX_TRACE, LAST_VOL_IDX_INIT, CDbIndex::Load(), CIndexedDb::locs_wrap_, CIndexedDb_New::mtx_, CIndexedDb_New::SVolumeDescriptor::n_oids, CIndexedDb_New::n_threads_, NCBI_THROW, CIndexedDb_New::queries_, CIndexedDb_New::SVolResults::ref_count, CIndexedDb_New::SVolResults::res, CIndexedDb_New::results_holder_, CDbIndex::Search(), CIndexedDb_New::sopt_, CIndexedDb_New::SVolumeDescriptor::start_oid, and CIndexedDb_New::volumes_.
Referenced by CIndexedDb_New::CheckOid().
◆ UseProteinCoords()
| void CBlastQueryFilteredFrames::UseProteinCoords | ( | TSeqPos | dna_length | ) |
Adjusts all stored masks from nucleotide to protein offsets.
Values stored here must be converted to protein offsets after a certain stage of processing. This method only has an effect for types of searches that need this service (which are those searches where the query sequence is translated.) Additional calls to this method will have no effect.
- Parameters
-
dna_length The query length in nucleotide bases.
Definition at line 1588 of file blast_setup_cxx.cpp.
References _ASSERT, CODON_LENGTH, CSeqLocInfo::eFrameMinus1, CSeqLocInfo::eFrameMinus2, CSeqLocInfo::eFrameMinus3, CSeqLocInfo::eFramePlus1, CSeqLocInfo::eFramePlus2, CSeqLocInfo::eFramePlus3, int, ITERATE, CBlastQueryFilteredFrames::m_Seqlocs, CBlastQueryFilteredFrames::m_TranslateCoords, and BlastSeqLoc::next.
Referenced by BOOST_AUTO_TEST_CASE(), and s_AddMask().
◆ USING_SCOPE() [1/6]
| USING_SCOPE | ( | blast | ) |
◆ USING_SCOPE() [2/6]
| USING_SCOPE | ( | ncbi | ) |
◆ USING_SCOPE() [3/6]
| USING_SCOPE | ( | ncbi::blast | ) |
◆ USING_SCOPE() [4/6]
| USING_SCOPE | ( | ncbi::blastdbindex | ) |
◆ USING_SCOPE() [5/6]
| USING_SCOPE | ( | ncbi::objects | ) |
◆ USING_SCOPE() [6/6]
| USING_SCOPE | ( | objects | ) |
◆ Validate() [1/5]
| bool CBlastOptions::Validate | ( | void | ) | const |
Validate the options.
Definition at line 825 of file blast_options_cxx.cpp.
References CBlastOptions::m_Local, and CBlastOptionsLocal::Validate().
Referenced by BlastSetupPreliminarySearchEx(), CBlastOptionsHandle::Validate(), and CBlastTracebackSearch::x_Init().
◆ Validate() [2/5]
| bool CBlastOptionsHandle::Validate | ( | void | ) | const |
Validate the options contained in this object.
- Note
- This method is meant to be used before calling any code that processes the BLAST options classes
Definition at line 92 of file blast_options_handle.cpp.
References CBlastOptionsHandle::m_Opts, and CBlastOptions::Validate().
Referenced by CBlastDemoApplication::Run(), CBlastAppArgs::SetOptions(), CBlastAppArgs::SetOptionsForSavedStrategy(), CSplignApp::x_SetupBlastOptions(), and CPsiBlastImpl::x_Validate().
◆ Validate() [3/5]
| bool CBlastOptionsLocal::Validate | ( | void | ) | const |
Validate the options.
Definition at line 374 of file blast_options_local_priv.cpp.
References BLAST_ValidateOptions(), eBlastn, eMapper, eMegablast, CBlastOptionsLocal::GetProgramType(), CBlastOptionsLocal::m_ExtnOpts, CBlastOptionsLocal::m_HitSaveOpts, CBlastOptionsLocal::m_InitWordOpts, CBlastOptionsLocal::m_LutOpts, CBlastOptionsLocal::m_Program, CBlastOptionsLocal::m_ScoringOpts, CBlastOptionsLocal::m_UseMBIndex, NCBI_THROW, NULL, and s_BlastMessageToException().
Referenced by CBlastOptions::Validate().
◆ Validate() [4/5]
| bool CCddInputData::CHitSegment::Validate | ( | void | ) | const |
Validate hit segment.
- Returns
- True if hit segment is valid, false otherwise
Check whether range on query and subject have the same lengths, MSA data is set and corresponds to subject range
Definition at line 766 of file cdd_pssm_input.cpp.
References _ASSERT, ITERATE, CCddInputData::kAlphabetSize, and CCddInputData::m_MsaData.
◆ Validate() [5/5]
| bool CCddInputData::CHit::Validate | ( | void | ) | const |
Validate hit.
- Returns
- True if hit is valid, false otherwise
Definition at line 480 of file cdd_pssm_input.cpp.
◆ WindowMaskerPathGet()
| string WindowMaskerPathGet | ( | ) |
Retrieves the path to the windowmasker data files.
Definition at line 93 of file winmask_filter.cpp.
References s_WINDOW_MASKER_PATH().
Referenced by s_FindPathToWM(), and CBLASTSeqToolJob::x_CreateProjectItems().
◆ WindowMaskerPathInit()
Initialize the path to the windowmasker data files.
- Parameters
-
window_masker_path path to window masker data files [in]
- Returns
- 0 in case of success, 1 if the path does not exist or is a file
Definition at line 77 of file winmask_filter.cpp.
References CDirEntry::eDir, and s_WINDOW_MASKER_PATH().
Referenced by BOOST_AUTO_TEST_CASE(), s_CallAligner(), and CBLASTSeqToolJob::x_CreateProjectItems().
◆ WindowMaskerPathReset()
| void WindowMaskerPathReset | ( | ) |
Resets the path to the windowmasker data files.
Definition at line 88 of file winmask_filter.cpp.
References s_WINDOW_MASKER_PATH().
Referenced by BOOST_AUTO_TEST_CASE().
◆ WindowMaskerTaxidToDb() [1/2]
Get the windowmasker file path for a given taxid and base path.
- Parameters
-
taxid NCBI taxonomy ID to get windowmasker files for [in]
- Returns
- empty string if not found
- Note
- Needed for GBench to ensure MT-safety, it this is not a concern, use the other overloaded version of WindowMaskerTaxidToDb
Definition at line 401 of file winmask_filter.cpp.
References CDirEntry::GetPathSeparator(), NStr::IntToString(), kEmptyStr, and s_WINDOW_MASKER_STAT_FILE_NAME().
◆ WindowMaskerTaxidToDb() [2/2]
Get the windowmasker file path for a given taxid.
- Parameters
-
taxid NCBI taxonomy ID to get windowmasker files for [in]
- Returns
- empty string if not found
Definition at line 411 of file winmask_filter.cpp.
References s_FindPathToWM().
Referenced by Blast_FindWindowMaskerLocTaxId(), and BOOST_AUTO_TEST_CASE().
◆ WrapStruct()
| CStructWrapper<TData>* WrapStruct | ( | TData * | obj, |
| TData *(*)(TData *) | del | ||
| ) |
Auxiliary function to create a CStructWrapper for a pointer to an object.
- Parameters
-
obj pointer to wrap [in] del deallocation function [in]
Definition at line 155 of file setup_factory.hpp.
Referenced by BOOST_AUTO_TEST_CASE(), CBlastTracebackSearch::Run(), CMagicBlast::Run(), CMagicBlast::RunEx(), CTracebackSearchTestFixture::x_GetSampleHspStream(), and CTracebackSearchTestFixture::x_GetSelfHitHspStream().
◆ Write()
| int CBlastHSPListQueueData::Write | ( | BlastHSPList ** | hsp_list | ) |
Write to the queue.
◆ x_AddParameterToProgramOptions() [1/4]
|
private |
Definition at line 682 of file search_strategy.cpp.
References _ASSERT, CExportStrategy::m_QueueSearchRequest, CBlast4_value_Base::SetInteger(), and CBlast4_queue_search_request_Base::SetProgram_options().
Referenced by CExportStrategy::x_Process_Query(), and CExportStrategy::x_Process_SearchDb().
◆ x_AddParameterToProgramOptions() [2/4]
|
private |
Definition at line 731 of file search_strategy.cpp.
References _ASSERT, CExportStrategy::m_QueueSearchRequest, CBlast4_queue_search_request_Base::SetProgram_options(), CBlast4_value_Base::SetString(), and str().
◆ x_AddParameterToProgramOptions() [3/4]
|
private |
Definition at line 696 of file search_strategy.cpp.
References _ASSERT, copy(), CExportStrategy::m_QueueSearchRequest, CBlast4_value_Base::SetInteger_list(), and CBlast4_queue_search_request_Base::SetProgram_options().
◆ x_AddParameterToProgramOptions() [4/4]
|
private |
Definition at line 713 of file search_strategy.cpp.
References _ASSERT, copy(), CExportStrategy::m_QueueSearchRequest, CBlast4_value_Base::SetBig_integer_list(), and CBlast4_queue_search_request_Base::SetProgram_options().
◆ x_AddPsiNumOfIterationsToFormatOptions()
|
private |
Definition at line 745 of file search_strategy.cpp.
References eBlastOpt_Web_StepNumber, CBlast4Field::GetName(), CExportStrategy::m_QueueSearchRequest, CBlast4_queue_search_request_Base::SetFormat_options(), and CBlast4_value_Base::SetInteger().
Referenced by CExportStrategy::CExportStrategy().
◆ x_AdjustProgram()
|
private |
Adjust the EProgram based on option values.
The blast4 protocol uses a notion of program and service to represent the type of search to do. However, for some values of program and service, it is necessary to look at options values in order to determine the precise EProgram value. This is particularly true when dealing with discontiguous megablast for example.
- Parameters
-
L The list of options used for this search. pstr The program string used by the blast4 protocol. program The EProgram suggested by program+service.
- Returns
- The EProgram value as adjusted by options.
◆ x_AnnotateC()
|
private |
Definition at line 1500 of file igblast.cpp.
References eNa_strand_minus, IAlnExplorer::eRight, CSeq_align_set_Base::Get(), CScope::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), CSeq_align_Base::C_Segs::GetDenseg(), CSeq_align_Base::GetSegs(), CSeq_align::GetSeq_id(), CSearchResults::GetSeqAlign(), CAlnMap::GetSeqPosFromSeqPos(), CSeq_align::GetSeqStart(), CSeq_align::GetSeqStop(), CSeq_align::GetSeqStrand(), CSeq_align_set::IsEmpty(), CIgBlast::m_IgOptions, CIgBlastOptions::m_NumAlign, CIgBlast::m_Scope, max(), min(), NON_CONST_ITERATE, CConstRef< C, Locker >::NotEmpty(), and s_MakeTopHitsId().
Referenced by CIgBlast::Run().
◆ x_AnnotateD()
|
private |
Definition at line 1473 of file igblast.cpp.
References CSeq_id::AsFastaString(), CConstRef< C, Locker >::Empty(), CSeq_align_set_Base::Get(), CIgAnnotationInfo::GetFrameOffset(), CSeq_align::GetSeq_id(), CSearchResults::GetSeqAlign(), CSeq_align::GetSeqStart(), CSeq_align::GetSeqStop(), CSeq_align_set::IsEmpty(), CIgBlast::m_AnnotationInfo, CIgBlast::m_IgOptions, CIgBlastOptions::m_NumAlign, NON_CONST_ITERATE, s_MakeTopHitsId(), and s_RemoveLocalPrefix().
Referenced by CIgBlast::Run().
◆ x_AnnotateDJ()
|
private |
Annotate the D and J genes based on blast results.
Definition at line 1595 of file igblast.cpp.
References CSeq_id::AsFastaString(), CSeq_align_set_Base::Get(), CIgAnnotationInfo::GetFrameOffset(), CSeq_align::GetSeq_id(), CSearchResults::GetSeqAlign(), CSeq_align::GetSeqStart(), CSeq_align::GetSeqStop(), CSeq_align_set::IsEmpty(), CIgBlast::m_AnnotationInfo, CIgBlast::m_IgOptions, CIgBlastOptions::m_NumAlign, NON_CONST_ITERATE, CConstRef< C, Locker >::NotEmpty(), s_MakeTopHitsId(), s_RemoveLocalPrefix(), and CIgBlast::x_FillJDomain().
Referenced by CIgBlast::Run().
◆ x_AnnotateDomain()
|
private |
Annotate the query chaintype and domains based on blast results.
Definition at line 1645 of file igblast.cpp.
References abs, CScope::AddBioseq(), IAlnExplorer::eBackwards, eBlastn, eBlastp, IAlnExplorer::eForward, eNa_strand_minus, CSeqDB::eNucleotide, CSeqDB::eProtein, CAlnMap::GetAlnPosFromSeqPos(), CLocalDbAdapter::GetDatabaseName(), CSeq_align_Base::C_Segs::GetDenseg(), CIgAnnotationInfo::GetDomainChainType(), CIgAnnotationInfo::GetDomainInfo(), CIgAnnotationInfo::GetFrameOffset(), CObjectManager::GetInstance(), CAlnMap::GetSeg(), CSeq_align_Base::GetSegs(), CSeq_align::GetSeq_id(), CAlnMap::GetSeqPosFromSeqPos(), CSeq_align::GetSeqStart(), CSeq_align::GetSeqStop(), CSeq_align::GetSeqStrand(), CAlnMap::GetStart(), i, CLocalDbAdapter::IsBlastDb(), ITERATE, CIgBlast::m_AnnotationInfo, CIgAnnotation::m_ChainType, CIgAnnotation::m_ChainTypeToShow, CIgBlastOptions::m_CustomInternalData, CIgBlastOptions::m_Db, CIgAnnotation::m_DomainInfo, CIgAnnotation::m_DomainInfo_S, CIgAnnotation::m_FrameInfo, CIgBlast::m_IgOptions, CIgBlastOptions::m_IsProtein, CIgAnnotation::m_MinusStrand, max(), min(), NcbiEmptyString, query, CScope::RemoveBioseq(), CRef< C, Locker >::Reset(), result, CBl2Seq::RunEx(), s_RemoveLocalPrefix(), CSeqDB::SeqidToBioseq(), and subject.
Referenced by CIgBlast::Run().
◆ x_AnnotateJ()
|
private |
Definition at line 1561 of file igblast.cpp.
References CSeq_id::AsFastaString(), CSeq_align_set_Base::Get(), CIgAnnotationInfo::GetFrameOffset(), CSeq_align::GetSeq_id(), CSearchResults::GetSeqAlign(), CSeq_align::GetSeqStart(), CSeq_align::GetSeqStop(), CSeq_align_set::IsEmpty(), CIgBlast::m_AnnotationInfo, CIgBlast::m_IgOptions, CIgBlastOptions::m_NumAlign, NON_CONST_ITERATE, CConstRef< C, Locker >::NotEmpty(), s_MakeTopHitsId(), s_RemoveLocalPrefix(), and CIgBlast::x_FillJDomain().
Referenced by CIgBlast::Run().
◆ x_AnnotateV()
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private |
Annotate the V gene based on blast results.
Definition at line 839 of file igblast.cpp.
References CSeq_align::GetSeqStart(), CSeq_align::GetSeqStop(), ITERATE, CIgAnnotation::m_GeneInfo, CIgBlast::m_IgOptions, CIgBlastOptions::m_NumAlign, CIgAnnotation::m_TopGeneIds, result, results, and s_MakeTopHitsId().
Referenced by CIgBlast::Run().
◆ x_ApplyInteractions()
|
private |
Apply values directly to BlastOptions object.
This function applies the values of certain blast4 parameter list options to the BlastOptions object. It is called after all other options are set. This design allows options which interact with each other to be handled as a group.
- Parameters
-
boh Blast options handle.
Definition at line 561 of file blast_options_builder.cpp.
References CBlastOptionsBuilder::m_ForceMbIndex, CBlastOptionsBuilder::m_HspRangeMax, CBlastOptionsBuilder::m_MbIndexName, CBlastOptionsBuilder::m_PerformCulling, CBlastOptions::SetCullingLimit(), CBlastOptionsHandle::SetOptions(), and CBlastOptions::SetUseIndex().
Referenced by CBlastOptionsBuilder::GetSearchOptions().
◆ x_AttachValue()
|
inlineprivate |
Definition at line 257 of file blast_options_cxx.cpp.
References CBlastOptionsRemote::m_ReqOpts, and NON_CONST_ITERATE.
Referenced by CBlastOptionsRemote::x_SetOneParam().
◆ x_AutoDetectGeneticCodes()
|
private |
Tries to extract the genetic code using the CScope, if it succeeds, it supercedes what's specified in the {SSeqLoc,CBlastSearchQuery}::genetic_code_id field.
Definition at line 111 of file blast_objmgr_tools.cpp.
References _ASSERT, BLAST_GENETIC_CODE, Blast_QueryIsTranslated(), Blast_SubjectIsTranslated(), CSeqdesc_Base::e_Source, CBlastQueryVector::GetBlastSearchQuery(), CBioSource::GetGenCode(), CBlastOptions::GetQueryGeneticCode(), CSeqdesc_Base::GetSource(), i, CBlastQuerySourceOM::m_Options, CBlastQuerySourceOM::m_Program, CBlastQuerySourceOM::m_QueryVector, CBlastQuerySourceOM::m_TSeqLocVector, NON_CONST_ITERATE, CRef< C, Locker >::NotEmpty(), query, and CBlastQueryVector::Size().
Referenced by CBlastQuerySourceOM::CBlastQuerySourceOM().
◆ x_BioseqSanityCheck()
|
private |
Auxiliary method to do some sanity checks on the input Bioseqs.
- Parameters
-
bs Bioseqs to inspect
Definition at line 419 of file bioseq_extract_data_priv.cpp.
References ENUM_METHOD_NAME, CSeq_inst_Base::eRepr_raw, CEnumeratedTypeValues::FindName(), CBlastQuerySourceBioseqSet::m_IsProt, msg(), and NCBI_THROW.
Referenced by CBlastQuerySourceBioseqSet::CBlastQuerySourceBioseqSet().
◆ x_BioseqSetFromBioseq()
| CRef< CBioseq_set > x_BioseqSetFromBioseq | ( | const CBioseq & | bioseq | ) |
Auxiliary function to convert a CBioseq into a CRef<CBioseq_set>
Definition at line 240 of file objmgrfree_query_data.cpp.
References CSeq_entry_Base::SetSeq(), and CBioseq_set_Base::SetSeq_set().
◆ x_BlastDatabaseOptions_cmp()
| bool x_BlastDatabaseOptions_cmp | ( | const BlastDatabaseOptions * | a, |
| const BlastDatabaseOptions * | b | ||
| ) |
Definition at line 466 of file blast_options_local_priv.cpp.
Referenced by CBlastOptionsLocal::operator==().
◆ x_BlastEffectiveLengthsOptions_cmp()
| bool x_BlastEffectiveLengthsOptions_cmp | ( | const BlastEffectiveLengthsOptions * | a, |
| const BlastEffectiveLengthsOptions * | b | ||
| ) |
Definition at line 492 of file blast_options_local_priv.cpp.
References a, b, min(), and x_safe_memcmp().
Referenced by CBlastOptionsLocal::operator==().
◆ x_BlastScoringOptions_cmp()
| bool x_BlastScoringOptions_cmp | ( | const BlastScoringOptions * | a, |
| const BlastScoringOptions * | b | ||
| ) |
Definition at line 474 of file blast_options_local_priv.cpp.
References a, b, and x_safe_strcmp().
Referenced by CBlastOptionsLocal::operator==().
◆ x_BuildAncillaryData()
|
protected |
Populate the internal m_AncillaryData member.
Definition at line 186 of file bl2seq.cpp.
References ITERATE, CBl2Seq::m_AncillaryData, CBl2Seq::m_Results, r(), and CSearchResultSet::size().
Referenced by CBl2Seq::Run().
◆ x_BuildResultSet()
|
protected |
Definition at line 481 of file magicblast.cpp.
References _ASSERT, BlastQueryInfo::contexts, eFirstSegment, eLastSegment, CSeq_align_set_Base::Get(), ILocalQueryData::GetNumQueries(), CBlastPrelimSearch::GetQueryMasks(), ILocalQueryData::GetSeq_loc(), CMagicBlast::m_BtopSpliceSignals, CMagicBlast::m_InternalData, CMagicBlast::m_LocalDbAdapter, CMagicBlast::m_Options, CMagicBlast::m_PrelimSearch, CMagicBlast::m_Queries, SInternalData::m_QueryInfo, IQueryFactory::MakeLocalQueryData(), CLocalDbAdapter::MakeSeqInfoSrc(), NUM_STRANDS, BlastContextInfo::query_length, CRef< C, Locker >::Reset(), results, BlastContextInfo::segment_flags, CSeq_align_set_Base::Set(), and CMagicBlast::x_CreateSeqAlignSet().
Referenced by CMagicBlast::RunEx().
◆ x_BuildSeqAlignSet()
|
protected |
Definition at line 440 of file magicblast.cpp.
References _ASSERT, CSeq_align_set_Base::Get(), ILocalQueryData::GetNumQueries(), CMagicBlast::m_BtopSpliceSignals, CMagicBlast::m_InternalData, CMagicBlast::m_LocalDbAdapter, CMagicBlast::m_Options, CMagicBlast::m_Queries, SInternalData::m_QueryInfo, IQueryFactory::MakeLocalQueryData(), CLocalDbAdapter::MakeSeqInfoSrc(), CRef< C, Locker >::Reset(), results, CSeq_align_set_Base::Set(), and CMagicBlast::x_CreateSeqAlignSet().
Referenced by CMagicBlast::Run().
◆ x_BuildStdSegList()
Definition at line 402 of file prelim_stage.cpp.
References _TRACE, Blast_HSPResultsFree(), BLASTPrelminSearchHitListToStdSeg(), CBlastPrelimSearch::ComputeBlastHSPResults(), CRef< C, Locker >::Empty(), CBlastOptions::GetGappedMode(), CRef< C, Locker >::GetPointer(), ILocalQueryData::GetSeq_loc(), ILocalQueryData::GetSeqLength(), i, l(), CBlastPrelimSearch::m_DbAdapter, CBlastPrelimSearch::m_DbInfo, SInternalData::m_HspStream, CBlastPrelimSearch::m_InternalData, CBlastPrelimSearch::m_Options, CBlastPrelimSearch::m_QueryFactory, SInternalData::m_ScoreBlk, IQueryFactory::MakeLocalQueryData(), CLocalDbAdapter::MakeSeqInfoSrc(), NULL, BlastHSPStream::program, CRef< C, Locker >::Reset(), results, and s_GetBitScores().
Referenced by CBlastPrelimSearch::Run().
◆ x_CalculateMasks()
|
private |
Performs filtering on the query sequences to calculate the masked locations.
Definition at line 176 of file blast_objmgr_tools.cpp.
References Blast_FindDustFilterLoc(), Blast_FindRepeatFilterLoc(), Blast_FindWindowMaskerLoc(), Blast_QueryIsNucleotide(), Blast_QueryIsTranslated(), CBlastOptions::GetDustFiltering(), CBlastOptions::GetDustFilteringLevel(), CBlastOptions::GetDustFilteringLinker(), CBlastOptions::GetDustFilteringWindow(), CBlastOptions::GetProgramType(), CBlastOptions::GetRepeatFiltering(), CBlastOptions::GetRepeatFilteringDB(), CBlastOptions::GetWindowMaskerDatabase(), CBlastOptions::GetWindowMaskerTaxId(), CBlastQuerySourceOM::m_CalculatedMasks, CBlastQuerySourceOM::m_Options, CBlastQuerySourceOM::m_QueryVector, CBlastQuerySourceOM::m_TSeqLocVector, CRef< C, Locker >::NotEmpty(), and NULL.
Referenced by CBlastQuerySourceOM::GetMask(), and CBlastQuerySourceOM::GetMaskedRegions().
◆ x_CheckConfig()
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private |
Verify that search object contains mandatory fields.
Definition at line 153 of file remote_blast.cpp.
References CRemoteBlast::eProgram, CRemoteBlast::eQueries, CRemoteBlast::eService, CRemoteBlast::eSubject, CRemoteBlast::m_NeedConfig, and NCBI_THROW.
Referenced by CRemoteBlast::GetSearchStrategy(), and CRemoteBlast::x_SendRequest().
◆ x_CheckResults()
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private |
Try to get and process results.
Definition at line 669 of file remote_blast.cpp.
References CRemoteBlast::m_ErrIgn, CRemoteBlast::m_Errs, CRemoteBlast::m_Pending, CRemoteBlast::m_Reply, r(), s_SearchPending(), SleepSec(), CRemoteBlast::x_GetSearchResults(), and CRemoteBlast::x_SearchErrors().
Referenced by CRemoteBlast::CheckDone(), and CRemoteBlast::x_PollUntilDone().
◆ x_CheckResultsDC()
|
private |
Try to get and process results using disk cache.
Definition at line 2396 of file remote_blast.cpp.
References Info(), LOG_POST, CRemoteBlast::m_ErrIgn, CRemoteBlast::m_Errs, CRemoteBlast::m_Pending, CRemoteBlast::m_Reply, r(), s_SearchPending(), SleepSec(), CRemoteBlast::x_GetSearchResultsHTTP(), CRemoteBlast::x_GetSearchStatsOnly(), and CRemoteBlast::x_SearchErrors().
Referenced by CRemoteBlast::CheckDone(), and CRemoteBlast::x_PollUntilDone().
◆ x_ComplementData()
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private |
Complements the data in m_SequenceData in place.
Definition at line 201 of file bioseq_extract_data_priv.cpp.
References _ASSERT, CBlastSeqVectorFromCSeq_data::m_Encoding, CBlastSeqVectorFromCSeq_data::m_SequenceData, CSeqManip::ReverseComplement(), and IBlastSeqVector::size().
Referenced by CBlastSeqVectorFromCSeq_data::x_SetMinusStrand(), and CBlastSeqVectorFromCSeq_data::x_SetPlusStrand().
◆ x_ComputeChunkRanges()
|
private |
Compute all chunk ranges.
Definition at line 135 of file split_query_cxx.cpp.
References _ASSERT, _TRACE, Blast_QueryIsTranslated(), CODON_LENGTH, CBlastOptions::GetProgramType(), CQuerySplitter::m_ChunkSize, CQuerySplitter::m_NumChunks, CQuerySplitter::m_Options, CQuerySplitter::m_SplitBlk, CQuerySplitter::m_TotalQueryLength, CRef< C, Locker >::NotEmpty(), CSplitQueryBlk::SetChunkBounds(), CSplitQueryBlk::SetChunkOverlapSize(), and SplitQuery_GetOverlapChunkSize().
Referenced by CQuerySplitter::Split().
◆ x_ComputeContextOffsets_NonTranslatedQueries()
|
private |
Compute the context offsets which are used to adjust the results for non-translated queries.
Definition at line 580 of file split_query_cxx.cpp.
References _ASSERT, _TRACE, CSplitQueryBlk::AddContextOffsetToChunk(), Blast_QueryIsProtein(), Blast_QueryIsTranslated(), BlastQueryInfo::contexts, ctx, CContextTranslator::GetAbsoluteContext(), CBlastOptions::GetProgramType(), ILocalQueryData::GetQueryInfo(), ILocalQueryData::GetSequenceBlk(), CContextTranslator::GetStartingChunk(), INT4_MAX, is_valid(), kInvalidContext, CQuerySplitter::m_LocalQueryData, CQuerySplitter::m_NumChunks, CQuerySplitter::m_Options, CQuerySplitter::m_QueryChunkFactories, CQuerySplitter::m_SplitBlk, IQueryFactory::MakeLocalQueryData(), min(), BlastContextInfo::query_length, BlastContextInfo::query_offset, s_GetAbsoluteContextLength(), s_IsPlusStrand(), BLAST_SequenceBlk::sequence, and SplitQuery_GetOverlapChunkSize().
Referenced by CQuerySplitter::x_ComputeContextOffsetsForChunks().
◆ x_ComputeContextOffsets_TranslatedQueries()
|
private |
Compute the context offsets which are used to adjust the results for translated queries.
Definition at line 686 of file split_query_cxx.cpp.
References _ASSERT, _TRACE, CSplitQueryBlk::AddContextOffsetToChunk(), Blast_QueryIsProtein(), Blast_QueryIsTranslated(), CODON_LENGTH, BlastQueryInfo::contexts, ctx, CContextTranslator::GetAbsoluteContext(), CSplitQueryBlk::GetContextOffsets(), CQueryDataPerChunk::GetLastChunk(), CBlastOptions::GetProgramType(), ILocalQueryData::GetQueryInfo(), CQueryDataPerChunk::GetQueryLength(), ILocalQueryData::GetSequenceBlk(), CContextTranslator::GetStartingChunk(), INT4_MAX, is_valid(), kInvalidContext, CQuerySplitter::m_LocalQueryData, CQuerySplitter::m_NumChunks, CQuerySplitter::m_Options, CQuerySplitter::m_QueryChunkFactories, CQuerySplitter::m_SplitBlk, IQueryFactory::MakeLocalQueryData(), min(), NUM_FRAMES, BlastContextInfo::query_length, BlastContextInfo::query_offset, s_GetAbsoluteContextLength(), s_IsPlusStrand(), BLAST_SequenceBlk::sequence, and SplitQuery_GetOverlapChunkSize().
Referenced by CQuerySplitter::x_ComputeContextOffsetsForChunks().
◆ x_ComputeContextOffsetsForChunks()
|
private |
Compute the context offsets which are used to adjust the results.
Definition at line 568 of file split_query_cxx.cpp.
References Blast_QueryIsTranslated(), CBlastOptions::GetProgramType(), CQuerySplitter::m_Options, CQuerySplitter::x_ComputeContextOffsets_NonTranslatedQueries(), and CQuerySplitter::x_ComputeContextOffsets_TranslatedQueries().
Referenced by CQuerySplitter::Split().
◆ x_ComputeQueryContextsForChunks()
|
private |
Compute query contexts that correspond to each chunk.
Definition at line 339 of file split_query_cxx.cpp.
References _ASSERT, abort(), CSplitQueryBlk::AddContextToChunk(), Blast_QueryIsNucleotide(), Blast_QueryIsProtein(), Blast_QueryIsTranslated(), BlastSetup_GetStrand(), CODON_LENGTH, ctx, eNa_strand_minus, eNa_strand_plus, GetNumberOfContexts(), CBlastOptions::GetProgramType(), CSplitQueryBlk::GetQueryIndices(), ILocalQueryData::GetSeq_loc(), CBlastOptions::GetStrandOption(), i, kInvalidContext, NMacroArgs::kStrand, CQuerySplitter::m_LocalQueryData, CQuerySplitter::m_NumChunks, CQuerySplitter::m_Options, CQuerySplitter::m_SplitBlk, NUM_FRAMES, NUM_STRANDS, s_AddShift(), and s_GetShiftForTranslatedNegStrand().
Referenced by CQuerySplitter::Split().
◆ x_ComputeQueryIndicesForChunks()
|
private |
Compute query indices that correspond to each chunk.
Definition at line 214 of file split_query_cxx.cpp.
References _ASSERT, _TRACE, CSplitQueryBlk::AddQueryToChunk(), CSeq_id::AsFastaString(), BlastSetup_GetStrand(), Empty(), CSplitQueryBlk::GetChunkBounds(), CSeq_interval_Base::GetFrom(), CSeq_loc::GetId(), CSeq_loc_Base::GetInt(), ILocalQueryData::GetNumQueries(), CBlastOptions::GetProgramType(), ILocalQueryData::GetSeq_loc(), ILocalQueryData::GetSeqLength(), CSeq_loc::GetStrand(), CBlastOptions::GetStrandOption(), CSeq_interval_Base::GetTo(), i, COpenRange< Position >::IntersectingWith(), CSeq_loc_Base::IsInt(), NMacroArgs::kStrand, CQuerySplitter::m_LocalQueryData, CQuerySplitter::m_NumChunks, CQuerySplitter::m_Options, CQuerySplitter::m_Scopes, CQuerySplitter::m_SplitBlk, CQuerySplitter::m_SplitQueriesInChunk, CQuerySplitter::m_UserSpecifiedMasks, CRef< C, Locker >::NotEmpty(), s_SetSplitQuerySeqInterval(), CSeq_loc::SetId(), and CSeq_loc::SetStrand().
Referenced by CQuerySplitter::Split().
◆ x_ContextInChunkToQueryIndex()
|
private |
Convert a context in a chunk to a query index (within the chunk)
- Parameters
-
context_in_chunk context number [in]
- Returns
- query index
Definition at line 354 of file split_query_aux_priv.cpp.
References _ASSERT, Blast_GetQueryIndexFromContext(), and CQueryDataPerChunk::m_Program.
Referenced by CQueryDataPerChunk::GetLastChunk(), and CQueryDataPerChunk::GetQueryLength().
◆ x_ConvertResultType()
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private |
Convert bl2seq result to database search mode.
Definition at line 1948 of file igblast.cpp.
References ctll::empty(), eSequenceComparison, CSearchResults::GetAncillaryData(), CBlastQueryVector::GetBlastSearchQuery(), CSearchResults::GetErrors(), CSearchResults::GetSeqAlign(), CSearchResults::GetSeqId(), GetSeqId(), CIgBlast::m_Query, CSeq_id::Match(), CSearchResultSet::push_back(), r(), CRef< C, Locker >::Reset(), result, CSeq_align_set_Base::Set(), and CBlastQueryVector::Size().
Referenced by CIgBlast::Run().
◆ x_Copy_CBlastDatabaseOptions()
|
staticprivate |
Get a copy of CBlastDatabaseOptions.
- Parameters
-
dbOptsDst options structure to copy to. dbOptsSrc options structure to copy from.
Definition at line 304 of file blast_options_local_priv.cpp.
References BlastMemDup(), CBlastDatabaseOptions::Get(), and CBlastDatabaseOptions::Reset().
Referenced by CBlastOptionsLocal::x_DoDeepCopy().
◆ x_Copy_CBlastEffectiveLengthsOptions()
|
staticprivate |
Get a copy of CBlastEffectiveLengthsOptions.
- Parameters
-
effLenOptsDst options structure to copy to. effLenOptsSrc options structure to copy from.
Definition at line 325 of file blast_options_local_priv.cpp.
References BlastMemDup(), CBlastEffectiveLengthsOptions::Get(), BlastEffectiveLengthsOptions::num_searchspaces, CBlastEffectiveLengthsOptions::Reset(), and BlastEffectiveLengthsOptions::searchsp_eff.
Referenced by CBlastOptionsLocal::x_DoDeepCopy().
◆ x_Copy_CBlastExtensionOptions()
|
staticprivate |
Get a copy of CBlastExtensionOptions.
- Parameters
-
extnOptsDst options structure to copy to. extnOptsSrc options structure to copy from.
Definition at line 237 of file blast_options_local_priv.cpp.
References BlastMemDup(), CBlastExtensionOptions::Get(), and CBlastExtensionOptions::Reset().
Referenced by CBlastOptionsLocal::x_DoDeepCopy().
◆ x_Copy_CBlastHitSavingOptions()
|
staticprivate |
Get a copy of CBlastHitSavingOptions.
- Parameters
-
hitSaveOptsDst options structure to copy to. hitSaveOptsSrc options structure to copy from.
Definition at line 249 of file blast_options_local_priv.cpp.
References BlastHSPFilteringOptions::best_hit, BlastMemDup(), BlastHSPFilteringOptions::culling_opts, CBlastHitSavingOptions::Get(), BlastHitSavingOptions::hsp_filt_opt, NULL, and CBlastHitSavingOptions::Reset().
Referenced by CBlastOptionsLocal::x_DoDeepCopy().
◆ x_Copy_CBlastInitialWordOptions()
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staticprivate |
Get a copy of CBlastInitialWordOptions.
- Parameters
-
initWordOptsDst options structure to copy to. initWordOptsSrc options structure to copy from.
Definition at line 225 of file blast_options_local_priv.cpp.
References BlastMemDup(), CBlastInitialWordOptions::Get(), and CBlastInitialWordOptions::Reset().
Referenced by CBlastOptionsLocal::x_DoDeepCopy().
◆ x_Copy_CBlastScoringOptions()
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staticprivate |
Get a copy of CBlastScoringOptions.
- Parameters
-
scoringOptsDst options structure to copy to. scoringOptsSrc options structure to copy from.
Definition at line 316 of file blast_options_local_priv.cpp.
References BlastScoringOptionsDup(), CBlastScoringOptions::Get(), NULL, and CBlastScoringOptions::Reset().
Referenced by CBlastOptionsLocal::x_DoDeepCopy().
◆ x_Copy_CLookupTableOptions()
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staticprivate |
Get a copy of CLookupTableOptions.
- Parameters
-
lutOptsDst options structure to copy to. lutOptsSrc options structure to copy from.
Definition at line 207 of file blast_options_local_priv.cpp.
References BlastMemDup(), CLookupTableOptions::Get(), LookupTableOptions::phi_pattern, CLookupTableOptions::Reset(), and strdup.
Referenced by CBlastOptionsLocal::x_DoDeepCopy().
◆ x_Copy_CPSIBlastOptions()
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staticprivate |
Get a copy of CPSIBlastOptions.
- Parameters
-
psiBlastOptsDst options structure to copy to. psiBlastOptsSrc options structure to copy from.
Definition at line 292 of file blast_options_local_priv.cpp.
References BlastMemDup(), CPSIBlastOptions::Get(), and CPSIBlastOptions::Reset().
Referenced by CBlastOptionsLocal::x_DoDeepCopy().
◆ x_Copy_CQuerySetUpOptions()
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staticprivate |
Get a copy of CQuerySetUpOptions.
- Parameters
-
queryOptsDst options structure to copy to. queryOptsSrc options structure to copy from.
Definition at line 120 of file blast_options_local_priv.cpp.
References BlastMemDup(), SRepeatFilterOptions::database, SWindowMaskerOptions::database, SBlastFilterOptions::dustOptions, QuerySetUpOptions::filter_string, QuerySetUpOptions::filtering_options, CQuerySetUpOptions::Get(), NULL, SBlastFilterOptions::readQualityOptions, SBlastFilterOptions::repeatFilterOptions, CQuerySetUpOptions::Reset(), SBlastFilterOptions::segOptions, strdup, and SBlastFilterOptions::windowMaskerOptions.
Referenced by CBlastOptionsLocal::x_DoDeepCopy().
◆ x_CopyQueryToMsa() [1/2]
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private |
Copies query sequence data to multiple alignment data structure.
Definition at line 311 of file msa_pssm_input.cpp.
References _ASSERT, PSIMsa::data, AutoPtr< X, Del >::get(), CPsiBlastInputClustalW::GetQueryLength(), PSIMsaCell::is_aligned, isupper(), ITERATE, kGapChar(), kQueryIndex, PSIMsaCell::letter, CPsiBlastInputClustalW::m_AsciiMsa, CPsiBlastInputClustalW::m_Msa, CPsiBlastInputClustalW::m_Query, and true.
Referenced by CPsiBlastInputClustalW::Process().
◆ x_CopyQueryToMsa() [2/2]
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private |
Copies query sequence data to multiple alignment data structure.
Definition at line 283 of file psi_pssm_input.cpp.
References _ASSERT, PSIMsa::data, CPsiBlastInputData::GetQueryLength(), i, PSIMsaCell::is_aligned, kQueryIndex, PSIMsaCell::letter, CPsiBlastInputData::m_Msa, and CPsiBlastInputData::m_Query.
Referenced by CPsiBlastInputData::Process().
◆ x_CountAndSelectQualifyingAlignments()
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private |
Examines the sequence alignment and keeps track of those hits which have an HSP with an e-value below the inclusion threshold specified in the PSIBlastOptions structure.
- Returns
- number of hits which qualify for constructing the multiple sequence alignment structure
Definition at line 178 of file psi_pssm_input.cpp.
References PSIBlastOptions::inclusion_ethresh, CPsiBlastInputData::m_Opts, CPsiBlastInputData::m_SeqAlignSet, proc, and set< Key, Compare >::size().
Referenced by CPsiBlastInputData::Process().
◆ x_CreateMsa()
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protected |
Create multiple alignment of CDs.
Definition at line 240 of file cdd_pssm_input.cpp.
References PSICdMsaCell::data, i, int, PSICdMsaCell::is_aligned, CCddInputData::m_CddData, CCddInputData::m_Hits, CCddInputData::m_Msa, CCddInputData::m_MsaData, CCddInputData::m_QueryData, PSICdMsa::msa, NCBI_THROW, NON_CONST_ITERATE, and NULL.
Referenced by CCddInputData::Process().
◆ x_CreatePssmFromCDD()
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private |
Using IPssmInputCdd as a delegate to provide data in the form of multiple alignment of CDs, creates PSSM using the CORE C PSSM engine API.
Definition at line 412 of file pssm_engine.cpp.
References _ASSERT, IPssmInputCdd::GetData(), IPssmInputCdd::GetDiagnosticsRequest(), IPssmInput_Base::GetMatrixName(), IPssmInputCdd::GetOptions(), IPssmInput_Base::GetQueryForPssm(), CPssmEngine::m_PssmInputCdd, CPssmEngine::m_ScoreBlk, msg(), NCBI_THROW, IPssmInputCdd::Process(), PSI_SUCCESS, PSICreatePssmFromCDD(), query, s_Validate(), CPssmWithParameters::SetQuery(), CSeq_entry_Base::SetSeq(), CPssmEngine::x_ErrorCodeToString(), and CPssmEngine::x_PSIMatrix2Asn1().
Referenced by CPssmEngine::Run().
◆ x_CreatePssmFromFreqRatios()
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private |
Using IPssmInputFreqRatios as a delegate to provide the input PSSM's frequency ratios, creates a PSSM using the CORE C PSSM engine API.
Definition at line 340 of file pssm_engine.cpp.
References _ASSERT, IPssmInputFreqRatios::GetData(), IPssmInputFreqRatios::GetImpalaScaleFactor(), IPssmInput_Base::GetMatrixName(), IPssmInput_Base::GetQuery(), IPssmInput_Base::GetQueryForPssm(), IPssmInput_Base::GetQueryLength(), CPssmEngine::m_PssmInputFreqRatios, CPssmEngine::m_ScoreBlk, msg(), NCBI_THROW, IPssmInputFreqRatios::Process(), PSI_SUCCESS, PSICreatePssmFromFrequencyRatios(), query, s_Validate(), CPssmWithParameters::SetQuery(), CSeq_entry_Base::SetSeq(), CPssmEngine::x_ErrorCodeToString(), and CPssmEngine::x_PSIMatrix2Asn1().
Referenced by CPssmEngine::Run().
◆ x_CreatePssmFromMsa()
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private |
Using IPssmInputData as a delegate to provide input data in the form of a multiple sequence alignment, creates a PSSM using the CORE C PSSM engine API.
Definition at line 376 of file pssm_engine.cpp.
References _ASSERT, IPssmInputData::GetData(), IPssmInputData::GetDiagnosticsRequest(), IPssmInput_Base::GetMatrixName(), IPssmInputData::GetOptions(), IPssmInput_Base::GetQueryForPssm(), CPssmEngine::m_PssmInput, CPssmEngine::m_ScoreBlk, msg(), NCBI_THROW, IPssmInputData::Process(), PSI_SUCCESS, PSICreatePssmWithDiagnostics(), query, s_Validate(), CPssmWithParameters::SetQuery(), CSeq_entry_Base::SetSeq(), CPssmEngine::x_ErrorCodeToString(), and CPssmEngine::x_PSIMatrix2Asn1().
Referenced by CPssmEngine::Run().
◆ x_CreatePssmScoresFromFrequencyRatios()
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private |
Computes the PSSM scores in case these are not available in the PSSM.
Definition at line 105 of file psiblast_impl.cpp.
References CBlastOptionsHandle::GetOptions(), CPsiBlastImpl::m_OptsHandle, CPsiBlastImpl::m_Pssm, and PsiBlastComputePssmScores().
◆ x_CreateSeqAlignSet()
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staticprotected |
Create results.
Definition at line 393 of file magicblast.cpp.
References CreateEmptySeq_align_set(), CSeq_align_Base::eType_partial, HSPChain::next, CRef< C, Locker >::Reset(), s_CreateSeqAlign(), CSeq_align_set_Base::Set(), CSeq_align_Base::SetDim(), CSeq_align_Base::SetSegs(), and CSeq_align_Base::SetType().
Referenced by CMagicBlast::x_BuildResultSet(), and CMagicBlast::x_BuildSeqAlignSet().
◆ x_DefaultTimeout()
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private |
The default timeout is 3.5 hours.
Definition at line 1635 of file remote_blast.cpp.
References int.
Referenced by CRemoteBlast::SubmitSync(), and CRemoteBlast::x_GetRequestInfoFromRID().
◆ x_DoDeepCopy() [1/3]
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private |
Perform a "deep copy" of Blast options.
- Parameters
-
opts Blast options object to copy from.
Definition at line 2721 of file blast_options_cxx.cpp.
References CBlastOptions::m_DefaultsMode, CBlastOptions::m_Local, CBlastOptions::m_ProgramName, CBlastOptions::m_Remote, and CBlastOptions::m_ServiceName.
Referenced by CBlastOptions::Clone().
◆ x_DoDeepCopy() [2/3]
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private |
Perform a "deep copy" of local Blast options.
- Parameters
-
optsLocal local Blast options object to copy from.
Definition at line 85 of file blast_options_local_priv.cpp.
References CBlastOptionsLocal::m_DbOpts, CBlastOptionsLocal::m_DeltaBlastOpts, CBlastOptionsLocal::m_EffLenOpts, CBlastOptionsLocal::m_ExtnOpts, CBlastOptionsLocal::m_ForceMBIndex, CBlastOptionsLocal::m_HitSaveOpts, CBlastOptionsLocal::m_InitWordOpts, CBlastOptionsLocal::m_LutOpts, CBlastOptionsLocal::m_MBIndexLoaded, CBlastOptionsLocal::m_MBIndexName, CBlastOptionsLocal::m_Program, CBlastOptionsLocal::m_PSIBlastOpts, CBlastOptionsLocal::m_QueryOpts, CBlastOptionsLocal::m_ScoringOpts, CBlastOptionsLocal::m_UseMBIndex, CBlastOptionsLocal::x_Copy_CBlastDatabaseOptions(), CBlastOptionsLocal::x_Copy_CBlastEffectiveLengthsOptions(), CBlastOptionsLocal::x_Copy_CBlastExtensionOptions(), CBlastOptionsLocal::x_Copy_CBlastHitSavingOptions(), CBlastOptionsLocal::x_Copy_CBlastInitialWordOptions(), CBlastOptionsLocal::x_Copy_CBlastScoringOptions(), CBlastOptionsLocal::x_Copy_CLookupTableOptions(), CBlastOptionsLocal::x_Copy_CPSIBlastOptions(), and CBlastOptionsLocal::x_Copy_CQuerySetUpOptions().
Referenced by CBlastOptionsLocal::CBlastOptionsLocal(), and CBlastOptionsLocal::operator=().
◆ x_DoDeepCopy() [3/3]
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inlineprivate |
Perform a "deep copy" of remote Blast options.
- Parameters
-
optsRemote remote Blast options object to copy from.
Definition at line 157 of file blast_options_cxx.cpp.
References CBlastOptionsRemote::m_DefaultsMode, CBlastOptionsRemote::m_ReqOpts, and CRef< C, Locker >::Reset().
Referenced by CBlastOptionsRemote::CBlastOptionsRemote(), and CBlastOptionsRemote::operator=().
◆ x_DoDestroy()
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private |
Deallocates the structure owned by this class.
Definition at line 133 of file rps_aux.cpp.
References BlastRPSAuxInfo::karlin_k, CBlastRPSAuxInfo::m_Data, NULL, BlastRPSAuxInfo::orig_score_matrix, and sfree.
Referenced by CBlastRPSAuxInfo::CBlastRPSAuxInfo(), and CBlastRPSAuxInfo::~CBlastRPSAuxInfo().
◆ x_Encoding_CSeq_data2CSeqUtil()
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private |
Auxiliary function to map the description of the encoding in CSeq_data::EChoice to CSeqUtil::ECoding.
Definition at line 210 of file bioseq_extract_data_priv.cpp.
References CSeq_data_Base::e_Ncbi2na, CSeqUtil::e_Ncbi2na_expand, CSeq_data_Base::e_Ncbi4na, CSeqUtil::e_Ncbi4na_expand, CSeq_data_Base::e_Ncbistdaa, CSeqUtil::e_Ncbistdaa, NCBI_CURRENT_FUNCTION, and NCBI_THROW.
Referenced by CBlastSeqVectorFromCSeq_data::SetCoding().
◆ x_ErrorCodeToString()
Convert a PSSM return status into a string.
- Parameters
-
error_code return value of a PSSM engine function as defined in blast_psi_priv.h [in]
- Returns
- string containing a description of the error
Definition at line 218 of file pssm_engine.cpp.
References NStr::IntToString(), PSI_SUCCESS, PSIERR_BADPARAM, PSIERR_BADPROFILE, PSIERR_BADSEQWEIGHTS, PSIERR_COLUMNOFGAPS, PSIERR_ENDINGGAP, PSIERR_GAPINQUERY, PSIERR_NOALIGNEDSEQS, PSIERR_NOFREQRATIOS, PSIERR_OUTOFMEM, PSIERR_POSITIVEAVGSCORE, PSIERR_STARTINGGAP, and PSIERR_UNALIGNEDCOLUMN.
Referenced by CPssmEngine::x_CreatePssmFromCDD(), CPssmEngine::x_CreatePssmFromFreqRatios(), CPssmEngine::x_CreatePssmFromMsa(), and CPssmCreateTestFixture::x_ErrorCodeToString().
◆ x_ExtendAlign3end()
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private |
Definition at line 275 of file igblast.cpp.
References eNa_strand_minus, eNa_strand_plus, CSeq_align::eScore_Score, extend_length3end, CScope::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), CIgBlast::m_Scope, min(), NON_CONST_ITERATE, result, and results.
Referenced by CIgBlast::Run().
◆ x_ExtendAlign5end()
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private |
Definition at line 190 of file igblast.cpp.
References count, eNa_strand_minus, eNa_strand_plus, CSeq_align::eScore_Score, extend_length5end, CScope::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), CIgBlast::m_Scope, min(), NON_CONST_ITERATE, result, and results.
Referenced by CIgBlast::Run().
◆ x_ExtractAlignmentData() [1/2]
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private |
Populates the multiple alignment data structure.
Definition at line 330 of file msa_pssm_input.cpp.
References _ASSERT, AMINOACID_TO_NCBISTDAA, PSIMsa::data, PSIMsa::dimensions, AutoPtr< X, Del >::get(), i, int, PSIMsaCell::is_aligned, isalpha(), kGapChar(), kQueryIndex, PSIMsaCell::letter, CPsiBlastInputClustalW::m_AsciiMsa, CPsiBlastInputClustalW::m_Msa, CPsiBlastInputClustalW::m_Query, NCBISTDAA_TO_AMINOACID, PSIMsaDimensions::num_seqs, PSIMsaDimensions::query_length, and toupper().
Referenced by CPsiBlastInputClustalW::Process().
◆ x_ExtractAlignmentData() [2/2]
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private |
Populates the multiple alignment data structure.
Definition at line 294 of file psi_pssm_input.cpp.
References _ASSERT, GetLowestEvalue(), CPsiBlastInputData::GetNumAlignedSequences(), PSIBlastOptions::inclusion_ethresh, ITERATE, kQueryIndex, CPsiBlastInputData::m_Opts, CPsiBlastInputData::m_SeqAlignSet, CSeq_id::Match(), NULL, and CPsiBlastInputData::x_ProcessDenseg().
Referenced by CPsiBlastInputData::Process().
◆ x_ExtractCScopesAndMasks()
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private |
Auxiliary method to extract the CScope objects from the query factory.
Definition at line 113 of file split_query_cxx.cpp.
References _ASSERT, CObjMgr_QueryFactory::ExtractScopes(), CObjMgr_QueryFactory::ExtractUserSpecifiedMasks(), ILocalQueryData::GetNumQueries(), CQuerySplitter::m_LocalQueryData, CQuerySplitter::m_NumChunks, CQuerySplitter::m_QueryFactory, CQuerySplitter::m_Scopes, CQuerySplitter::m_UserSpecifiedMasks, CRef< C, Locker >::NotEmpty(), and NULL.
◆ x_ExtractQueryForPssm() [1/3]
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private |
Extracts the query bioseq from m_SeqEntry.
Definition at line 183 of file msa_pssm_input.cpp.
References _ASSERT, Begin(), CRef< C, Locker >::Empty(), AutoPtr< X, Del >::get(), CPsiBlastInputClustalW::GetQueryLength(), CPsiBlastInputClustalW::m_Query, CPsiBlastInputClustalW::m_QueryBioseq, CPsiBlastInputClustalW::m_SeqEntry, CRef< C, Locker >::NotEmpty(), CRef< C, Locker >::Reset(), s_AreSequencesEqual(), and s_GetQuerySequenceData().
Referenced by CPsiBlastInputClustalW::Process().
◆ x_ExtractQueryForPssm() [2/3]
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private |
Extracts the query bioseq from m_SeqAlignSet.
Definition at line 144 of file psi_pssm_input.cpp.
References _ASSERT, CSeq_inst_Base::eMol_aa, CRef< C, Locker >::Empty(), CSeq_inst_Base::eRepr_raw, CPsiBlastInputData::GetQueryLength(), CSeq_align::GetSeq_id(), i, CPsiBlastInputData::m_Query, CPsiBlastInputData::m_QueryBioseq, CPsiBlastInputData::m_QueryTitle, CPsiBlastInputData::m_SeqAlignSet, CRef< C, Locker >::NotEmpty(), CConstRef< C, Locker >::NotEmpty(), CRef< C, Locker >::Reset(), CAliasBase< TPrim >::Set(), and CSeqdesc_Base::SetTitle().
Referenced by CPsiBlastInputData::Process().
◆ x_ExtractQueryForPssm() [3/3]
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protected |
Create query as Bioseq.
Definition at line 441 of file cdd_pssm_input.cpp.
References _ASSERT, CSeq_inst_Base::eMol_aa, CRef< C, Locker >::Empty(), CSeq_inst_Base::eRepr_raw, CCddInputData::GetQueryLength(), CSeq_align::GetSeq_id(), i, CCddInputData::m_QueryBioseq, CCddInputData::m_QueryData, CCddInputData::m_QueryTitle, CCddInputData::m_SeqalignSet, CRef< C, Locker >::NotEmpty(), CConstRef< C, Locker >::NotEmpty(), CRef< C, Locker >::Reset(), CAliasBase< TPrim >::Set(), and CSeqdesc_Base::SetTitle().
Referenced by CCddInputData::Process().
◆ x_ExtractQueryFromMsa()
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private |
Extracts the query sequence from the multiple sequence alignment, assuming it's the first one, into m_Query.
- Postcondition
- m_Query is not NULL and m_MsaDimensions.query_length is assigned
Definition at line 274 of file msa_pssm_input.cpp.
References _ASSERT, AMINOACID_TO_NCBISTDAA, AutoPtr< X, Del >::get(), isalpha(), ITERATE, kGapChar(), kQuery, CPsiBlastInputClustalW::m_AsciiMsa, CPsiBlastInputClustalW::m_MsaDimensions, CPsiBlastInputClustalW::m_Query, NCBI_THROW, NULL, PSIMsaDimensions::query_length, AutoPtr< X, Del >::reset(), and toupper().
◆ x_ExtractQueryFromPssm()
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private |
Auxiliary function to get the query sequence data from the ASN.1 PSSM Post-condition: (m_Query.Empty() == false)
Definition at line 115 of file psiblast_impl.cpp.
References CPsiBlastImpl::m_Pssm, CPsiBlastImpl::m_Query, and CRef< C, Locker >::Reset().
◆ x_ExtractQueryIds()
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private |
Extract the query IDs from the CBlast4_queries for a given search.
- Parameters
-
query_ids the query IDs to be returned [in|out]
Definition at line 2090 of file remote_blast.cpp.
References _ASSERT, CSeq_id::BestRank(), FindBestChoice(), CBlast4_queries_Base::GetBioseq_set(), CBioseq_Base::GetId(), CBlast4_queries::GetNumQueries(), CBlast4_queries_Base::GetPssm(), CRemoteBlast::GetQueries(), CPssmWithParameters::GetQuery(), CSeq_entry_Base::GetSeq(), CBlast4_queries_Base::GetSeq_loc_list(), CSeq_entry_Base::GetSet(), i, CBlast4_queries_Base::IsBioseq_set(), CBlast4_queries_Base::IsPssm(), CSeq_entry_Base::IsSeq(), CBlast4_queries_Base::IsSeq_loc_list(), CSeq_entry_Base::IsSet(), ITERATE, and s_ExtractQueryIdsFromBioseqSet().
Referenced by CRemoteBlast::GetResultSet(), and CRemoteBlast::GetSeqAlignSets().
◆ x_ExtractUserSpecifiedMasks()
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private |
Extract the user specified masking locations from the query factory.
- Note
- this method only extracts masking locations for CObjMgr_QueryFactory objects, for other types use the SetQueries method
- Parameters
-
query_factory source of query sequence data [in] masks masking locations extracted [out]
Definition at line 1369 of file remote_blast.cpp.
References CObjMgr_QueryFactory::ExtractUserSpecifiedMasks(), and NULL.
Referenced by CRemoteBlast::x_InitQueries().
◆ x_FillHitsData()
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protected |
Read data needed for PSSM computation from CDD and populate arrays.
Definition at line 221 of file cdd_pssm_input.cpp.
References _ASSERT, CSeqDB::eProtein, CBlastRPSInfo::fDeltaBlast, CCddInputData::m_DbName, CCddInputData::m_Hits, and NON_CONST_ITERATE.
Referenced by CCddInputData::Process().
◆ x_FillJDomain()
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private |
Definition at line 1238 of file igblast.cpp.
References CSeq_id::AsFastaString(), eNa_strand_minus, IAlnExplorer::eRight, CScope::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), CSeq_align_Base::C_Segs::GetDenseg(), CIgAnnotationInfo::GetFwr4EndOffset(), CIgAnnotationInfo::GetJDomain(), CSeq_align_Base::GetSegs(), CSeq_align::GetSeq_id(), CAlnMap::GetSeqPosFromSeqPos(), CSeq_align::GetSeqStart(), CSeq_align::GetSeqStop(), CSeq_align::GetSeqStrand(), CIgBlast::m_AnnotationInfo, CIgAnnotation::m_JDomain, CIgBlast::m_Scope, max(), min(), and s_RemoveLocalPrefix().
Referenced by CIgBlast::x_AnnotateDJ(), and CIgBlast::x_AnnotateJ().
◆ x_FillObservations()
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private |
Populate arrays of effective numbers of observations.
- Parameters
-
db_oid Subject index in CDD [in] profile_data Object accessing data in CDD [in]
Definition at line 851 of file cdd_pssm_input.cpp.
References _ASSERT, data, fabs, i, CCddInputData::kRpsScaleFactor, CCddInputData::m_MsaData, BlastRPSProfileHeader::num_profiles, offsets, BlastRPSProfileHeader::start_offsets, and val.
◆ x_FillResidueCounts()
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private |
Populate arrays of weighted residue counts.
- Parameters
-
db_oid Subject index in CDD [in] profile_data Object accessing data in CDD [in]
Definition at line 804 of file cdd_pssm_input.cpp.
References _ASSERT, i, int, CCddInputData::kAlphabetSize, CCddInputData::m_MsaData, BlastRPSProfileHeader::num_profiles, and BlastRPSProfileHeader::start_offsets.
◆ x_FindDbInfoFromAvailableDatabases()
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private |
Look for a database matching this method's argument and returned detailed information about it.
- Parameters
-
blastdb database description
- Returns
- detailed information about the database requested or an empty CRef<> if the database was not found
Definition at line 371 of file blast_services.cpp.
References _ASSERT, ITERATE, CBlastServices::m_AvailableDatabases, and CRef< C, Locker >::NotEmpty().
Referenced by CBlastServices::GetDatabaseInfo().
◆ x_FindDJ()
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private |
Definition at line 1169 of file igblast.cpp.
References CSerialObject::Assign(), CSeq_align::eScore_Score, CSeq_align_set_Base::Get(), CSearchResults::GetSeqAlign(), CSearchResults::HasAlignments(), CIgAnnotation::m_ChainType, CRef< C, Locker >::NotEmpty(), CRef< C, Locker >::Reset(), and CIgBlast::x_FindDJAln().
Referenced by CIgBlast::x_ProcessDJResult().
◆ x_FindDJAln()
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private |
Definition at line 972 of file igblast.cpp.
References CSeq_id::eContent, CSeq_align_set_Base::Get(), CIgAnnotationInfo::GetDJChainType(), CSeq_align_set::IsEmpty(), ITERATE, j_wordsize, CIgBlast::m_AnnotationInfo, CIgBlastOptions::m_D_penalty, CIgBlastOptions::m_DetectOverlap, CIgBlast::m_IgOptions, CIgBlastOptions::m_J_penalty, CIgBlastOptions::m_Min_D_match, CIgBlast::m_Scope, max_allowed_j_deletion, max_allowed_VD_distance, max_allowed_VJ_distance_with_D, max_allowed_VJ_distance_without_D, CRef< C, Locker >::NotEmpty(), s_CompareSeqAlignByScore(), s_CompareSeqAlignByScoreAndName(), s_DJNotCompatible(), CSeq_align_set_Base::Set(), and NStr::ToUpper().
Referenced by CIgBlast::x_FindDJ().
◆ x_FindDomainHits()
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protected |
Search domain database.
- Returns
- Domain database search results
Definition at line 195 of file deltablast.cpp.
References CBlastOptionsFactory::Create(), eRPSBlast, CDeltaBlastOptionsHandle::GetDomainInclusionThreshold(), CRef< C, Locker >::GetNonNullPointer(), CDeltaBlast::m_DomainDb, CDeltaBlast::m_Options, CDeltaBlast::m_Queries, CDeltaBlast::m_RpsOptions, CRef< C, Locker >::NotEmpty(), CRef< C, Locker >::Reset(), CLocalBlast::Run(), CBlastOptionsHandle::SetEvalueThreshold(), and CBlastOptionsHandle::SetFilterString().
Referenced by CDeltaBlast::Run().
◆ x_FixStrand()
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inlineprotected |
If the Seq-loc is on the minus strand and the user is asking for the minus strand, we change the user's request to the plus strand.
If we did not do this, we would get the plus strand (ie it would be reversed twice)
- Parameters
-
strand strand to handle [in|out]
Definition at line 554 of file blast_objmgr_tools.cpp.
References eNa_strand_minus, eNa_strand_plus, CSeq_loc::GetStrand(), and CBlastSeqVectorOM::m_SeqLoc.
Referenced by CBlastSeqVectorOM::GetStrandData(), and CBlastSeqVectorOM::x_SetStrand().
◆ x_GetAvailableDatabases()
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private |
Retrieve the BLAST databases available for searching.
Definition at line 406 of file blast_services.cpp.
References client, CBlastServices::m_AvailableDatabases, and NCBI_THROW.
Referenced by CBlastServices::GetDatabaseInfo(), and CBlastServices::GetOrganismSpecificRepeatsDatabases().
◆ x_GetBlast4SearchRequestBody()
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private |
Retrieve the request body for a search submission.
Definition at line 626 of file remote_blast.cpp.
References CRef< C, Locker >::Empty(), CRemoteBlast::m_Errs, CRemoteBlast::m_QSR, CRef< C, Locker >::Reset(), CBlast4_request_body_Base::SetQueue_search(), CRemoteBlast::x_QueryMaskingLocationsToNetwork(), and CRemoteBlast::x_SetAlgoOpts().
Referenced by CRemoteBlast::GetSearchStrategy(), and CRemoteBlast::x_SubmitSearch().
◆ x_GetGapExistence()
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private |
Private interface to retrieve gap existence cost from data source.
Definition at line 609 of file pssm_engine.cpp.
References IPssmInput_Base::GetGapExistence(), CPssmEngine::m_PssmInput, and CPssmEngine::m_PssmInputFreqRatios.
Referenced by CPssmEngine::CPssmEngine().
◆ x_GetGapExtension()
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private |
Private interface to retrieve gap extension cost from data source.
Definition at line 617 of file pssm_engine.cpp.
References IPssmInput_Base::GetGapExtension(), CPssmEngine::m_PssmInput, and CPssmEngine::m_PssmInputFreqRatios.
Referenced by CPssmEngine::CPssmEngine().
◆ x_GetGSRR()
|
private |
Poll until done, return the CBlast4_get_search_results_reply.
- Returns
- Pointer to GSR reply object or NULL if search failed.
Definition at line 373 of file remote_blast.cpp.
References CRemoteBlast::m_Archive, CRemoteBlast::m_ReadFile, CRemoteBlast::m_Reply, CRef< C, Locker >::NotEmpty(), NULL, and CRemoteBlast::SubmitSync().
Referenced by CRemoteBlast::GetAlignments(), CRemoteBlast::GetKABlocks(), CRemoteBlast::GetPhiAlignments(), CRemoteBlast::GetPSSM(), CRemoteBlast::GetSearchStats(), and CRemoteBlast::x_GetMasks().
◆ x_GetMasks()
|
private |
Get the query masks from the results.
- Returns
- list of references to Blast4_mask object.
Definition at line 548 of file remote_blast.cpp.
References CRemoteBlast::x_GetGSRR().
Referenced by CRemoteBlast::GetMasks().
◆ x_GetMatrixName()
|
private |
Private interface to retrieve matrix name from its data source interface.
Definition at line 601 of file pssm_engine.cpp.
References IPssmInput_Base::GetMatrixName(), CPssmEngine::m_PssmInput, and CPssmEngine::m_PssmInputFreqRatios.
Referenced by CPssmEngine::CPssmEngine().
◆ x_GetPatternRanges()
|
private |
Definition at line 199 of file seedtop.cpp.
References len, CSeedTop::m_Units, NCBISTDAA_TO_AMINOACID, and test.
Referenced by CSeedTop::Run().
◆ x_GetProgramOptionIntegerList()
|
private |
Definition at line 264 of file search_strategy.cpp.
References CBlast4Field::GetName(), CImportStrategy::GetProgramOptions(), CRef< C, Locker >::NotEmpty(), and NULL.
Referenced by CImportStrategy::GetNegativeTaxidList(), and CImportStrategy::GetTaxidList().
◆ x_GetPsiIterationsFromServer()
|
private |
Definition at line 2664 of file remote_blast.cpp.
References kBlast4SearchInfoReqName_Search, kBlast4SearchInfoReqValue_PsiIterationNum, CRemoteBlast::m_RID, s_BuildSearchInfoRequest(), NStr::StringToUInt(), CRemoteBlast::x_GetStringFromSearchInfoReply(), and CRemoteBlast::x_SendRequest().
Referenced by CRemoteBlast::GetPsiNumberOfIterations().
◆ x_GetQuery()
|
private |
Private interface to retrieve query sequence from its data source interface.
Definition at line 586 of file pssm_engine.cpp.
References IPssmInput_Base::GetQuery(), CPssmEngine::m_PssmInput, and CPssmEngine::m_PssmInputFreqRatios.
Referenced by CPssmEngine::CPssmEngine().
◆ x_GetQueryLength()
|
private |
Private interface to retrieve query length from its data source interface.
Definition at line 593 of file pssm_engine.cpp.
References IPssmInput_Base::GetQueryLength(), CPssmEngine::m_PssmInput, and CPssmEngine::m_PssmInputFreqRatios.
Referenced by CPssmEngine::CPssmEngine().
◆ x_GetRequestInfo()
|
private |
Fetch the request info (wait for completion if necessary).
Definition at line 1647 of file remote_blast.cpp.
References CRemoteBlast::m_ReadFile, CRemoteBlast::x_GetRequestInfoFromFile(), and CRemoteBlast::x_GetRequestInfoFromRID().
Referenced by CRemoteBlast::GetCreatedBy(), CRemoteBlast::GetDatabases(), CRemoteBlast::GetProgram(), CRemoteBlast::GetQueries(), CRemoteBlast::GetService(), CRemoteBlast::GetSubjectSeqLocs(), CRemoteBlast::GetSubjectSequences(), and CRemoteBlast::IsDbSearch().
◆ x_GetRequestInfoFromFile()
|
private |
Fetch the requested info from an archive file.
Definition at line 1709 of file remote_blast.cpp.
References CRef< C, Locker >::Empty(), CRemoteBlast::GetSearchOptions(), kNoArchiveFile(), CRemoteBlast::m_AlgoOpts, CRemoteBlast::m_Archive, CRemoteBlast::m_CreatedBy, CRemoteBlast::m_FormatOpts, CRemoteBlast::m_Program, CRemoteBlast::m_ProgramOpts, CRemoteBlast::m_Queries, CRemoteBlast::m_Service, CRemoteBlast::m_SubjectSequences, NCBI_THROW, CRef< C, Locker >::Reset(), and CRemoteBlast::x_SetDatabase().
Referenced by CRemoteBlast::LoadFromArchive(), and CRemoteBlast::x_GetRequestInfo().
◆ x_GetRequestInfoFromRID()
|
private |
Fetch the requested info from splitd.
Definition at line 1748 of file remote_blast.cpp.
References CBlast4Client_Base::Ask(), CRemoteBlast::eDebug, CRemoteBlast::eDone, CStopWatch::Elapsed(), CRemoteBlast::ePollAsync, CStopWatch::eStart, kNoRIDSpecified(), CRemoteBlast::m_AlgoOpts, CRemoteBlast::m_ClientId, CRemoteBlast::m_CreatedBy, CRemoteBlast::m_Dbs, CRemoteBlast::m_FormatOpts, CRemoteBlast::m_Program, CRemoteBlast::m_ProgramOpts, CRemoteBlast::m_Queries, CRemoteBlast::m_RID, CRemoteBlast::m_Service, CRemoteBlast::m_Verbose, MSerial_AsnText, NCBI_THROW, NcbiCout, CRef< C, Locker >::Reset(), CBlast4_request_Base::SetBody(), CBlast4_request_body_Base::SetGet_request_info(), CBlast4_request_Base::SetIdent(), CBlast4_get_request_info_request_Base::SetRequest_id(), sw, CRemoteBlast::x_DefaultTimeout(), CRemoteBlast::x_GetState(), CRemoteBlast::x_GetSubjects(), and CRemoteBlast::x_PollUntilDone().
Referenced by CRemoteBlast::x_GetRequestInfo().
◆ x_GetSearchResults()
|
private |
Try to get the search results.
- Returns
- The blast4 server response.
Definition at line 246 of file remote_blast.cpp.
References CRemoteBlast::m_RID, CBlast4_request_body_Base::SetGet_search_results(), and CRemoteBlast::x_SendRequest().
Referenced by CRemoteBlast::x_CheckResults(), and CRemoteBlast::x_GetSearchResultsHTTP().
◆ x_GetSearchResultsHTTP()
| CRef< objects::CBlast4_reply > CRemoteBlast::x_GetSearchResultsHTTP | ( | void | ) |
Definition at line 2485 of file remote_blast.cpp.
References CDirEntry::CreateTmpFile(), CObjectIStream::eNoFileHeader, env, Error(), eSerial_AsnBinary, failure, fSERV_HttpPost, Info(), kEmptyStr, LOG_POST, CRemoteBlast::m_disk_cache_error_flag, CRemoteBlast::m_disk_cache_error_msg, CRemoteBlast::m_RID, CRemoteBlast::m_use_disk_cache, MSerial_AsnBinary, ObjectInfo(), CObjectIStream::Open(), CStreamUtils::Readsome(), CStopWatch::Restart(), CBlast4_request_Base::SetBody(), CBlast4_request_body_Base::SetGet_search_results(), CStopWatch::Start(), CStopWatch::Stop(), and CRemoteBlast::x_GetSearchResults().
Referenced by CRemoteBlast::x_CheckResultsDC().
◆ x_GetSearchStatsOnly()
| CRef< objects::CBlast4_reply > CRemoteBlast::x_GetSearchStatsOnly | ( | void | ) |
Definition at line 2466 of file remote_blast.cpp.
References CRemoteBlast::m_RID, CBlast4_request_body_Base::SetGet_search_results(), and CRemoteBlast::x_SendRequest().
Referenced by CRemoteBlast::x_CheckResultsDC().
◆ x_GetState()
|
private |
Determine what state the search is in.
Definition at line 603 of file remote_blast.cpp.
References CRemoteBlast::eDone, CRemoteBlast::eFailed, CRemoteBlast::eStart, CRemoteBlast::eWait, CRemoteBlast::m_Errs, CRemoteBlast::m_Pending, and CRemoteBlast::m_RID.
Referenced by CRemoteBlast::CheckDone(), CRemoteBlast::Submit(), CRemoteBlast::SubmitSync(), and CRemoteBlast::x_GetRequestInfoFromRID().
◆ x_GetStringFromSearchInfoReply()
|
private |
Definition at line 2347 of file remote_blast.cpp.
References Blast4SearchInfo_BuildReplyName(), CBlast4_get_search_info_reply_Base::CanGetInfo(), CBlast4_get_search_info_reply_Base::CanGetRequest_id(), CRef< C, Locker >::Empty(), CBlast4_get_search_info_reply_Base::GetInfo(), CBlast4_parameters::GetParamByName(), CBlast4_get_search_info_reply_Base::GetRequest_id(), CRemoteBlast::m_RID, CRef< C, Locker >::NotEmpty(), and rapidjson::value.
Referenced by CRemoteBlast::GetTitle(), and CRemoteBlast::x_GetPsiIterationsFromServer().
◆ x_GetSubjects()
|
private |
Definition at line 2571 of file remote_blast.cpp.
References CBlast4Client_Base::Ask(), Blast4SearchInfo_BuildReplyName(), CBlast4_get_search_info_reply_Base::CanGetInfo(), CBlast4_get_search_info_reply_Base::CanGetRequest_id(), CRemoteBlast::eDebug, CStopWatch::Elapsed(), CStopWatch::eStart, CBlast4_get_search_info_reply_Base::GetInfo(), CBlast4_parameters::GetParamByName(), CBlast4_get_search_info_reply_Base::GetRequest_id(), kBlast4SearchInfoReqName_Search, kBlast4SearchInfoReqValue_Subjects, CRemoteBlast::m_RID, CRemoteBlast::m_SubjectSeqLocs, CRemoteBlast::m_SubjectSequences, CRemoteBlast::m_Verbose, MSerial_AsnText, NCBI_THROW, NcbiCout, CRef< C, Locker >::NotEmpty(), s_BuildSearchInfoRequest(), CBlast4_request_Base::SetBody(), sw, and CRemoteBlast::x_SetSubjectSequences().
Referenced by CRemoteBlast::x_GetRequestInfoFromRID().
◆ x_GetSubjectSequence()
|
staticprivate |
Tries to fetch the sequence data for the subject for the segments specified in the Dense-seg.
If the sequence cannot be retrieved from the scope, a warning is printed and an empty string is returned in sequence_data
- Parameters
-
ds dense seg for which the sequence data is needed [in] scope scope from which to obtain the sequence data [in] sequence_data string which will contain the sequence data.
Definition at line 411 of file psi_pssm_input.cpp.
References _ASSERT, CSeq_id::AsFastaString(), CSeq_data_Base::e_Ncbistdaa, ERR_POST, GAP_IN_ALIGNMENT, CSeq_interval_Base::GetId(), CSeq_loc_Base::GetInt(), CSeqVector::GetSeqData(), i, kInvalidSeqPos, CSeqVector::SetCoding(), and Warning().
Referenced by CPssmCreateTestFixture::x_GetSubjectSequence(), and CPsiBlastInputData::x_ProcessDenseg().
◆ x_GuardProteinQuery()
|
staticprivate |
Copies query sequence and adds protein sentinel bytes at the beginning and at the end of the sequence.
- Parameters
-
query sequence to copy [in] query_length length of the sequence above [in]
- Exceptions
-
CBlastException if does not have enough memory
- Returns
- copy of query guarded by protein sentinel bytes
Definition at line 449 of file pssm_engine.cpp.
References _ASSERT, eBlastEncodingProtein, GetSentinelByte(), malloc(), NCBI_THROW, NULL, and query.
Referenced by CPssmCreateTestFixture::x_GuardProteinQuery(), and CPssmEngine::x_InitializeScoreBlock().
◆ x_HasRetrievedSubjects()
|
inlineprivate |
Definition at line 495 of file remote_blast.hpp.
References CRemoteBlast::m_SubjectSeqLocs, and CRemoteBlast::m_SubjectSequences.
Referenced by CRemoteBlast::GetSubjectSeqLocs(), and CRemoteBlast::GetSubjectSequences().
◆ x_Init() [1/10]
|
private |
Called by new search constructors: initialize a new search.
Definition at line 826 of file remote_blast.cpp.
References CBlastOptionsHandle::GetOptions(), CBlastOptions::GetRemoteProgramAndService_Blast3(), and CRemoteBlast::x_Init().
◆ x_Init() [2/10]
|
private |
Called by new search constructors: initialize a new search.
Definition at line 835 of file remote_blast.cpp.
References CRemoteBlast::eNeedAll, CRemoteBlast::eProgram, CRemoteBlast::eService, CRemoteBlast::eSilent, CBlastOptions::GetBlast4AlgoOpts(), kEmptyStr, CRemoteBlast::m_CBOH, CRemoteBlast::m_ClientId, CRemoteBlast::m_DbFilteringAlgorithmId, CRemoteBlast::m_DbFilteringAlgorithmKey, CRemoteBlast::m_ErrIgn, CRemoteBlast::m_NeedConfig, CRemoteBlast::m_Pending, CRemoteBlast::m_Program, CRemoteBlast::m_QSR, CRemoteBlast::m_QueryMaskingLocations, CRemoteBlast::m_ReadFile, CRemoteBlast::m_Service, CRemoteBlast::m_Verbose, NCBI_THROW, CRef< C, Locker >::Reset(), and CBlastOptionsHandle::SetOptions().
◆ x_Init() [3/10]
|
private |
Uses the file to populate results.
The file may be text or binary ASN.1 or XML. type is automatically detected.
- Parameters
-
f istream to archive file
Definition at line 796 of file remote_blast.cpp.
References CFormatGuess::eBinaryASN, eSerial_Xml, CRemoteBlast::eSilent, CFormatGuess::eTextASN, CFormatGuess::eXml, f, kEmptyStr, CRemoteBlast::m_DbFilteringAlgorithmId, CRemoteBlast::m_DbFilteringAlgorithmKey, CRemoteBlast::m_ErrIgn, CRemoteBlast::m_ObjectStream, CRemoteBlast::m_ObjectType, CRemoteBlast::m_ReadFile, CRemoteBlast::m_Verbose, NCBI_THROW, and CObjectIStream::Open().
Referenced by CRemoteBlast::CRemoteBlast(), and CRemoteBlast::x_Init().
◆ x_Init() [4/10]
Called by RID constructor: set up monitoring of existing search.
Definition at line 879 of file remote_blast.cpp.
References CRemoteBlast::eNoConfig, CRemoteBlast::eSilent, kEmptyStr, CRemoteBlast::m_DbFilteringAlgorithmId, CRemoteBlast::m_DbFilteringAlgorithmKey, CRemoteBlast::m_ErrIgn, CRemoteBlast::m_NeedConfig, CRemoteBlast::m_Pending, CRemoteBlast::m_QueryMaskingLocations, CRemoteBlast::m_ReadFile, CRemoteBlast::m_RID, CRemoteBlast::m_Verbose, and NCBI_THROW.
◆ x_Init() [5/10]
Initialize attributes.
Definition at line 518 of file rps_aux.cpp.
References _ASSERT, CSeqDB::eProtein, CBlastRPSInfo::fAuxInfoFile, CBlastRPSInfo::fFreqRatiosFile, CBlastRPSInfo::fFrequenciesFile, CSeqDB::FindVolumePaths(), flags, CBlastRPSInfo::fLookupTableFile, CBlastRPSInfo::fObservationsFile, CBlastRPSInfo::fPssmFile, CBlastRPSInfo::m_AuxFile, CBlastRPSInfo::m_FreqRatiosFile, CBlastRPSInfo::m_FreqsFile, CBlastRPSInfo::m_LutFile, CBlastRPSInfo::m_ObsrFile, CBlastRPSInfo::m_PssmFile, CBlastRPSInfo::m_RpsInfo, msg(), NCBI_RETHROW, NCBI_THROW, NULL, and CRef< C, Locker >::Reset().
Referenced by CBlastRPSInfo::CBlastRPSInfo().
◆ x_Init() [6/10]
|
private |
Common initialization code for all c-tors.
Definition at line 128 of file bl2seq.cpp.
References CBl2Seq::m_tQueries, CBl2Seq::m_tSubjects, CBl2Seq::mi_pDiagnostics, and NULL.
Referenced by CBl2Seq::CBl2Seq().
◆ x_Init() [7/10]
|
private |
Initialize a search with a database and options handle.
- Parameters
-
opts_handle Blast options handle. db Database used for this search.
Definition at line 1394 of file remote_blast.cpp.
References copy(), CRef< C, Locker >::Empty(), CSearchDatabase::GetDatabaseName(), CSearchDatabase::GetEntrezQueryLimitation(), CSearchDatabase::GetFilteringAlgorithm(), CSearchDatabase::GetFilteringAlgorithmKey(), CSearchDatabase::GetGiListLimitation(), CSearchDatabase::GetNegativeGiListLimitation(), NCBI_THROW, CRemoteBlast::SetDatabase(), CRemoteBlast::SetDbFilteringAlgorithmId(), CRemoteBlast::SetDbFilteringAlgorithmKey(), CRemoteBlast::SetEntrezQuery(), CRemoteBlast::SetGIList(), CRemoteBlast::SetNegativeGIList(), and CRemoteBlast::x_Init().
◆ x_Init() [8/10]
|
private |
Common initialization performed when doing traceback only.
Definition at line 126 of file traceback_stage.cpp.
References _ASSERT, Blast_DiagnosticsFree(), Blast_ProgramIsPhiBlast(), Blast_ProgramIsRpsBlast(), BlastScoreBlkFree(), CSetupFactory::CreateDiagnosticsStructure(), CSetupFactory::CreateLookupTable(), CSetupFactory::CreateRpsStructures(), CSetupFactory::CreateScoreBlock(), CBlastOptions::CreateSnapshot(), dbname(), ILocalQueryData::GetMessages(), CBlastOptions::GetProgramType(), ILocalQueryData::GetQueryInfo(), ILocalQueryData::GetSequenceBlk(), LookupTableWrapFree(), SInternalData::m_Diagnostics, SInternalData::m_HspStream, CBlastTracebackSearch::m_InternalData, SInternalData::m_LookupTable, CBlastTracebackSearch::m_Messages, CBlastTracebackSearch::m_OptsMemento, CBlastOptionsMemento::m_ProgramType, SInternalData::m_Queries, SInternalData::m_QueryInfo, SInternalData::m_RpsData, SInternalData::m_ScoreBlk, IQueryFactory::MakeLocalQueryData(), CConstRef< C, Locker >::NotEmpty(), NULL, PsiBlastSetupScoreBlock(), true, and CBlastOptions::Validate().
◆ x_Init() [9/10]
|
private |
Internal initialization function Initializes internal data structures except the BlastSeqSrc.
- Parameters
-
query_factory Contains query related data [in] options BLAST algorithm options [in] pssm PSSM to initialize PSI-BLAST seqsrc Wrapper for source of database sequences [in] num_threads Number of threads to use [in]
Definition at line 126 of file prelim_stage.cpp.
References BlastSetupPreliminarySearchEx(), copy(), CBlastPrelimSearch::m_InternalData, CBlastPrelimSearch::m_MasksForAllQueries, and CBlastPrelimSearch::m_Messages.
Referenced by CBlastPrelimSearch::CBlastPrelimSearch().
◆ x_Init() [10/10]
|
private |
Initialize the result set.
Definition at line 558 of file blast_results.cpp.
References _ASSERT, eSequenceComparison, i, kEmptyStr, CSearchResultSet::m_IsPhiBlast, CSearchResultSet::m_NumQueries, CSearchResultSet::m_Results, CSearchResultSet::m_ResultType, NULL, and CSearchResultSet::SetFilteredQueryRegions().
Referenced by CSearchResultSet::CSearchResultSet().
◆ x_InitCLocalBlast()
|
private |
Common initialization of the CLocalBlast object.
Definition at line 60 of file bl2seq.cpp.
References _ASSERT, CRef< C, Locker >::Empty(), CBl2Seq::m_Blast, CBl2Seq::m_DbScanMode, CBl2Seq::m_InterruptFnx, CBl2Seq::m_InterruptUserData, CBl2Seq::m_OptsHandle, CBl2Seq::m_tQueries, CBl2Seq::m_tSubjects, NULL, CRef< C, Locker >::Reset(), CBlastOptionsHandle::SetHitlistSize(), and CLocalBlast::SetInterruptCallback().
Referenced by CBl2Seq::RunEx().
◆ x_InitDiskCache()
|
private |
Initialize disk caching.
Definition at line 1439 of file remote_blast.cpp.
References NStr::CompareNocase(), env, Info(), kEmptyStr, LOG_POST, CRemoteBlast::m_disk_cache_error_flag, CRemoteBlast::m_disk_cache_error_msg, and CRemoteBlast::m_use_disk_cache.
Referenced by CRemoteBlast::CRemoteBlast().
◆ x_InitializeDb()
|
private |
Initialize the database.
Definition at line 251 of file uniform_search.cpp.
References _ASSERT, CSeqDBNegativeList::AddSi(), CSeqDBNegativeList::AddTaxIds(), CSeqDBIdSet::eGi, CSeqDBGiList::Empty(), CRef< C, Locker >::Empty(), CSeqDB::eNucleotide, CSeqDB::eProtein, CSeqDBGiList::GetGiList(), CSeqDBGiList::GetListInfo(), CSeqDBGiList::GetNumGis(), CSeqDBGiList::GetNumPigs(), CSeqDBGiList::GetNumSis(), CSeqDBGiList::GetNumTaxIds(), CSeqDBGiList::GetPigList(), CRef< C, Locker >::GetPointer(), CSeqDBGiList::GetSiList(), CSeqDBGiList::GetTaxIdsList(), CSearchDatabase::IsProtein(), ITERATE, CSearchDatabase::m_DbInitialized, CSearchDatabase::m_DbName, CSearchDatabase::m_GiList, CSearchDatabase::m_NegativeGiList, CSearchDatabase::m_SeqDb, CRef< C, Locker >::NotEmpty(), CSeqDBNegativeList::ReserveSis(), CRef< C, Locker >::Reset(), CSeqDBNegativeList::SetListInfo(), CSeqDBNegativeList::SetPigList(), and CSearchDatabase::x_ValidateMaskingAlgorithm().
Referenced by CSearchDatabase::GetSeqDb(), and CSearchDatabase::x_TranslateFilteringAlgorithm().
◆ x_InitializeQueryInfo()
|
private |
Initialiazes the core BlastQueryInfo structure for a single protein sequence.
- Parameters
-
query_length length of the sequence above [in]
Definition at line 466 of file pssm_engine.cpp.
References BlastQueryInfoNew(), BlastQueryInfo::contexts, eBlastTypeBlastp, BlastQueryInfo::max_length, NCBI_THROW, BlastContextInfo::query_length, and BlastContextInfo::query_offset.
Referenced by CPssmEngine::x_InitializeScoreBlock().
◆ x_InitializeScoreBlock()
|
private |
Initializes the BlastScoreBlk data member required to run the PSSM engine.
- Parameters
-
query sequence [in] query_length length of the sequence above [in] matrix_name name of the underlying scoring matrix to use [in] gap_existence cost to open a gap gap_extension cost to open a gap
- Exceptions
-
CBlastException if does not have enough memory or if there was an error when setting up the return value
Definition at line 512 of file pssm_engine.cpp.
References _ASSERT, abort(), Blast_MessageFree(), BlastFindMatrixPath(), BlastScoreBlkFree(), BlastScoringOptionsNew(), BlastScoringOptionsSetMatrix(), BlastSeqBlkNew(), BlastSeqBlkSetSequence(), BlastSetup_ScoreBlkInit(), eBlastTypePsiBlast, BlastScoringOptions::gap_extend, BlastScoringOptions::gap_open, BlastScoreBlk::kbp, BlastScoreBlk::kbp_gap, BlastScoreBlk::kbp_gap_psi, BlastScoreBlk::kbp_ideal, BlastScoreBlk::kbp_psi, kScaleFactor, CPssmEngine::m_ScoreBlk, Blast_Message::message, msg(), NCBI_THROW, NULL, query, AutoPtr< X, Del >::release(), CBlastScoreBlk::Reset(), CPssmEngine::x_GuardProteinQuery(), and CPssmEngine::x_InitializeQueryInfo().
Referenced by CPssmEngine::CPssmEngine().
◆ x_InitQueries()
|
private |
Initialize queries based on a query factory.
- Parameters
-
queries Query factory from which to pull queries.
Definition at line 1307 of file remote_blast.cpp.
References _ASSERT, CBioseq_set_Base::CanGetSeq_set(), eBlastOpt_RequiredEnd, eBlastOpt_RequiredStart, eExtreme_Positional, CRef< C, Locker >::Empty(), CBlast4Field::Get(), IRemoteQueryData::GetBioseqSet(), CBioseq_set_Base::GetSeq_set(), IRemoteQueryData::GetSeqLocs(), IsLocalId(), ITERATE, kStart(), IQueryFactory::MakeRemoteQueryData(), NCBI_THROW, CRemoteBlast::SetQueries(), CRemoteBlast::x_ExtractUserSpecifiedMasks(), and CRemoteBlast::x_SetOneParam().
Referenced by CRemoteBlast::CRemoteBlast().
◆ x_InitSubject()
|
private |
Auxiliary method to initialize the subject.
- Parameters
-
subject query factory describing the subject sequence(s) [in] options PSI-BLAST options [in]
- Exceptions
-
CBlastException if options is empty
- Postcondition
- the m_Subject member will be initialized
Definition at line 74 of file psibl2seq.cpp.
References CPsiBl2Seq::m_Subject, NCBI_THROW, CRef< C, Locker >::Reset(), and subject.
Referenced by CPsiBl2Seq::CPsiBl2Seq().
◆ x_IsUnknownRID()
|
private |
Determine if this is an unknown RID.
- Note
- caller must have contacted the server for this method to work (e.g.: via CheckDone());
Definition at line 340 of file remote_blast.cpp.
References NStr::Find(), CRemoteBlast::GetErrors(), and NPOS.
Referenced by CRemoteBlast::CheckDone().
◆ x_LaunchMultiThreadedSearch()
|
private |
Runs the preliminary search in multi-threaded mode.
- Parameters
-
internal_data internal preliminary data structures
Definition at line 142 of file prelim_stage.cpp.
References _TRACE, BLASTERR_DB_MEMORY_MAP, BLASTERR_DB_OPEN_FILES, BlastErrorCode2String(), BlastSeqSrcSetNumberOfThreads(), CBlastOptions::CreateSnapshot(), GetDbIndexSetNumThreadsFn(), CThreadable::GetNumberOfThreads(), CBlastPrelimSearch::m_InternalData, CBlastPrelimSearch::m_Options, SInternalData::m_SeqSrc, NCBI_THROW, NON_CONST_ITERATE, and result.
Referenced by CBlastPrelimSearch::Run().
◆ x_LookupTableOptions_cmp()
| bool x_LookupTableOptions_cmp | ( | const LookupTableOptions * | a, |
| const LookupTableOptions * | b | ||
| ) |
Definition at line 453 of file blast_options_local_priv.cpp.
References a, b, and x_safe_strcmp().
Referenced by CBlastOptionsLocal::operator==().
◆ x_MakeLocalQueryData() [1/3]
|
protectedvirtual |
factory method to create an ILocalQueryData, only called if the data members above are not set
Implements IQueryFactory.
Definition at line 467 of file objmgr_query_data.cpp.
References abort(), CObjMgr_QueryFactory::m_QueryVector, CObjMgr_QueryFactory::m_SSeqLocVector, CRef< C, Locker >::NotEmpty(), and CRef< C, Locker >::Reset().
◆ x_MakeLocalQueryData() [2/3]
|
protectedvirtual |
factory method to create an ILocalQueryData, only called if the data members above are not set
Implements IQueryFactory.
Definition at line 260 of file objmgrfree_query_data.cpp.
References CObjMgrFree_QueryFactory::m_Bioseqs, NCBI_CURRENT_FUNCTION, NCBI_THROW, CConstRef< C, Locker >::NotEmpty(), and CRef< C, Locker >::Reset().
◆ x_MakeLocalQueryData() [3/3]
|
protectedpure virtual |
factory method to create an ILocalQueryData, only called if the data members above are not set
Implemented in CObjMgrFree_QueryFactory, and CObjMgr_QueryFactory.
Referenced by IQueryFactory::MakeLocalQueryData().
◆ x_MakeLookupTable()
|
private |
Definition at line 81 of file seedtop.cpp.
References LookupTableOptionsNew(), LookupTableWrapInit(), CSeedTop::m_Lookup, CSeedTop::m_Pattern, CSeedTop::m_Program, CSeedTop::m_ScoreBlk, NULL, LookupTableOptions::phi_pattern, and strdup.
◆ x_MakeRemoteQueryData() [1/3]
|
protectedvirtual |
factory method to create an IRemoteQueryData, only called if the data members above are not set
Implements IQueryFactory.
Definition at line 483 of file objmgr_query_data.cpp.
References abort(), CObjMgr_QueryFactory::m_QueryVector, CObjMgr_QueryFactory::m_SSeqLocVector, CRef< C, Locker >::NotEmpty(), and CRef< C, Locker >::Reset().
◆ x_MakeRemoteQueryData() [2/3]
|
protectedvirtual |
factory method to create an IRemoteQueryData, only called if the data members above are not set
Implements IQueryFactory.
Definition at line 276 of file objmgrfree_query_data.cpp.
References CObjMgrFree_QueryFactory::m_Bioseqs, NCBI_CURRENT_FUNCTION, NCBI_THROW, CConstRef< C, Locker >::NotEmpty(), and CRef< C, Locker >::Reset().
◆ x_MakeRemoteQueryData() [3/3]
|
protectedpure virtual |
factory method to create an IRemoteQueryData, only called if the data members above are not set
Implemented in CObjMgrFree_QueryFactory, and CObjMgr_QueryFactory.
Referenced by IQueryFactory::MakeRemoteQueryData().
◆ x_MakeScoreBlk()
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private |
Definition at line 92 of file seedtop.cpp.
References BlastFindMatrixPath(), BlastQueryInfoNew(), BlastScoringOptionsNew(), BlastSetup_ScoreBlkInit(), CSeedTop::m_Program, CSeedTop::m_ScoreBlk, msg(), and NULL.
◆ x_NeedsTrans()
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private |
Returns true if this program needs coordinate translation.
Definition at line 1506 of file blast_setup_cxx.cpp.
References eBlastTypeBlastx, eBlastTypeRpsTblastn, eBlastTypeTblastx, and CBlastQueryFilteredFrames::m_Program.
Referenced by CBlastQueryFilteredFrames::CBlastQueryFilteredFrames().
◆ x_NonTranslatedHSPToStdSeg()
| CRef<CStd_seg> x_NonTranslatedHSPToStdSeg | ( | BlastHSP * | hsp, |
| CRef< CSeq_id > | query_id, | ||
| CRef< CSeq_id > | subject_id, | ||
| Int4 | query_length, | ||
| Int4 | subject_length, | ||
| const vector< string > & | seqid_list | ||
| ) |
Creates a Std-seg object from HSP information and sequence identifiers for a non-translated ungapped search.
- Parameters
-
hsp An HSP structure [in] query_id Query sequence identifier [in] subject_id Subject sequence identifier [in] query_length Length of the query [in] subject_length Length of the subject [in] gi_list List of GIs for the subject sequence.
- Returns
- Resulting Std-seg object.
Definition at line 2040 of file blast_seqalign.cpp.
References BlastSeg::end, BlastSeg::frame, kBlastAlignmentDim, BlastSeg::offset, BlastHSP::query, s_BuildScoreList(), s_Frame2Strand(), CSeq_loc::SetInt(), and BlastHSP::subject.
Referenced by BLASTPrelminSearchHitListToStdSeg().
◆ x_ParsePattern()
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private |
Definition at line 62 of file seedtop.cpp.
References i, ITERATE, CSeedTop::m_Pattern, CSeedTop::m_Units, NStr::Split(), NStr::ToUpper(), and NStr::TruncateSpacesInPlace().
◆ x_PollUntilDone()
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private |
Poll until results are found, error occurs, or timeout expires.
Definition at line 734 of file remote_blast.cpp.
References CRemoteBlast::eDebug, CRemoteBlast::ePollAsync, CRemoteBlast::m_Pending, CRemoteBlast::m_use_disk_cache, CRemoteBlast::m_Verbose, SleepSec(), CRemoteBlast::x_CheckResults(), and CRemoteBlast::x_CheckResultsDC().
Referenced by CRemoteBlast::SubmitSync(), and CRemoteBlast::x_GetRequestInfoFromRID().
◆ x_Process_BlastOptions()
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private |
Definition at line 371 of file search_strategy.cpp.
References CRef< C, Locker >::Empty(), CBlastOptions::GetBlast4AlgoOpts(), CBlastOptionsHandle::GetOptions(), CBlastOptions::GetRemoteProgramAndService_Blast3(), CExportStrategy::m_QueueSearchRequest, NCBI_THROW, NULL, CBlast4_queue_search_request_Base::SetAlgorithm_options(), CBlastOptionsHandle::SetOptions(), CBlast4_queue_search_request_Base::SetProgram(), and CBlast4_queue_search_request_Base::SetService().
Referenced by CExportStrategy::CExportStrategy().
◆ x_Process_Pssm()
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private |
Definition at line 525 of file search_strategy.cpp.
References CRef< C, Locker >::Empty(), CBlast4_queue_search_request_Base::GetProgram(), CBlast4_queue_search_request_Base::GetService(), CExportStrategy::m_QueueSearchRequest, NCBI_THROW, CPsiBlastValidate::Pssm(), CBlast4_queries_Base::SetPssm(), CBlast4_queue_search_request_Base::SetQueries(), and CBlast4_queue_search_request_Base::SetService().
Referenced by CExportStrategy::CExportStrategy().
◆ x_Process_Query()
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private |
Definition at line 563 of file search_strategy.cpp.
References _ASSERT, CBioseq_set_Base::CanGetSeq_set(), CRemoteBlast::ConvertToRemoteMasks(), eBlastOpt_LCaseMask, eBlastOpt_RequiredEnd, eBlastOpt_RequiredStart, eExtreme_Positional, CRef< C, Locker >::Empty(), CObjMgr_QueryFactory::ExtractUserSpecifiedMasks(), CBlast4Field::Get(), IRemoteQueryData::GetBioseqSet(), CBlast4Field::GetName(), CBlast4_queue_search_request_Base::GetProgram(), CBioseq_set_Base::GetSeq_set(), IRemoteQueryData::GetSeqLocs(), CBlast4_queue_search_request_Base::GetService(), IsLocalId(), ITERATE, kStart(), CExportStrategy::m_QueueSearchRequest, NCBI_THROW, NetworkProgram2BlastProgramType(), NON_CONST_ITERATE, NULL, query, CBlast4_queries_Base::SetBioseq_set(), CBlast4_queue_search_request_Base::SetProgram_options(), CBlast4_queue_search_request_Base::SetQueries(), CBlast4_value_Base::SetQuery_mask(), CBlast4_queries_Base::SetSeq_loc_list(), and CExportStrategy::x_AddParameterToProgramOptions().
Referenced by CExportStrategy::CExportStrategy().
◆ x_Process_SearchDb()
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private |
Definition at line 408 of file search_strategy.cpp.
References _ASSERT, set< Key, Compare >::begin(), eBlastOpt_DbFilteringAlgorithmId, eBlastOpt_DbFilteringAlgorithmKey, eBlastOpt_EntrezQuery, eBlastOpt_GiList, eBlastOpt_NegativeGiList, eBlastOpt_NegativeTaxidList, eBlastOpt_SubjectMaskingType, eBlastOpt_TaxidList, CRef< C, Locker >::Empty(), set< Key, Compare >::end(), CBlast4Field::Get(), CSearchDatabase::GetDatabaseName(), CSearchDatabase::GetEntrezQueryLimitation(), CSearchDatabase::GetFilteringAlgorithm(), CSearchDatabase::GetFilteringAlgorithmKey(), CSearchDatabase::GetGiList(), CSearchDatabase::GetGiListLimitation(), CSearchDatabase::GetMaskType(), CBlast4Field::GetName(), CSearchDatabase::GetNegativeGiList(), CSearchDatabase::GetNegativeGiListLimitation(), CSeqDBGiList::GetTaxIdsList(), GI_TO, int, ITERATE, kEmptyStr, CExportStrategy::m_QueueSearchRequest, NCBI_THROW, CRef< C, Locker >::NotEmpty(), CBlast4_subject_Base::SetDatabase(), CBlast4_queue_search_request_Base::SetProgram_options(), CBlast4_value_Base::SetString(), CBlast4_queue_search_request_Base::SetSubject(), TAX_ID_TO, and CExportStrategy::x_AddParameterToProgramOptions().
Referenced by CExportStrategy::CExportStrategy().
◆ x_Process_Subject()
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private |
Definition at line 661 of file search_strategy.cpp.
References CRef< C, Locker >::Empty(), FlattenBioseqSet(), IRemoteQueryData::GetBioseqSet(), CExportStrategy::m_QueueSearchRequest, NCBI_THROW, CBlast4_subject_Base::SetSequences(), CBlast4_queue_search_request_Base::SetSubject(), and subject.
Referenced by CExportStrategy::CExportStrategy().
◆ x_ProcessAlignments()
|
protected |
Process RPS-BLAST hits.
Convert hits to internal representation.
- Parameters
-
min_evalue Min e-value for inclusion of CD hit in PSSM calculation [in] max_evalue Max e-value for inclusion of CD hit in PSSM calculation [in]
Definition at line 152 of file cdd_pssm_input.cpp.
References CSeq_align::eScore_EValue, ITERATE, CCddInputData::m_Hits, CCddInputData::m_SeqalignSet, and NCBI_THROW.
Referenced by CCddInputData::Process().
◆ x_ProcessCResult()
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private |
Definition at line 1425 of file igblast.cpp.
References eNa_strand_minus, eNa_strand_plus, CSeq_align_set_Base::Get(), CSearchResults::GetSeqAlign(), CSearchResults::HasAlignments(), NON_CONST_ITERATE, CRef< C, Locker >::Reset(), and CSeq_align_set_Base::Set().
Referenced by CIgBlast::Run().
◆ x_ProcessDenseg()
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private |
Iterates over the Dense-seg passed in and extracts alignment information to multiple alignment data structure.
- Parameters
-
denseg source alignment segment (HSP) [in] msa_index index of the sequence aligned with the query in the desc_matrix field of the m_AlignmentData data member [in] evalue evalue for this sequence aligned with the query (used for debugging only) [in] bit_score bit score for this sequence aligned with the query (used for debugging only) [in]
Definition at line 325 of file psi_pssm_input.cpp.
References _ASSERT, AMINOACID_TO_NCBISTDAA, PSIMsa::data, GAP_IN_ALIGNMENT, CPsiBlastInputData::GetQueryLength(), i, PSIMsaCell::is_aligned, PSIMsaCell::letter, CPsiBlastInputData::m_Msa, CPsiBlastInputData::m_Query, CPsiBlastInputData::m_Scope, and CPsiBlastInputData::x_GetSubjectSequence().
Referenced by CPsiBlastInputData::x_ExtractAlignmentData().
◆ x_ProcessDGeneResult()
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private |
Definition at line 1319 of file igblast.cpp.
References CSeq_id::eContent, eNa_strand_minus, eNa_strand_plus, CIgAnnotationInfo::GetDJChainType(), CSearchResults::HasAlignments(), CSeq_align_set::IsEmpty(), ITERATE, CIgBlast::m_AnnotationInfo, CIgBlast::m_IgOptions, CIgBlastOptions::m_Min_D_match, max_allowed_VD_distance, NON_CONST_ITERATE, CRef< C, Locker >::NotEmpty(), s_CompareSeqAlignByScoreAndName(), s_DJNotCompatible(), CSeq_align_set_Base::Set(), CSearchResults::SetSeqAlign(), and NStr::ToUpper().
Referenced by CIgBlast::Run().
◆ x_ProcessDJResult()
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private |
Definition at line 1454 of file igblast.cpp.
References eNa_strand_minus, eNa_strand_plus, NON_CONST_ITERATE, and CIgBlast::x_FindDJ().
Referenced by CIgBlast::Run().
◆ x_ProcessOneOption() [1/2]
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private |
Add an algorithm or program option to the provided handle.
◆ x_ProcessOneOption() [2/2]
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private |
Apply the value of one option to the CBlastOptionsHandle.
- Parameters
-
opts The blast options handle. p The parameter to apply to the options handle.
Definition at line 140 of file blast_options_builder.cpp.
References _ASSERT, Blast_QueryIsNucleotide(), eBlastOpt_BestHitOverhang, eBlastOpt_BestHitScoreEdge, eBlastOpt_CompositionBasedStats, eBlastOpt_Culling, eBlastOpt_CullingLimit, eBlastOpt_CutoffScore, eBlastOpt_DbFilteringAlgorithmId, eBlastOpt_DbFilteringAlgorithmKey, eBlastOpt_DbGeneticCode, eBlastOpt_DbLength, eBlastOpt_DomainInclusionThreshold, eBlastOpt_DustFiltering, eBlastOpt_DustFilteringLevel, eBlastOpt_DustFilteringLinker, eBlastOpt_DustFilteringWindow, eBlastOpt_EffectiveSearchSpace, eBlastOpt_EntrezQuery, eBlastOpt_EvalueThreshold, eBlastOpt_FilterString, eBlastOpt_FinalDbSeq, eBlastOpt_FirstDbSeq, eBlastOpt_ForceMbIndex, eBlastOpt_GapExtensionCost, eBlastOpt_GapExtnAlgorithm, eBlastOpt_GapOpeningCost, eBlastOpt_GappedMode, eBlastOpt_GapTracebackAlgorithm, eBlastOpt_GapTrigger, eBlastOpt_GapXDropoff, eBlastOpt_GapXDropoffFinal, eBlastOpt_GiList, eBlastOpt_HitlistSize, eBlastOpt_HspRangeMax, eBlastOpt_IgnoreMsaMaster, eBlastOpt_InclusionThreshold, eBlastOpt_LCaseMask, eBlastOpt_LongestIntronLength, eBlastOpt_MaskAtHash, eBlastOpt_MatchReward, eBlastOpt_MatrixName, eBlastOpt_MatrixTable, eBlastOpt_MaxHspsPerSubject, eBlastOpt_MbIndexName, eBlastOpt_MBTemplateLength, eBlastOpt_MBTemplateType, eBlastOpt_MismatchPenalty, eBlastOpt_NegativeGiList, eBlastOpt_NegativeTaxidList, eBlastOpt_OutOfFrameMode, eBlastOpt_PercentIdentity, eBlastOpt_PHIPattern, eBlastOpt_PseudoCount, eBlastOpt_QueryCovHspPerc, eBlastOpt_QueryGeneticCode, eBlastOpt_RepeatFiltering, eBlastOpt_RepeatFilteringDB, eBlastOpt_RequiredEnd, eBlastOpt_RequiredStart, eBlastOpt_SegFiltering, eBlastOpt_SegFilteringHicut, eBlastOpt_SegFilteringLocut, eBlastOpt_SegFilteringWindow, eBlastOpt_SmithWatermanMode, eBlastOpt_StrandOption, eBlastOpt_SubjectBestHit, eBlastOpt_SubjectMaskingType, eBlastOpt_SumStatisticsMode, eBlastOpt_TaxidList, eBlastOpt_UnifiedP, eBlastOpt_WindowMaskerTaxId, eBlastOpt_WindowSize, eBlastOpt_WordSize, eBlastOpt_WordThreshold, CBlast4Field::Get(), CBlast4_value_Base::GetBig_integer(), CBlast4_value_Base::GetBig_integer_list(), CBlast4_value_Base::GetBoolean(), CBlast4_value_Base::GetCutoff(), CBlast4_cutoff_Base::GetE_value(), CBlast4_value_Base::GetInteger(), CBlast4_value_Base::GetInteger_list(), CBlastOptions::GetProgramType(), CBlast4_value_Base::GetQuery_mask(), CBlast4_value_Base::GetReal(), CBlastOptionsBuilder::SOptional< T >::GetRef(), CBlast4_value_Base::GetStrand_type(), CBlast4_value_Base::GetString(), GI_FROM, CBlastOptionsBuilder::SOptional< T >::Have(), NStr::IntToString(), CBlast4_value_Base::IsBig_integer_list(), CBlast4_value_Base::IsCutoff(), CBlast4_cutoff_Base::IsE_value(), CBlast4_value_Base::IsQuery_mask(), CBlast4_value_Base::IsReal(), ITERATE, CBlastOptionsBuilder::m_DbFilteringAlgorithmId, CBlastOptionsBuilder::m_DbFilteringAlgorithmKey, CBlastOptionsBuilder::m_EntrezQuery, CBlastOptionsBuilder::m_FinalDbSeq, CBlastOptionsBuilder::m_FirstDbSeq, CBlastOptionsBuilder::m_ForceMbIndex, CBlastOptionsBuilder::m_GiList, CBlastOptionsBuilder::m_HspRangeMax, CBlastOptionsBuilder::m_IgnoreQueryMasks, CBlastOptionsBuilder::m_IgnoreUnsupportedOptions, CBlastOptionsBuilder::m_MbIndexName, CBlastOptionsBuilder::m_NegativeGiList, CBlastOptionsBuilder::m_NegativeTaxidList, CBlastOptionsBuilder::m_PerformCulling, CBlastOptionsBuilder::m_QueryMasks, CBlastOptionsBuilder::m_QueryRange, CBlastOptionsBuilder::m_SubjectMaskingType, CBlastOptionsBuilder::m_TaxidList, CBlast4Field::Match(), msg(), NCBI_THROW, CBlastOptions::SetBestHitOverhang(), CBlastOptions::SetBestHitScoreEdge(), CBlastOptions::SetCompositionBasedStats(), CBlastOptions::SetCullingLimit(), CBlastOptionsHandle::SetCutoffScore(), CBlastOptions::SetDbGeneticCode(), CBlastOptionsHandle::SetDbLength(), CBlastOptions::SetDomainInclusionThreshold(), CBlastOptions::SetDustFiltering(), CBlastOptions::SetDustFilteringLevel(), CBlastOptions::SetDustFilteringLinker(), CBlastOptions::SetDustFilteringWindow(), CBlastOptionsHandle::SetEffectiveSearchSpace(), CBlastOptionsHandle::SetEvalueThreshold(), CBlastOptionsHandle::SetFilterString(), CRange_Base::SetFrom(), CBlastOptions::SetGapExtensionCost(), CBlastOptions::SetGapExtnAlgorithm(), CBlastOptions::SetGapOpeningCost(), CBlastOptionsHandle::SetGappedMode(), CBlastOptions::SetGapTracebackAlgorithm(), CBlastOptions::SetGapTrigger(), CBlastOptions::SetGapXDropoff(), CBlastOptions::SetGapXDropoffFinal(), CBlastOptionsHandle::SetHitlistSize(), CBlastOptions::SetIgnoreMsaMaster(), CBlastOptions::SetInclusionThreshold(), CBlastOptions::SetLongestIntronLength(), CBlastOptions::SetMaskAtHash(), CBlastOptions::SetMatchReward(), CBlastOptions::SetMatrixName(), CBlastOptions::SetMaxHspsPerSubject(), CBlastOptions::SetMBTemplateLength(), CBlastOptions::SetMBTemplateType(), CBlastOptions::SetMismatchPenalty(), CBlastOptionsHandle::SetOptions(), CBlastOptions::SetOutOfFrameMode(), CBlastOptionsHandle::SetPercentIdentity(), CBlastOptions::SetPHIPattern(), CBlastOptions::SetPseudoCount(), CBlastOptionsHandle::SetQueryCovHspPerc(), CBlastOptions::SetQueryGeneticCode(), CBlastOptions::SetRepeatFiltering(), CBlastOptions::SetRepeatFilteringDB(), CBlastOptions::SetSegFiltering(), CBlastOptions::SetSegFilteringHicut(), CBlastOptions::SetSegFilteringLocut(), CBlastOptions::SetSegFilteringWindow(), CBlastOptions::SetSmithWatermanMode(), CBlastOptions::SetStrandOption(), CBlastOptions::SetSubjectBestHit(), CBlastOptions::SetSumStatisticsMode(), COpenRange< Position >::SetToOpen(), CBlastOptions::SetUnifiedP(), CBlastOptions::SetWindowMaskerTaxId(), CBlastOptionsHandle::SetWindowSize(), CBlastOptions::SetWordSize(), CBlastOptions::SetWordThreshold(), TAX_ID_FROM, and CBlast4_value_Base::Which().
Referenced by CBlastOptionsBuilder::x_ProcessOptions().
◆ x_ProcessOptions() [1/2]
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private |
Add algorithm and program options to the provided handle.
◆ x_ProcessOptions() [2/2]
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private |
Apply the value of all options to the CBlastOptionsHandle.
A list of blast4 parameters is used to configure the provided CBlastOptionsHandle object.
- Parameters
-
opts The blast options handle. L The list of parameters to add to the options.
Definition at line 548 of file blast_options_builder.cpp.
References ITERATE, and CBlastOptionsBuilder::x_ProcessOneOption().
Referenced by CBlastOptionsBuilder::GetSearchOptions().
◆ x_PSIMatrix2Asn1()
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staticprivate |
Converts the PSIMatrix structure into a ASN.1 CPssmWithParameters object.
- Parameters
-
pssm input PSIMatrix structure [in] opts options to be used in the PSSM engine [in] matrix_name name of the underlying scoring matrix used diagnostics contains diagnostics data from PSSM creation process to save into the return value [in]
- Returns
- CPssmWithParameters object with equivalent contents to those in pssm argument
Definition at line 625 of file pssm_engine.cpp.
References _ASSERT, PSIDiagnosticsResponse::alphabet_size, PSIDiagnosticsResponse::frequency_ratios, PSIDiagnosticsResponse::gapless_column_weights, CPssm_Base::GetByRow(), PSIMatrix::h, i, PSIBlastOptions::impala_scaling_factor, PSIDiagnosticsResponse::independent_observations, PSIDiagnosticsResponse::information_content, PSIDiagnosticsResponse::interval_sizes, PSIMatrix::kappa, kPSSM_NoImpalaScaling, PSIMatrix::lambda, mtx, PSIMatrix::ncols, PSIMatrix::nrows, PSIDiagnosticsResponse::num_matching_seqs, PSIBlastOptions::pseudo_count, PSIMatrix::pssm, PSIDiagnosticsResponse::query_length, PSIDiagnosticsResponse::residue_freqs, CPssm_Base::SetByRow(), CPssm_Base::SetFinalData(), CPssm::SetH(), CPssm::SetHUngapped(), CPssm_Base::SetIntermediateData(), CPssm_Base::SetIsProtein(), CPssm::SetKappa(), CPssm::SetKappaUngapped(), CPssm::SetLambda(), CPssm::SetLambdaUngapped(), CPssm_Base::SetNumColumns(), CPssm_Base::SetNumRows(), CPssmWithParameters_Base::SetParams(), CPssmWithParameters_Base::SetPssm(), PSIDiagnosticsResponse::sigma, NStr::ToUpper(), PSIMatrix::ung_h, PSIMatrix::ung_kappa, PSIMatrix::ung_lambda, and PSIDiagnosticsResponse::weighted_residue_freqs.
Referenced by CPssmEngine::x_CreatePssmFromCDD(), CPssmEngine::x_CreatePssmFromFreqRatios(), and CPssmEngine::x_CreatePssmFromMsa().
◆ x_QueryMaskingLocationsToNetwork()
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private |
Converts the provided query masking locations (if any) to the network representation following the BLAST 4 ASN.1 spec.
Definition at line 1142 of file remote_blast.cpp.
References CRemoteBlast::ConvertToRemoteMasks(), eBlastOpt_LCaseMask, CBlast4Field::Get(), ITERATE, CRemoteBlast::m_CBOH, CRemoteBlast::m_Program, CRemoteBlast::m_QueryMaskingLocations, CRemoteBlast::m_Service, CRemoteBlast::m_Warn, NetworkProgram2BlastProgramType(), and CRemoteBlast::x_SetOneParam().
Referenced by CRemoteBlast::x_GetBlast4SearchRequestBody().
◆ x_QuerySetupOptions_cmp()
| bool x_QuerySetupOptions_cmp | ( | const QuerySetUpOptions * | a, |
| const QuerySetUpOptions * | b | ||
| ) |
Definition at line 442 of file blast_options_local_priv.cpp.
References a, b, and x_safe_strcmp().
Referenced by CBlastOptionsLocal::operator==().
◆ x_ReadAsciiMsa()
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private |
Reads the multiple sequence alignment from the input file.
- Parameters
-
input_file Input file containing the multiple sequence alignment. [in]
- Postcondition
- m_AsciiMsa and m_SeqEntry are not empty
Definition at line 119 of file msa_pssm_input.cpp.
References _ASSERT, CAlnReader::eAlpha_Protein, CObjReaderParseException::eFormat, CRef< C, Locker >::Empty(), NStr::Find(), CParseTemplException< TBase >::GetErrCode(), CAlnReader::GetSeqEntry(), CAlnReader::GetSeqs(), input_file, CPsiBlastInputClustalW::m_AsciiMsa, CPsiBlastInputClustalW::m_SeqEntry, msg(), NCBI_THROW, NPOS, CAlnReader::Read(), and CAlnReader::SetClustal().
◆ x_ReadFromFile()
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private |
Auxiliary method to read the contents of the file into m_Data.
Definition at line 195 of file rps_aux.cpp.
References input().
Referenced by CRpsAuxFile::CRpsAuxFile().
◆ x_RemoteBlast() [1/2]
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private |
Method to construct and run the remote blast search.
Definition at line 82 of file remote_search.cpp.
References _ASSERT, CRef< C, Locker >::Empty(), CConstRef< C, Locker >::Empty(), IRemoteQueryData::GetBioseqSet(), CSearchDatabase::GetDatabaseName(), CSearchDatabase::GetEntrezQueryLimitation(), CSearchDatabase::GetGiListLimitation(), IRemoteQueryData::GetSeqLocs(), CRemoteSeqSearch::m_Queries, CRemoteSeqSearch::m_RemoteBlast, CRemoteSeqSearch::m_SearchOpts, CRemoteSeqSearch::m_Subject, NCBI_THROW, CRef< C, Locker >::NotEmpty(), CRef< C, Locker >::Reset(), CRemoteBlast::SetDatabase(), CRemoteBlast::SetEntrezQuery(), CRemoteBlast::SetGIList(), and CRemoteBlast::SetQueries().
Referenced by CRemoteSeqSearch::Run().
◆ x_RemoteBlast() [2/2]
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private |
Method to construct and run the remote blast search.
Definition at line 301 of file remote_search.cpp.
References CRef< C, Locker >::Empty(), CConstRef< C, Locker >::Empty(), CSearchDatabase::GetDatabaseName(), CSearchDatabase::GetEntrezQueryLimitation(), CSearchDatabase::GetGiListLimitation(), CRemotePssmSearch::m_Pssm, CRemotePssmSearch::m_RemoteBlast, CRemotePssmSearch::m_SearchOpts, CRemotePssmSearch::m_Subject, NCBI_THROW, CRef< C, Locker >::Reset(), CRemoteBlast::SetDatabase(), CRemoteBlast::SetEntrezQuery(), CRemoteBlast::SetGIList(), and CRemoteBlast::SetQueries().
Referenced by CRemotePssmSearch::Run().
◆ x_RemoveMultipleCdHits()
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protected |
Remove multiple hits to the same CD.
For each pair of hits to the same CD the intersection between hits in CD ranges is subtracted using query ranges from the CD with worse e-value
Definition at line 168 of file cdd_pssm_input.cpp.
References CCddInputData::CHit::eSubject, i, CCddInputData::CHit::IntersectWith(), CCddInputData::m_Hits, NULL, and ct::sort().
Referenced by CCddInputData::Process().
◆ x_ResetInternalDs()
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private |
Clean up structures and results from any previous search.
Definition at line 141 of file bl2seq.cpp.
References Blast_DiagnosticsFree(), CBl2Seq::m_AncillaryData, CBl2Seq::m_Messages, CBl2Seq::m_Results, CBl2Seq::mi_pDiagnostics, and CRef< C, Locker >::Reset().
Referenced by CBl2Seq::SetOptionsHandle(), CBl2Seq::SetQueries(), CBl2Seq::SetQuery(), CBl2Seq::SetSubject(), CBl2Seq::SetSubjects(), and CBl2Seq::~CBl2Seq().
◆ x_ResetValue()
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inlineprivate |
Remove values for a given Blast4 field.
- Parameters
-
f Field to search for and remove.
Definition at line 273 of file blast_options_cxx.cpp.
References f, and CBlastOptionsRemote::m_ReqOpts.
Referenced by CBlastOptionsRemote::ResetValue().
◆ x_Run()
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protected |
Definition at line 104 of file magicblast.cpp.
References CBlastPrelimSearch::CheckInternalData(), TSearchMessages::Combine(), CBlastException::eCoreBlastError, CException::GetErrCode(), CThreadable::GetNumberOfThreads(), ILocalQueryData::GetNumQueries(), ILocalQueryData::GetQueryMessages(), CBlastPrelimSearch::GetSearchMessages(), ILocalQueryData::GetSeq_loc(), i, CLocalDbAdapter::IsBlastDb(), CLocalDbAdapter::IsDbScanMode(), CMagicBlast::m_InternalData, CMagicBlast::m_LocalDbAdapter, CMagicBlast::m_Options, CMagicBlast::m_PrelimSearch, CMagicBlast::m_Queries, IQueryFactory::MakeLocalQueryData(), CLocalDbAdapter::MakeSeqInfoSrc(), msg(), CRef< C, Locker >::NotEmpty(), NULL, CRef< C, Locker >::Reset(), CBlastPrelimSearch::Run(), CBlastPrelimSearch::SetNumberOfThreads(), and IBlastSeqInfoSrc::Size().
Referenced by CMagicBlast::Run(), and CMagicBlast::RunEx().
◆ x_safe_memcmp()
Definition at line 429 of file blast_options_local_priv.cpp.
References a, b, NULL, and ncbi::grid::netcache::search::fields::size.
Referenced by CBlastOptionsLocal::operator==(), and x_BlastEffectiveLengthsOptions_cmp().
◆ x_safe_strcmp()
Definition at line 416 of file blast_options_local_priv.cpp.
References a, b, NULL, and util::strcmp().
Referenced by x_BlastScoringOptions_cmp(), x_LookupTableOptions_cmp(), and x_QuerySetupOptions_cmp().
◆ x_ScreenByAlignLength()
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private |
Definition at line 173 of file igblast.cpp.
References NON_CONST_ITERATE, result, and results.
Referenced by CIgBlast::Run().
◆ x_SearchErrors()
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private |
Iterate over error list, splitting into errors and warnings.
Definition at line 100 of file remote_blast.cpp.
References eBlast4_error_code_bad_request, eBlast4_error_code_bad_request_id, eBlast4_error_code_conversion_warning, eBlast4_error_code_internal_error, eBlast4_error_code_not_allowed, eBlast4_error_code_not_implemented, NStr::eNocase, i, CRemoteBlast::m_Errs, CRemoteBlast::m_Warn, NStr::MatchesMask(), msg(), and TRUE.
Referenced by CRemoteBlast::x_CheckResults(), CRemoteBlast::x_CheckResultsDC(), and CRemoteBlast::x_SubmitSearch().
◆ x_SendRequest()
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private |
Send a Blast4 request and get a reply.
- Returns
- The blast4 server response.
Definition at line 199 of file remote_blast.cpp.
References CBlast4Client_Base::Ask(), CRemoteBlast::eDebug, CStopWatch::Elapsed(), CStopWatch::eStart, CRemoteBlast::m_ClientId, CRemoteBlast::m_Verbose, MSerial_AsnText, NCBI_THROW, NcbiCout, CBlast4_request_Base::SetBody(), CBlast4_request_Base::SetIdent(), sw, and CRemoteBlast::x_CheckConfig().
Referenced by CRemoteBlast::GetTitle(), CRemoteBlast::x_GetPsiIterationsFromServer(), CRemoteBlast::x_GetSearchResults(), CRemoteBlast::x_GetSearchStatsOnly(), and CRemoteBlast::x_SubmitSearch().
◆ x_SetAlgoOpts()
|
private |
Configure new search from options handle passed to constructor.
Definition at line 897 of file remote_blast.cpp.
References CBlast4_parameters::Add(), env, kEmptyStr, CRemoteBlast::m_CBOH, and CRemoteBlast::m_QSR.
Referenced by CRemoteBlast::x_GetBlast4SearchRequestBody().
◆ x_SetAnnotation()
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private |
Append annotation info to the final results.
Definition at line 2069 of file igblast.cpp.
References CIgAnnotation::m_GeneInfo, CIgBlast::m_IgOptions, CIgBlastOptions::m_MinJLength, NON_CONST_ITERATE, CRef< C, Locker >::Reset(), result, and CIgBlastResults::SetIgAnnotation().
Referenced by CIgBlast::Run().
◆ x_SetChainType()
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private |
Set the subject chain type and frame info.
Definition at line 1904 of file igblast.cpp.
References i, ITERATE, CIgAnnotation::m_ChainType, CIgBlastResults::m_NumActualC, CIgBlastResults::m_NumActualD, CIgBlastResults::m_NumActualJ, CIgBlastResults::m_NumActualV, result, and results.
Referenced by CIgBlast::Run().
◆ x_SetDatabase()
Sets a subset (only m_Dbs) of what the public SetDatabase sets.
- Parameters
-
x name of database.
Definition at line 1535 of file remote_blast.cpp.
References eBlast4_residue_type_nucleotide, eBlast4_residue_type_protein, eBlast4_residue_type_unknown, CRemoteBlast::m_Dbs, CRemoteBlast::m_Program, CRemoteBlast::m_Service, CRemoteBlast::m_SubjectSequences, and CRef< C, Locker >::Reset().
Referenced by CRemoteBlast::SetDatabase(), and CRemoteBlast::x_GetRequestInfoFromFile().
◆ x_SetInfo()
|
private |
Definition at line 651 of file magicblast.cpp.
References ASSERT, eNa_strand_minus, eNa_strand_plus, CMagicBlastResults::fFiltered, CMagicBlastResults::fUnaligned, CSeq_align_set_Base::Get(), COpenRange< Position >::GetLength(), CSeq_align::GetSeqStart(), CSeq_align::GetSeqStrand(), CMagicBlastResults::m_Aligns, CMagicBlastResults::m_Concordant, CMagicBlastResults::m_FirstInfo, CMagicBlastResults::m_LastInfo, CMagicBlastResults::m_MateId, CMagicBlastResults::m_Paired, and CMagicBlastResults::m_QueryId.
Referenced by CMagicBlastResults::CMagicBlastResults().
◆ x_SetMaskingLocationsForQueries()
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private |
Set the masking locations AFTER the queries have been set in the m_QSR field.
Definition at line 1039 of file remote_blast.cpp.
References _ASSERT, CRemoteBlast::m_QSR, CRemoteBlast::m_QueryMaskingLocations, and NCBI_THROW.
Referenced by CRemoteBlast::SetQueries(), and CRemoteBlast::SetQueryMasks().
◆ x_SetMinusStrand() [1/3]
|
protectedvirtual |
@inheritDoc
Implements IBlastSeqVector.
Definition at line 193 of file bioseq_extract_data_priv.cpp.
References eNa_strand_minus, IBlastSeqVector::GetStrand(), and CBlastSeqVectorFromCSeq_data::x_ComplementData().
◆ x_SetMinusStrand() [2/3]
|
inlineprotectedvirtual |
@inheritDoc
Implements IBlastSeqVector.
Definition at line 533 of file blast_objmgr_tools.cpp.
References eNa_strand_minus, and CBlastSeqVectorOM::x_SetStrand().
◆ x_SetMinusStrand() [3/3]
|
protectedpure virtual |
Method which does the work for setting the minus strand of the nucleotide sequence data.
Implemented in CBlastSeqVectorOM, and CBlastSeqVectorFromCSeq_data.
Referenced by IBlastSeqVector::GetStrandData(), and IBlastSeqVector::SetMinusStrand().
◆ x_SetOneParam() [1/12]
|
inlineprivate |
Definition at line 197 of file blast_options_cxx.cpp.
References CBlast4Field::GetName(), and CBlastOptionsRemote::x_AttachValue().
◆ x_SetOneParam() [2/12]
|
inlineprivate |
Definition at line 185 of file blast_options_cxx.cpp.
References CBlast4Field::GetName(), and CBlastOptionsRemote::x_AttachValue().
◆ x_SetOneParam() [3/12]
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inlineprivate |
Definition at line 221 of file blast_options_cxx.cpp.
References CBlast4Field::GetName(), and CBlastOptionsRemote::x_AttachValue().
◆ x_SetOneParam() [4/12]
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inlineprivate |
Definition at line 173 of file blast_options_cxx.cpp.
References CBlast4Field::GetName(), and CBlastOptionsRemote::x_AttachValue().
Referenced by CBlastOptionsRemote::x_SetParam().
◆ x_SetOneParam() [5/12]
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inlineprivate |
Definition at line 233 of file blast_options_cxx.cpp.
References CBlast4Field::GetName(), and CBlastOptionsRemote::x_AttachValue().
◆ x_SetOneParam() [6/12]
|
inlineprivate |
Definition at line 209 of file blast_options_cxx.cpp.
References CBlast4Field::GetName(), and CBlastOptionsRemote::x_AttachValue().
◆ x_SetOneParam() [7/12]
|
inlineprivate |
Definition at line 245 of file blast_options_cxx.cpp.
References CBlast4Field::GetName(), and CBlastOptionsRemote::x_AttachValue().
◆ x_SetOneParam() [8/12]
|
private |
Set a string parameter.
- Parameters
-
field CBlast4Field object corresponding to option. value Pointer to pointer to null delimited string.
Definition at line 972 of file remote_blast.cpp.
References _ASSERT, CRemoteBlast::m_QSR, and CBlast4_value_Base::SetString().
◆ x_SetOneParam() [9/12]
Set an integer parameter (not used yet).
- Parameters
-
field CBlast4Field object corresponding to option. value Pointer to integer value to use.
Definition at line 914 of file remote_blast.cpp.
References _ASSERT, CRemoteBlast::m_QSR, and CBlast4_value_Base::SetInteger().
Referenced by CRemoteBlast::SetDbFilteringAlgorithmId(), CRemoteBlast::SetDbFilteringAlgorithmKey(), CRemoteBlast::SetEntrezQuery(), CRemoteBlast::SetGIList(), CRemoteBlast::SetNegativeGIList(), CRemoteBlast::x_InitQueries(), and CRemoteBlast::x_QueryMaskingLocationsToNetwork().
◆ x_SetOneParam() [10/12]
|
private |
Set a list of integers.
- Parameters
-
field CBlast4Field object corresponding to option. value Pointer to list of integers to use.
Definition at line 943 of file remote_blast.cpp.
References _ASSERT, CRemoteBlast::m_QSR, and CBlast4_value_Base::SetInteger_list().
◆ x_SetOneParam() [11/12]
|
private |
Set a list of 8 byte integers.
- Parameters
-
field CBlast4Field object corresponding to option. value Pointer to list of integers to use.
Definition at line 957 of file remote_blast.cpp.
References _ASSERT, CRemoteBlast::m_QSR, and CBlast4_value_Base::SetBig_integer_list().
◆ x_SetOneParam() [12/12]
|
private |
Set a masking location for query.
- Parameters
-
field CBlast4Field object corresponding to option. mask masking location [in]
Definition at line 928 of file remote_blast.cpp.
References _ASSERT, CRemoteBlast::m_QSR, mask, and CBlast4_value_Base::SetQuery_mask().
◆ x_SetParam()
|
inlineprivate |
Definition at line 168 of file blast_options_cxx.cpp.
References rapidjson::value, and CBlastOptionsRemote::x_SetOneParam().
Referenced by CBlastOptionsRemote::SetValue().
◆ x_SetPlusStrand() [1/3]
|
protectedvirtual |
@inheritDoc
Implements IBlastSeqVector.
Definition at line 185 of file bioseq_extract_data_priv.cpp.
References eNa_strand_plus, IBlastSeqVector::GetStrand(), and CBlastSeqVectorFromCSeq_data::x_ComplementData().
◆ x_SetPlusStrand() [2/3]
|
inlineprotectedvirtual |
@inheritDoc
Implements IBlastSeqVector.
Definition at line 529 of file blast_objmgr_tools.cpp.
References eNa_strand_plus, and CBlastSeqVectorOM::x_SetStrand().
◆ x_SetPlusStrand() [3/3]
|
protectedpure virtual |
Method which does the work for setting the plus strand of the nucleotide sequence data.
Implemented in CBlastSeqVectorOM, and CBlastSeqVectorFromCSeq_data.
Referenced by IBlastSeqVector::GetStrandData(), and IBlastSeqVector::SetPlusStrand().
◆ x_SetStrand()
|
inlineprotected |
@inheritDoc
- Note
- for this class, this might be inefficient, please use GetStrandData with the appropriate strand
Definition at line 540 of file blast_objmgr_tools.cpp.
References _ASSERT, CBioseq_Handle::eCoding_Ncbi, CSeqVector::GetStrand(), CBlastSeqVectorOM::m_Scope, CBlastSeqVectorOM::m_SeqLoc, CBlastSeqVectorOM::m_SeqVector, IBlastSeqVector::m_Strand, and CBlastSeqVectorOM::x_FixStrand().
Referenced by CBlastSeqVectorOM::x_SetMinusStrand(), and CBlastSeqVectorOM::x_SetPlusStrand().
◆ x_SetSubjectSequences()
Set a list of subject sequences to search against (only m_SubjectSequences)
- Parameters
-
subj subject bioseqs
Definition at line 1600 of file remote_blast.cpp.
References CRemoteBlast::m_Dbs, CRemoteBlast::m_SubjectSequences, and CRef< C, Locker >::Reset().
Referenced by CRemoteBlast::SetSubjectSequences(), and CRemoteBlast::x_GetSubjects().
◆ x_SetupCRegionSearch()
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private |
Definition at line 575 of file igblast.cpp.
References CBlastQueryVector::GetBlastSearchQuery(), ITERATE, len, CIgBlast::m_IgOptions, CIgBlastOptions::m_NumAlign, CIgBlast::m_Query, mask, ms(), query, CRef< C, Locker >::Reset(), CBlastOptionsHandle::SetEvalueThreshold(), CBlastOptionsHandle::SetFilterString(), CBlastOptions::SetGapExtensionCost(), CBlastOptions::SetGapOpeningCost(), CBlastOptionsHandle::SetHitlistSize(), CBlastQueryVector::SetMaskedRegions(), CBlastOptions::SetMatchReward(), CBlastOptions::SetMismatchPenalty(), CBlastOptionsHandle::SetOptions(), and CBlastOptions::SetWordSize().
Referenced by CIgBlast::Run().
◆ x_SetupDbSearch()
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private |
Prepare blast option handle and query for specified database search.
Definition at line 754 of file igblast.cpp.
References CBlastQueryVector::GetBlastSearchQuery(), ITERATE, len, CIgBlastOptions::m_FocusV, CIgBlast::m_IgOptions, CIgBlast::m_Query, mask, query, CRef< C, Locker >::Reset(), and CBlastQueryVector::SetMaskedRegions().
Referenced by CIgBlast::Run().
◆ x_SetupDJSearch()
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private |
Prepare blast option handle and query for D, J germline database search.
Definition at line 622 of file igblast.cpp.
References CBlastQueryVector::AddMask(), CBlastQueryVector::GetBlastSearchQuery(), ITERATE, j_wordsize, len, CIgBlastOptions::m_D_penalty, CIgBlastOptions::m_DetectOverlap, CIgBlast::m_IgOptions, CIgBlastOptions::m_J_penalty, CIgBlastOptions::m_Min_D_match, CIgBlastOptions::m_NumAlign, CIgBlast::m_Query, mask, max(), max_allowed_V_end_to_J_end, max_v_j_overlap, ms(), query, CRef< C, Locker >::Reset(), CBlastOptionsHandle::SetEvalueThreshold(), CBlastOptionsHandle::SetFilterString(), CBlastOptions::SetGapExtensionCost(), CBlastOptions::SetGapOpeningCost(), CBlastOptionsHandle::SetHitlistSize(), CBlastQueryVector::SetMaskedRegions(), CBlastOptions::SetMatchReward(), CBlastOptions::SetMismatchPenalty(), CBlastOptionsHandle::SetOptions(), and CBlastOptions::SetWordSize().
Referenced by CIgBlast::Run().
◆ x_SetupNoOverlapDSearch()
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private |
Definition at line 692 of file igblast.cpp.
References CBlastQueryVector::AddMask(), CRef< C, Locker >::Empty(), CBlastQueryVector::GetBlastSearchQuery(), CSeq_align_set::IsEmpty(), ITERATE, len, CIgBlastOptions::m_D_penalty, CIgBlast::m_IgOptions, CIgBlastOptions::m_Min_D_match, CIgBlastOptions::m_NumAlign, CIgBlast::m_Query, mask, max(), max_allowed_V_end_to_J_end, min(), ms(), query, CRef< C, Locker >::Reset(), CBlastOptionsHandle::SetEvalueThreshold(), CBlastOptionsHandle::SetFilterString(), CBlastOptions::SetGapExtensionCost(), CBlastOptions::SetGapOpeningCost(), CBlastOptionsHandle::SetHitlistSize(), CBlastQueryVector::SetMaskedRegions(), CBlastOptions::SetMatchReward(), CBlastOptions::SetMismatchPenalty(), CBlastOptionsHandle::SetOptions(), and CBlastOptions::SetWordSize().
Referenced by CIgBlast::Run().
◆ x_SetupVSearch()
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private |
Prepare blast option handle and query for V germline database search.
Definition at line 553 of file igblast.cpp.
References eNoCompositionBasedStats, CBlastOptions::GetEvalueThreshold(), CBlastOptionsHandle::GetOptions(), CBlastOptions::GetWordSize(), CIgBlast::m_IgOptions, CIgBlastOptions::m_IsProtein, CIgBlastOptions::m_NumAlign, CIgBlast::m_Options, CIgBlast::m_Query, CIgBlastOptions::m_V_penalty, CRef< C, Locker >::Reset(), CBlastOptions::SetCompositionBasedStats(), CBlastOptionsHandle::SetEvalueThreshold(), CBlastOptionsHandle::SetFilterString(), CBlastOptions::SetGapExtensionCost(), CBlastOptions::SetGapOpeningCost(), CBlastOptionsHandle::SetHitlistSize(), CBlastOptions::SetMatchReward(), CBlastOptions::SetMismatchPenalty(), CBlastOptionsHandle::SetOptions(), and CBlastOptions::SetWordSize().
Referenced by CIgBlast::Run().
◆ x_Size() [1/3]
|
inlineprotectedvirtual |
@inheritDoc
Implements IBlastSeqVector.
Definition at line 156 of file bioseq_extract_data_priv.cpp.
References CBlastSeqVectorFromCSeq_data::m_SequenceData.
Referenced by CBlastSeqVectorFromCSeq_data::operator[]().
◆ x_Size() [2/3]
|
inlineprotectedvirtual |
@inheritDoc
Implements IBlastSeqVector.
Definition at line 525 of file blast_objmgr_tools.cpp.
References CBlastSeqVectorOM::m_SeqVector, and CSeqVector::size().
◆ x_Size() [3/3]
|
protectedpure virtual |
Method which retrieves the size of the sequence vector, as described in the size() method above.
Implemented in CBlastSeqVectorOM, and CBlastSeqVectorFromCSeq_data.
Referenced by IBlastSeqVector::GetStrandData(), and IBlastSeqVector::size().
◆ x_SubmitSearch()
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private |
Submit the search and process results (of submit action).
Definition at line 643 of file remote_blast.cpp.
References CRemoteBlast::m_Errs, CRemoteBlast::m_Pending, CRemoteBlast::m_RID, CRemoteBlast::x_GetBlast4SearchRequestBody(), CRemoteBlast::x_SearchErrors(), and CRemoteBlast::x_SendRequest().
Referenced by CRemoteBlast::Submit(), and CRemoteBlast::SubmitSync().
◆ x_ThrowExceptionOnLogicError()
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private |
After the iteration state object has converged or exhausted its iterations, it shouldn't be modified, so it throws a CBlastException if this happens.
Definition at line 100 of file psiblast_iteration.cpp.
References msg(), and NCBI_THROW.
Referenced by CPsiBlastIterationState::Advance().
◆ x_Throwx() [1/2]
Auxiliary to throw CBlastExceptions.
- Parameters
-
msg message to pass in the exception [in]
Definition at line 2700 of file blast_options_cxx.cpp.
References msg(), and NCBI_THROW.
Referenced by CBlastOptions::GetBestHitOverhang(), CBlastOptions::GetBestHitScoreEdge(), CBlastOptions::GetChaining(), CBlastOptions::GetComplexityAdjMode(), CBlastOptions::GetCompositionBasedStats(), CBlastOptions::GetCullingLimit(), CBlastOptions::GetCutoffScore(), CBlastOptions::GetCutoffScoreCoeffs(), CBlastOptions::GetDbGeneticCode(), CBlastOptions::GetDbLength(), CBlastOptions::GetDbSeqNum(), CBlastOptions::GetDomainInclusionThreshold(), CBlastOptions::GetDustFiltering(), CBlastOptions::GetDustFilteringLevel(), CBlastOptions::GetDustFilteringLinker(), CBlastOptions::GetDustFilteringWindow(), CBlastOptions::GetEffectiveSearchSpace(), CBlastOptions::GetEvalueThreshold(), CBlastOptions::GetFilterString(), CBlastOptions::GetForceIndex(), CBlastOptions::GetFrameShiftPenalty(), CBlastOptions::GetGapExtensionCost(), CBlastOptions::GetGapExtnAlgorithm(), CBlastOptions::GetGapOpeningCost(), CBlastOptions::GetGappedMode(), CBlastOptions::GetGapTracebackAlgorithm(), CBlastOptions::GetGapTrigger(), CBlastOptions::GetGapXDropoff(), CBlastOptions::GetGapXDropoffFinal(), CBlastOptions::GetHitlistSize(), CBlastOptions::GetIgnoreMsaMaster(), CBlastOptions::GetInclusionThreshold(), CBlastOptions::GetIndexName(), CBlastOptions::GetIsOldStyleMBIndex(), CBlastOptions::GetLongestIntronLength(), CBlastOptions::GetLookupDbFilter(), CBlastOptions::GetLookupTableStride(), CBlastOptions::GetLookupTableType(), CBlastOptions::GetLowScorePerc(), CBlastOptions::GetMaskAtHash(), CBlastOptions::GetMaskLevel(), CBlastOptions::GetMatchReward(), CBlastOptions::GetMatrixName(), CBlastOptions::GetMaxDbWordCount(), CBlastOptions::GetMaxEditDistance(), CBlastOptions::GetMaxHspsPerSubject(), CBlastOptions::GetMaxMismatches(), CBlastOptions::GetMaxNumHspPerSequence(), CBlastOptions::GetMBIndexLoaded(), CBlastOptions::GetMBTemplateLength(), CBlastOptions::GetMBTemplateType(), CBlastOptions::GetMinDiagSeparation(), CBlastOptions::GetMismatchPenalty(), CBlastOptions::GetMismatchWindow(), CBlastOptions::GetOffDiagonalRange(), CBlastOptions::GetOutOfFrameMode(), CBlastOptions::GetPaired(), CBlastOptions::GetPercentIdentity(), CBlastOptions::GetPHIPattern(), CBlastOptions::GetProgram(), CBlastOptions::GetProgramType(), CBlastOptions::GetPseudoCount(), CBlastOptions::GetQueryCovHspPerc(), CBlastOptions::GetQueryGeneticCode(), CBlastOptions::GetReadMaxFractionAmbiguous(), CBlastOptions::GetReadMinDimerEntropy(), CBlastOptions::GetReadQualityFiltering(), CBlastOptions::GetRepeatFiltering(), CBlastOptions::GetRepeatFilteringDB(), CBlastOptions::GetSegFiltering(), CBlastOptions::GetSegFilteringHicut(), CBlastOptions::GetSegFilteringLocut(), CBlastOptions::GetSegFilteringWindow(), CBlastOptions::GetSmithWatermanMode(), CBlastOptions::GetSpliceAlignments(), CBlastOptions::GetStrandOption(), CBlastOptions::GetSubjectBestHit(), CBlastOptions::GetSumStatisticsMode(), CBlastOptions::GetUnifiedP(), CBlastOptions::GetUseIndex(), CBlastOptions::GetWindowMaskerDatabase(), CBlastOptions::GetWindowMaskerTaxId(), CBlastOptions::GetWindowSize(), CBlastOptions::GetWordSize(), CBlastOptions::GetWordThreshold(), CBlastOptions::GetXDropoff(), CBlastOptions::SetChaining(), CBlastOptions::SetCutoffScoreCoeffs(), CBlastOptions::SetLookupDbFilter(), CBlastOptions::SetLookupTableStride(), CBlastOptions::SetMaxDbWordCount(), CBlastOptions::SetMaxEditDistance(), CBlastOptions::SetMaxMismatches(), CBlastOptions::SetMBIndexLoaded(), CBlastOptions::SetMinDiagSeparation(), CBlastOptions::SetMismatchWindow(), CBlastOptions::SetPaired(), CBlastOptions::SetReadMaxFractionAmbiguous(), CBlastOptions::SetReadMinDimerEntropy(), CBlastOptions::SetReadQualityFiltering(), and CBlastOptions::SetSpliceAlignments().
◆ x_Throwx() [2/2]
Definition at line 292 of file blast_options_cxx.cpp.
References msg(), and NCBI_THROW.
Referenced by CBlastOptionsRemote::SetValue().
◆ x_TranslateFilteringAlgorithm()
|
private |
Translate string algorithm id to numeric id.
Definition at line 223 of file uniform_search.cpp.
References eNoSubjMasking, CSeqDB::GetMaskAlgorithmId(), CSearchDatabase::m_DbInitialized, CSearchDatabase::m_FilteringAlgorithmId, CSearchDatabase::m_FilteringAlgorithmString, CSearchDatabase::m_MaskType, CSearchDatabase::m_NeedsFilteringTranslation, CSearchDatabase::m_SeqDb, and CSearchDatabase::x_InitializeDb().
Referenced by CSearchDatabase::GetFilteringAlgorithm().
◆ x_UngappedHSPToDenseDiag()
| CRef<CDense_diag> x_UngappedHSPToDenseDiag | ( | BlastHSP * | hsp, |
| CRef< CSeq_id > | query_id, | ||
| CRef< CSeq_id > | subject_id, | ||
| Int4 | query_length, | ||
| Int4 | subject_length, | ||
| const vector< string > & | seqid_list | ||
| ) |
Creates a Dense-diag object from HSP information and sequence identifiers for a non-translated ungapped search.
- Parameters
-
hsp An HSP structure [in] query_id Query sequence identifier [in] subject_id Subject sequence identifier [in] query_length Length of the query [in] subject_length Length of the subject [in] gi_list List of GIs for the subject sequence.
- Returns
- Resulting Dense-diag object.
Definition at line 1274 of file blast_seqalign.cpp.
References BlastSeg::end, BlastSeg::frame, kBlastAlignmentDim, BlastSeg::offset, BlastHSP::query, s_BuildScoreList(), s_Frame2Strand(), and BlastHSP::subject.
Referenced by BLASTUngappedHspListToSeqAlign().
◆ x_UngappedHSPToStdSeg()
| CRef<CStd_seg> x_UngappedHSPToStdSeg | ( | BlastHSP * | hsp, |
| CRef< CSeq_id > | query_id, | ||
| CRef< CSeq_id > | subject_id, | ||
| Int4 | query_length, | ||
| Int4 | subject_length, | ||
| const vector< string > & | seqid_list | ||
| ) |
Creates a Std-seg object from HSP information and sequence identifiers for a translated ungapped search.
- Parameters
-
hsp An HSP structure [in] query_id Query sequence identifier [in] subject_id Subject sequence identifier [in] query_length Length of the query [in] subject_length Length of the subject [in] gi_list List of GIs for the subject sequence.
- Returns
- Resulting Std-seg object.
Definition at line 1324 of file blast_seqalign.cpp.
References CODON_LENGTH, BlastSeg::end, BlastSeg::frame, kBlastAlignmentDim, BlastSeg::offset, BlastHSP::query, s_BuildScoreList(), s_Frame2Strand(), CSeq_loc::SetInt(), and BlastHSP::subject.
Referenced by BLASTPrelminSearchHitListToStdSeg(), and BLASTUngappedHspListToSeqAlign().
◆ x_Validate() [1/3]
|
private |
Perform sanity checks on input parameters.
Definition at line 80 of file psiblast_impl.cpp.
References CRef< C, Locker >::Empty(), CConstRef< C, Locker >::Empty(), CPsiBlastImpl::m_OptsHandle, CPsiBlastImpl::m_Pssm, CPsiBlastImpl::m_Query, CPsiBlastImpl::m_Subject, NCBI_THROW, CRef< C, Locker >::NotEmpty(), CPsiBlastValidate::Pssm(), CPsiBlastValidate::QueryFactory(), and CBlastOptionsHandle::Validate().
Referenced by CPsiBlastImpl::CPsiBlastImpl().
◆ x_Validate() [2/3]
|
protected |
Perform sanity checks on input parameters.
Definition at line 215 of file deltablast.cpp.
References CRef< C, Locker >::Empty(), CConstRef< C, Locker >::Empty(), CDeltaBlast::m_DomainDb, CDeltaBlast::m_Options, CDeltaBlast::m_Queries, CDeltaBlast::m_Subject, and NCBI_THROW.
Referenced by CDeltaBlast::CDeltaBlast().
◆ x_Validate() [3/3]
|
protected |
Perform sanity checks on input arguments.
Definition at line 190 of file magicblast.cpp.
References CRef< C, Locker >::Empty(), CMagicBlast::m_LocalDbAdapter, CMagicBlast::m_Options, CMagicBlast::m_Queries, and NCBI_THROW.
Referenced by CMagicBlast::CMagicBlast().
◆ x_ValidateHits()
|
protected |
Validate internal representation of RPS-BLAST hits.
Definition at line 431 of file cdd_pssm_input.cpp.
References _ASSERT, ITERATE, and CCddInputData::m_Hits.
Referenced by CCddInputData::Process().
◆ x_ValidateIndex()
|
private |
Definition at line 74 of file query_data.cpp.
References ILocalQueryData::GetNumQueries(), and NStr::SizetToString().
Referenced by ILocalQueryData::GetQueryMessages(), and ILocalQueryData::IsValidQuery().
◆ x_ValidateMaskingAlgorithm()
|
private |
Validates that the specified filtering algorithm ID is supported by the specified BLAST database.
- Exceptions
-
CBlastException if validation fails
Definition at line 301 of file uniform_search.cpp.
References CRef< C, Locker >::Empty(), CSeqDB::GetAvailableMaskAlgorithms(), CSearchDatabase::GetDatabaseName(), CSearchDatabase::IsProtein(), CSearchDatabase::m_FilteringAlgorithmId, CSearchDatabase::m_SeqDb, msg(), and NCBI_THROW.
Referenced by CSearchDatabase::SetFilteringAlgorithm(), and CSearchDatabase::x_InitializeDb().
◆ x_ValidateMsa()
|
protected |
Validate multiple alignment of CDs.
Definition at line 286 of file cdd_pssm_input.cpp.
References _ASSERT, AMINOACID_TO_NCBISTDAA, PSICdMsaCell::data, data, fabs, i, int, bm::is_aligned(), CCddInputData::kAlphabetSize, kGapChar(), CCddInputData::m_Hits, CCddInputData::m_Msa, CCddInputData::m_QueryData, and NCBI_THROW.
Referenced by CCddInputData::Process().
◆ x_ValidateQueryInMsa()
|
private |
Searches the query sequence (m_Query) in the aligned sequences (m_AsciiMsa) and moves the first instance it finds to the front of this data structure.
- Exceptions
-
CBlastException if the query sequence is not found.
Definition at line 226 of file msa_pssm_input.cpp.
References _ASSERT, AutoPtr< X, Del >::get(), CPsiBlastInputClustalW::GetQueryLength(), kGapChar(), kProtMask, CPsiBlastInputClustalW::m_AsciiMsa, CPsiBlastInputClustalW::m_Query, msg(), NCBI_THROW, NCBISTDAA_TO_AMINOACID, swap(), and toupper().
◆ x_VerifyFrame()
|
private |
Verify the specified frame value.
Definition at line 1654 of file blast_setup_cxx.cpp.
References eBlastTypeBlastn, eBlastTypeBlastp, eBlastTypeBlastx, eBlastTypeMapping, eBlastTypePhiBlastp, eBlastTypePsiBlast, eBlastTypePsiTblastn, eBlastTypeRpsBlast, eBlastTypeRpsTblastn, eBlastTypeTblastn, eBlastTypeTblastx, CSeqLocInfo::eFrameMinus1, CSeqLocInfo::eFramePlus1, CBlastQueryFilteredFrames::m_Program, and NCBI_THROW.
Referenced by CBlastQueryFilteredFrames::AddSeqLoc(), and CBlastQueryFilteredFrames::operator[]().
◆ ~CAutomaticGenCodeSingleton()
| CAutomaticGenCodeSingleton::~CAutomaticGenCodeSingleton | ( | ) |
destructor
Definition at line 645 of file blast_aux.cpp.
References GenCodeSingletonFini(), and CAutomaticGenCodeSingleton::m_RefCounter.
◆ ~CAutoNcbiConfigFile()
|
inline |
Definition at line 97 of file blast_input_unit_test_aux.hpp.
References CMetaRegistry::fAlwaysReload, CAutoNcbiConfigFile::kDataLoaders, kEmptyStr, CAutoNcbiConfigFile::kNuclBlastDbDataLoader, CAutoNcbiConfigFile::kProtBlastDbDataLoader, CAutoNcbiConfigFile::kSection, CAutoNcbiConfigFile::m_App, CAutoNcbiConfigFile::m_BlastDb, CAutoNcbiConfigFile::m_Registry, CNcbiApplicationAPI::ReloadConfig(), and IRWRegistry::Set().
◆ ~CBl2Seq()
|
virtual |
◆ ~CBlast_ExtendWord()
|
inlinevirtual |
Definition at line 322 of file blast_aux.hpp.
◆ ~CBlast_Message()
|
inlinevirtual |
Definition at line 352 of file blast_aux.hpp.
◆ ~CBLAST_SequenceBlk()
|
inlinevirtual |
Definition at line 309 of file blast_aux.hpp.
◆ ~CBlastAncillaryData()
| CBlastAncillaryData::~CBlastAncillaryData | ( | ) |
Destructor.
Definition at line 163 of file blast_results.cpp.
References Blast_KarlinBlkFree(), CBlastAncillaryData::m_GappedKarlinBlk, CBlastAncillaryData::m_GumbelBlk, CBlastAncillaryData::m_PsiGappedKarlinBlk, CBlastAncillaryData::m_PsiUngappedKarlinBlk, CBlastAncillaryData::m_UngappedKarlinBlk, and sfree.
◆ ~CBlastAppDiagHandler()
| CBlastAppDiagHandler::~CBlastAppDiagHandler | ( | ) |
Destructor.
Definition at line 1181 of file blast_aux.cpp.
References CBlastAppDiagHandler::m_handler, NULL, and SetDiagHandler().
◆ ~CBlastDatabaseOptions()
|
inlinevirtual |
Definition at line 331 of file blast_aux.hpp.
◆ ~CBlastEffectiveLengthsOptions()
|
inlinevirtual |
Definition at line 338 of file blast_aux.hpp.
◆ ~CBlastEffectiveLengthsParameters()
|
inlinevirtual |
Definition at line 340 of file blast_aux.hpp.
◆ ~CBlastExtensionOptions()
|
inlinevirtual |
Definition at line 323 of file blast_aux.hpp.
◆ ~CBlastExtensionParameters()
|
inlinevirtual |
Definition at line 324 of file blast_aux.hpp.
◆ ~CBlastGapAlignStruct()
|
inlinevirtual |
Definition at line 342 of file blast_aux.hpp.
◆ ~CBlastHitSavingOptions()
|
inlinevirtual |
Definition at line 326 of file blast_aux.hpp.
◆ ~CBlastHitSavingParameters()
|
inlinevirtual |
Definition at line 328 of file blast_aux.hpp.
◆ ~CBlastHSPListQueueData()
| CBlastHSPListQueueData::~CBlastHSPListQueueData | ( | ) |
Destructor.
◆ ~CBlastHSPResults()
|
inlinevirtual |
Definition at line 343 of file blast_aux.hpp.
◆ ~CBlastInitialWordOptions()
|
inlinevirtual |
Definition at line 318 of file blast_aux.hpp.
◆ ~CBlastInitialWordParameters()
|
inlinevirtual |
Definition at line 320 of file blast_aux.hpp.
◆ ~CBlastMaskLoc()
|
inlinevirtual |
Definition at line 354 of file blast_aux.hpp.
◆ ~CBlastOptions()
| CBlastOptions::~CBlastOptions | ( | ) |
Destructor.
Definition at line 315 of file blast_options_cxx.cpp.
References CBlastOptions::m_Local, and CBlastOptions::m_Remote.
◆ ~CBlastOptionsLocal()
| CBlastOptionsLocal::~CBlastOptionsLocal | ( | ) |
Definition at line 70 of file blast_options_local_priv.cpp.
◆ ~CBlastOptionsMemento()
|
inline |
Note the no-op destructor, this class does not own any of its data members!
Definition at line 61 of file blast_memento_priv.hpp.
◆ ~CBlastOptionsRemote()
|
inline |
Definition at line 69 of file blast_options_cxx.cpp.
◆ ~CBlastpKmerOptionsHandle()
|
inline |
Definition at line 60 of file blastp_kmer_options.hpp.
◆ ~CBlastQueryFilteredFrames()
| CBlastQueryFilteredFrames::~CBlastQueryFilteredFrames | ( | ) |
Destructor; frees any BlastSeqLoc lists not released by the caller.
Definition at line 1570 of file blast_setup_cxx.cpp.
References BlastSeqLocFree(), ITERATE, and CBlastQueryFilteredFrames::m_Seqlocs.
◆ ~CBlastQueryInfo()
|
inlinevirtual |
Definition at line 311 of file blast_aux.hpp.
◆ ~CBlastQuerySourceOM()
|
virtual |
dtor which determines if the internal pointer to its data should be deleted or not.
Definition at line 230 of file blast_objmgr_tools.cpp.
References CBlastQuerySourceOM::m_OwnTSeqLocVector, CBlastQuerySourceOM::m_TSeqLocVector, and NULL.
◆ ~CBlastRPSAuxInfo()
| CBlastRPSAuxInfo::~CBlastRPSAuxInfo | ( | ) |
◆ ~CBlastRPSInfo()
| CBlastRPSInfo::~CBlastRPSInfo | ( | ) |
Destructor.
Definition at line 610 of file rps_aux.cpp.
◆ ~CBlastScopeSourceWrapper()
|
inline |
Definition at line 130 of file blast_input_unit_test_aux.hpp.
References CBlastScopeSourceWrapper::m_ScopeSrc, and CRef< C, Locker >::Reset().
◆ ~CBlastScoreBlk()
|
inlinevirtual |
Definition at line 333 of file blast_aux.hpp.
◆ ~CBlastScoringOptions()
|
inlinevirtual |
Definition at line 334 of file blast_aux.hpp.
◆ ~CBlastScoringParameters()
|
inlinevirtual |
Definition at line 335 of file blast_aux.hpp.
◆ ~CBlastSeqLoc()
|
inlinevirtual |
Definition at line 355 of file blast_aux.hpp.
◆ ~CBlastSeqSrc()
|
inlinevirtual |
Definition at line 350 of file blast_aux.hpp.
◆ ~CBlastSeqSrcIterator()
|
inlinevirtual |
Definition at line 351 of file blast_aux.hpp.
◆ ~CBlastTracebackSearch()
|
virtual |
Destructor.
Definition at line 108 of file traceback_stage.cpp.
References CBlastTracebackSearch::m_OptsMemento.
◆ ~CCddInputData()
|
virtual |
Virtual destructor.
Definition at line 104 of file cdd_pssm_input.cpp.
References i, CCddInputData::m_Hits, and CCddInputData::m_Msa.
◆ ~CDeltaBlast()
|
inline |
Destructor.
Definition at line 98 of file deltablast.hpp.
◆ ~CDeltaBlastOptionsHandle()
|
inline |
Destructor.
Definition at line 59 of file deltablast_options.hpp.
◆ ~CEffectiveSearchSpacesMemento()
|
inline |
Destructor.
Definition at line 132 of file blast_memento_priv.hpp.
References _ASSERT, CBlastOptionsLocal::m_EffLenOpts, CEffectiveSearchSpacesMemento::m_EffLenOrig, CEffectiveSearchSpacesMemento::m_EffLenReplace, CBlastOptions::m_Local, CEffectiveSearchSpacesMemento::m_Options, NULL, and CBlastEffectiveLengthsOptions::Reset().
◆ ~CFilteringMemento()
|
inline |
Destructor.
Definition at line 68 of file effsearchspace_calc.cpp.
References SBlastFilterOptionsFree().
◆ ~CHit()
| CCddInputData::CHit::~CHit | ( | ) |
◆ ~CIgBlast()
|
inline |
Destructor.
Definition at line 283 of file igblast.hpp.
◆ ~CIndexedDb()
|
virtual |
Object destructor.
Definition at line 1031 of file blast_dbindex.cpp.
◆ ~CIndexedDb_New()
|
virtual |
◆ ~CLocalDbAdapter()
|
virtual |
Destructor.
Definition at line 92 of file local_db_adapter.cpp.
References BlastSeqSrcFree(), and CLocalDbAdapter::m_SeqSrc.
◆ ~CLookupTableOptions()
|
inlinevirtual |
Definition at line 314 of file blast_aux.hpp.
◆ ~CLookupTableWrap()
|
inlinevirtual |
Definition at line 315 of file blast_aux.hpp.
◆ ~CMagicBlast()
|
inline |
Destructor.
Definition at line 74 of file magicblast.hpp.
◆ ~CMultiSeqInfo()
| CMultiSeqInfo::~CMultiSeqInfo | ( | ) |
Destructor.
Definition at line 187 of file seqsrc_multiseq.cpp.
References BlastSequenceBlkFree(), CMultiSeqInfo::m_ivSeqBlkVec, and NON_CONST_ITERATE.
◆ ~CPHIBlastNuclOptionsHandle()
|
inline |
Definition at line 59 of file phiblast_nucl_options.hpp.
◆ ~CPHIBlastProtOptionsHandle()
|
inline |
Definition at line 60 of file phiblast_prot_options.hpp.
◆ ~CPrelimSearchRunner()
|
inline |
Definition at line 61 of file prelim_search_runner.hpp.
◆ ~CPrelimSearchThread()
|
inlineprotectedvirtual |
Definition at line 134 of file prelim_search_runner.hpp.
References BlastQueryInfoFree(), CPrelimSearchThread::m_InternalData, and SInternalData::m_QueryInfo.
◆ ~CPsiBl2Seq()
| CPsiBl2Seq::~CPsiBl2Seq | ( | ) |
◆ ~CPsiBlast()
| CPsiBlast::~CPsiBlast | ( | ) |
◆ ~CPsiBlastInputClustalW()
|
virtual |
virtual destructor
Definition at line 112 of file msa_pssm_input.cpp.
References CPsiBlastInputClustalW::m_DiagnosticsRequest, CPsiBlastInputClustalW::m_Msa, PSIDiagnosticsRequestFree(), and PSIMsaFree().
◆ ~CPsiBlastInputData()
|
virtual |
virtual destructor
Definition at line 115 of file psi_pssm_input.cpp.
References CPsiBlastInputData::m_Msa, CPsiBlastInputData::m_Query, and PSIMsaFree().
◆ ~CPsiBlastIterationState()
| CPsiBlastIterationState::~CPsiBlastIterationState | ( | ) |
Destructor.
Definition at line 54 of file psiblast_iteration.cpp.
◆ ~CPSIBlastOptions()
|
inlinevirtual |
Definition at line 330 of file blast_aux.hpp.
◆ ~CPSIBlastOptionsHandle()
|
inline |
Destructor.
Definition at line 62 of file psiblast_options.hpp.
◆ ~CPSIDiagnosticsRequest()
|
inlinevirtual |
Definition at line 347 of file blast_aux.hpp.
◆ ~CPSIDiagnosticsResponse()
|
inlinevirtual |
Definition at line 348 of file blast_aux.hpp.
◆ ~CPSIMatrix()
|
inlinevirtual |
Definition at line 346 of file blast_aux.hpp.
◆ ~CPSIMsa()
|
inlinevirtual |
Definition at line 345 of file blast_aux.hpp.
◆ ~CPssmEngine()
| CPssmEngine::~CPssmEngine | ( | ) |
Destructor.
Definition at line 213 of file pssm_engine.cpp.
◆ ~CQueryFactoryInfo()
| CQueryFactoryInfo::~CQueryFactoryInfo | ( | ) |
Destructor.
Definition at line 151 of file seqsrc_query_factory.cpp.
References BlastSequenceBlkFree(), CQueryFactoryInfo::m_QuerySource, CQueryFactoryInfo::m_SeqBlkVector, NON_CONST_ITERATE, and CRef< C, Locker >::Reset().
◆ ~CQuerySetUpOptions()
|
inlinevirtual |
Definition at line 312 of file blast_aux.hpp.
◆ ~CRemoteBlast()
| CRemoteBlast::~CRemoteBlast | ( | ) |
Destruct the search object.
Definition at line 1456 of file remote_blast.cpp.
◆ ~CRpsFreqRatiosFile()
|
inlinevirtual |
Definition at line 474 of file rps_aux.cpp.
◆ ~CRPSTBlastnOptionsHandle()
|
inline |
Definition at line 59 of file rpstblastn_options.hpp.
◆ ~CSBlastProgress()
|
inlinevirtual |
Definition at line 357 of file blast_aux.hpp.
◆ ~CSearchResults()
| CSearchResults::~CSearchResults | ( | ) |
Our destructor.
Definition at line 220 of file blast_results.cpp.
References CSearchResults::m_PhiQueryInfo, and SPHIQueryInfoFree().
◆ ~CSeqDbSeqInfoSrc()
|
virtual |
Our destructor.
Definition at line 63 of file seqinfosrc_seqdb.cpp.
◆ ~CSeqVecSeqInfoSrc()
|
virtual |
Destructor.
Definition at line 57 of file seqinfosrc_seqvec.cpp.
◆ ~CSplitQueryBlk()
| CSplitQueryBlk::~CSplitQueryBlk | ( | ) |
Destructor.
Definition at line 54 of file split_query_blk.cpp.
References CSplitQueryBlk::m_SplitQueryBlk, and SplitQueryBlkFree().
◆ ~CStructWrapper()
|
inline |
Destructor.
Definition at line 111 of file setup_factory.hpp.
References CStructWrapper< TData >::m_Data, CStructWrapper< TData >::m_DeleteFunction, and NULL.
◆ ~CTBlastnOptionsHandle()
|
inline |
Definition at line 60 of file tblastn_options.hpp.
◆ ~CTBlastxOptionsHandle()
|
inline |
Definition at line 62 of file tblastx_options.hpp.
◆ ~CThreadable()
|
inlinevirtual |
Our virtual destructor.
Definition at line 171 of file setup_factory.hpp.
◆ ~IBlastQuerySource()
|
inlinevirtual |
Our no-op virtual destructor.
Definition at line 104 of file blast_setup.hpp.
◆ ~IBlastSeqInfoSrc()
|
inlinevirtual |
Definition at line 61 of file blast_seqinfosrc.hpp.
◆ ~IBlastSeqVector()
|
inlinevirtual |
Our no-op virtual destructor.
Definition at line 183 of file blast_setup.hpp.
◆ ~ILocalQueryData()
|
inlinevirtual |
virtual destructor
Definition at line 61 of file query_data.hpp.
◆ ~IPssmInput_Base()
|
inlinevirtual |
virtual destructor
Definition at line 58 of file pssm_input.hpp.
◆ ~IPssmInputCdd()
|
inlinevirtual |
Definition at line 76 of file cdd_pssm_input.hpp.
◆ ~IPssmInputData()
|
inlinevirtual |
virtual destructor
Definition at line 108 of file pssm_input.hpp.
◆ ~IPssmInputFreqRatios()
|
inlinevirtual |
virtual destructor
Definition at line 133 of file pssm_input.hpp.
◆ ~IQueryFactory()
|
inlinevirtual |
Definition at line 149 of file query_data.hpp.
◆ ~IRemoteQueryData()
|
inlinevirtual |
Definition at line 117 of file query_data.hpp.
◆ ~ISeqSearch()
|
inlinevirtual |
Destructor.
Definition at line 251 of file uniform_search.hpp.
◆ ~SNcbiMatrix2DoubleMatrix()
|
inline |
Destructor.
Definition at line 322 of file pssm_engine.cpp.
References SNcbiMatrix2DoubleMatrix::m_Data, and SNcbiMatrix2DoubleMatrix::m_NumCols.
Variable Documentation
◆ allowed_letters
| string SPatternUnit::allowed_letters |
Definition at line 51 of file seedtop.hpp.
◆ AMINOACID_TO_NCBISTDAA
Translates between ncbieaa and ncbistdaa.
Definition at line 105 of file blast_encoding.c.
Referenced by _PSICalculateMatchWeights(), _PSICalculateNormalizedSequenceWeights(), _PSICheckSequenceWeights(), _PSIComputeAlignedRegionLengths(), _PSIComputeFreqRatios(), _PSIComputeFreqRatiosFromCDs(), _PSIComputeFrequenciesFromCDs(), _PSIComputePositionExtents(), _PSIComputeScoreProbabilities(), _PSIConvertFreqRatiosToPSSM(), _PSIGetAlignedSequencesForPosition(), _PSIGetLeftExtents(), _PSIGetRightExtents(), _PSISaveDiagnostics(), _PSISequenceLengthWithoutX(), _PSISpreadGapWeights(), _PSIValidateCdMSA(), Blast_FillResidueProbability(), Blast_GetStdAlphabet(), BLAST_ScoreSetAmbigRes(), BlastKmerGetCompressedTranslationTable(), BlastScoreBlkProteinMatrixLoad(), BlastScoreBlkProteinMatrixRead(), BOOST_AUTO_TEST_CASE(), TKmerMethods< TKmerCounts >::BuildCompressedTranslation(), CConservationScoringMethod::CalculateScores(), CPssmInputFlankingGaps::CPssmInputFlankingGaps(), CPssmInputGapsInQuery::CPssmInputGapsInQuery(), CPssmInputWithGapsInQuery::CPssmInputWithGapsInQuery(), CPssmInputWithNegativeFreqs::CPssmInputWithNegativeFreqs(), CPssmInputWithUnnormalizedFreqs::CPssmInputWithUnnormalizedFreqs(), CPssmInputTestData::FindNonIdenticalHighScoringResidue(), CScoreBuilder::GetBlastScoreProtToNucl(), GetSequenceProtein(), CBlastFormatUtil::PrintAsciiPssm(), RPSFillScores(), RPSRescalePssm(), s_BuildCompressedTranslation(), s_CodonToAA(), s_CreateBioseq(), s_IsResidueOnlyColumn(), s_PSIPurgeSimilarAlignments(), s_PSIValidateAlignedColumns(), s_PSIValidateNoFlankingGaps(), s_PSIValidateNoGapsInQuery(), s_TestCreatePssmFromFreqs(), CPssmInputTestData::SetupQueryAlignedWithInternalGaps(), SPHIPatternSearchBlkNew(), CPsiBlastInputClustalW::x_ExtractAlignmentData(), CPsiBlastInputClustalW::x_ExtractQueryFromMsa(), CPsiBlastInputData::x_ProcessDenseg(), CPhiblastTestFixture::x_SetupSequenceBlk(), and CCddInputData::x_ValidateMsa().
◆ at_least
| size_t SPatternUnit::at_least |
Definition at line 53 of file seedtop.hpp.
◆ at_most
| size_t SPatternUnit::at_most |
Definition at line 54 of file seedtop.hpp.
◆ BLASTNA_TO_IUPACNA
|
extern |
Translates between blastna and iupacna.
Definition at line 75 of file blast_encoding.c.
Referenced by MakeSplicedSeg(), and s_ComputeBtopAndIdentity().
◆ BLASTNA_TO_NCBI4NA
Translates between blastna and ncbi4na.
Definition at line 56 of file blast_encoding.c.
Referenced by BlastScoreBlkNuclMatrixCreate().
◆ copied
| bool SSeqDB_SeqSrc_Data::copied |
Definition at line 96 of file seqsrc_seqdb.cpp.
◆ ctable
|
static |
Definition at line 424 of file blast_objmgr_tools.cpp.
Referenced by s_BuildNa4ToNa2Table(), s_Ncbi4naToNcbi2na(), and WriteDB_Ncbi4naToBinary().
◆ data
| TAutoUint1Ptr SBlastSequence::data |
Sequence data.
Definition at line 64 of file blast_setup.hpp.
Referenced by AascanTestFixture::AascanTestFixture(), BOOST_AUTO_TEST_CASE(), CompressedAascanTestFixture::CompressedAascanTestFixture(), CompressNcbi2na(), CPssmCddInputTest::CreatePssmInput(), CBlastSeqVectorFromCSeq_data::GetCompressedPlusStrand(), CBlastSeqVectorOM::GetCompressedPlusStrand(), CompressedAalookupTestFixture::GetSeqBlk(), AalookupTestFixture::GetSeqBlk(), PsiBlastComputePssmFromAlignment(), SBlastSequence::SBlastSequence(), LinkHspTestFixture::setupLinkHspInputBlastn(), SetupQueries_OMF(), NtlookupTestFixture::SetUpQuery(), TestFixture::SetUpQuery(), NuclWordFinderTextFixture::setupSequences(), TestFixture::SetUpSubject(), and SetupSubjects_OMF().
◆ dbscan_mode
| bool SMultiSeqSrcNewArgs::dbscan_mode |
Database mode (not pairwise)
Definition at line 465 of file seqsrc_multiseq.cpp.
Referenced by s_MultiSeqSrcNew().
◆ disallowed_letters
| string SPatternUnit::disallowed_letters |
Definition at line 52 of file seedtop.hpp.
◆ extend_length3end
|
static |
Definition at line 59 of file igblast.cpp.
Referenced by CIgBlast::x_ExtendAlign3end().
◆ extend_length5end
|
static |
Definition at line 58 of file igblast.cpp.
Referenced by CIgBlast::x_ExtendAlign5end().
◆ has_index
| bool CIndexedDb_New::SVolumeDescriptor::has_index |
'true' if the volume is indexed.
Definition at line 347 of file blast_dbindex.cpp.
◆ index_
Currently loaded index.
Definition at line 241 of file blast_dbindex.cpp.
Referenced by CIndexedDb_Old::PreSearch().
◆ index_names_
|
private |
List of index volume names.
Definition at line 240 of file blast_dbindex.cpp.
Referenced by CIndexedDb_Old::CIndexedDb_Old(), CIndexedDb_Old::MinIndexWordSize(), and CIndexedDb_Old::PreSearch().
◆ Index_Set_Instance
|
static |
Shared representation of currently loaded index volumes.
Definition at line 149 of file blast_dbindex.cpp.
Referenced by DbIndexInit(), IndexedDbRunSearch(), IndexedDbSetNumThreads(), IndexedDbSetQueryInfo(), IndexedDbSetUsingThreads(), s_CheckMinWordSize(), s_MB_IdbCheckOid(), s_MB_IdbGetResults(), and s_MB_IdxEndSearchIndication().
◆ is_x
| bool SPatternUnit::is_x |
Definition at line 55 of file seedtop.hpp.
◆ isProtein
| bool SSeqDB_SeqSrc_Data::isProtein |
Definition at line 97 of file seqsrc_seqdb.cpp.
◆ IUPACNA_TO_BLASTNA
Translates between iupacna and blastna.
Definition at line 85 of file blast_encoding.c.
Referenced by BLAST_ScoreSetAmbigRes(), BlastScoreBlkNucleotideMatrixRead(), and BlastScoreBlkProteinMatrixRead().
◆ IUPACNA_TO_NCBI4NA
Translates between iupacna and ncbi4na.
Definition at line 95 of file blast_encoding.c.
Referenced by BLAST_ScoreSetAmbigRes(), and SPHIPatternSearchBlkNew().
◆ j_wordsize
|
static |
Definition at line 63 of file igblast.cpp.
Referenced by CIgBlast::x_FindDJAln(), and CIgBlast::x_SetupDJSearch().
◆ kAlphabetSize
Definition at line 487 of file cdd_pssm_input.hpp.
Referenced by CPssmCddInputTest::GetAlphabetSize(), CCddInputData::CHitSegment::Validate(), CCddInputData::CHitSegment::x_FillResidueCounts(), and CCddInputData::x_ValidateMsa().
◆ kBlastAlignmentDim
BLAST alignments have always 2 dimensions (i.e.
: Pairwise alignment is 2 dimensional)
Definition at line 71 of file blast_seqalign.cpp.
Referenced by s_BlastHSP2SeqAlign(), s_CollectSeqAlignData(), s_CreateDenseg(), s_CreateSeqAlign(), s_CreateStdSegs(), s_OOFBlastHSP2SeqAlign(), x_NonTranslatedHSPToStdSeg(), x_UngappedHSPToDenseDiag(), and x_UngappedHSPToStdSeg().
◆ kDataLoaders
|
static |
Definition at line 57 of file blast_input_unit_test_aux.hpp.
Referenced by CAutoNcbiConfigFile::CAutoNcbiConfigFile(), and CAutoNcbiConfigFile::~CAutoNcbiConfigFile().
◆ kExtension [1/6]
Extension associated with the RPS-BLAST database auxiliary file.
Definition at line 162 of file rps_aux.cpp.
Referenced by CRpsAuxFile::CRpsAuxFile().
◆ kExtension [2/6]
Extension associated with the RPS-BLAST database lookup table file.
Definition at line 275 of file rps_aux.cpp.
Referenced by CRpsLookupTblFile::CRpsLookupTblFile().
◆ kExtension [3/6]
Extension associated with the RPS-BLAST database PSSM file.
Definition at line 322 of file rps_aux.cpp.
Referenced by CRpsPssmFile::CRpsPssmFile().
◆ kExtension [4/6]
Extension associated with the RPS-BLAST database PSSM file.
Definition at line 370 of file rps_aux.cpp.
Referenced by CRpsFreqsFile::CRpsFreqsFile().
◆ kExtension [5/6]
Extension associated with the RPS-BLAST database PSSM file.
Definition at line 420 of file rps_aux.cpp.
Referenced by CRpsObsrFile::CRpsObsrFile().
◆ kExtension [6/6]
Extension associated with the RPS-BLAST database PSSM file.
Definition at line 468 of file rps_aux.cpp.
Referenced by CRpsFreqRatiosFile::CRpsFreqRatiosFile().
◆ kInvalidFilterValue
Definition at line 53 of file blast_options_local_priv.hpp.
Referenced by CBlastOptionsLocal::GetDustFilteringLevel(), CBlastOptionsLocal::GetDustFilteringLinker(), CBlastOptionsLocal::GetDustFilteringWindow(), CBlastOptionsLocal::GetSegFilteringHicut(), CBlastOptionsLocal::GetSegFilteringLocut(), and CBlastOptionsLocal::GetSegFilteringWindow().
◆ kNoPhiBlastPattern
set to -1 in ctor, indicate that m_NumPatOccurInDB is unset or not applicable.
Definition at line 360 of file setup_factory.hpp.
Referenced by CBlastTracebackSearch::Run(), CBlastTracebackSearch::RunSimple(), and SDatabaseScanData::SDatabaseScanData().
◆ kNuclBlastDbDataLoader
|
static |
Definition at line 59 of file blast_input_unit_test_aux.hpp.
Referenced by CAutoNcbiConfigFile::SetNucleotideBlastDbDataLoader(), and CAutoNcbiConfigFile::~CAutoNcbiConfigFile().
◆ kNuclSentinel
Sentinel nibble for nucleotide sequences.
Definition at line 121 of file blast_encoding.c.
Referenced by GetSentinelByte(), s_GetSeq4na(), s_GetSeq4naChunkSeq(), and s_GetSeq4naChunkSeq_PartialFetching().
◆ kProtBlastDbDataLoader
|
static |
Definition at line 58 of file blast_input_unit_test_aux.hpp.
Referenced by CAutoNcbiConfigFile::SetProteinBlastDbDataLoader(), and CAutoNcbiConfigFile::~CAutoNcbiConfigFile().
◆ kProtSentinel
Sentinel byte for protein sequences.
Definition at line 120 of file blast_encoding.c.
Referenced by GetSentinelByte().
◆ kPubMedUrls
|
static |
Pubmed URLs to retrieve the references defined above.
Definition at line 87 of file version.cpp.
Referenced by CReference::GetPubmedUrl().
◆ kReferences
|
static |
References for the various BLAST publications.
Definition at line 47 of file version.cpp.
Referenced by CReference::GetString().
◆ kRpsScaleFactor
Scale of residue frequencies and number of independent observations stored in CDD.
Definition at line 491 of file cdd_pssm_input.hpp.
Referenced by CPssmCddInputTest::GetProfilesDataScale(), and CCddInputData::CHitSegment::x_FillObservations().
◆ kSection
|
static |
Definition at line 56 of file blast_input_unit_test_aux.hpp.
Referenced by CAutoNcbiConfigFile::CAutoNcbiConfigFile(), CAutoNcbiConfigFile::RemoveBLASTDBEnvVar(), CAutoNcbiConfigFile::SetNucleotideBlastDbDataLoader(), CAutoNcbiConfigFile::SetProteinBlastDbDataLoader(), and CAutoNcbiConfigFile::~CAutoNcbiConfigFile().
◆ length
| TSeqPos SBlastSequence::length |
Length of the buffer above (not necessarily sequence length!)
Definition at line 65 of file blast_setup.hpp.
Referenced by AascanTestFixture::AascanTestFixture(), BOOST_AUTO_TEST_CASE(), CompressedAascanTestFixture::CompressedAascanTestFixture(), CompressNcbi2na(), CPssmCddInputTest::CreatePssmInput(), CompressedAalookupTestFixture::GetSeqBlk(), AalookupTestFixture::GetSeqBlk(), PsiBlastComputePssmFromAlignment(), SetupQueries_OMF(), NtlookupTestFixture::SetUpQuery(), TestFixture::SetUpQuery(), NuclWordFinderTextFixture::setupSequences(), TestFixture::SetUpSubject(), and SetupSubjects_OMF().
◆ locs_wrap_
|
protected |
Current set of unmasked query locations.
Definition at line 145 of file blast_dbindex.cpp.
Referenced by CIndexedDb_Old::DoPreSearch(), CIndexedDb::SetQueryInfo(), and CIndexedDb_New::UpdateIndex().
◆ m_AbsoluteContexts
|
private |
Definition at line 167 of file split_query_aux_priv.hpp.
Referenced by CContextTranslator::CContextTranslator(), and operator<<().
◆ m_AirrField
| list<string> CIgBlastOptions::m_AirrField |
Definition at line 90 of file igblast.hpp.
Referenced by CIgBlastnApp::CIgFormatter::Main().
◆ m_AlgoOpts
|
private |
Options relevant to the search algorithm.
Definition at line 794 of file remote_blast.hpp.
Referenced by CRemoteBlast::GetSearchOptions(), CRemoteBlast::x_GetRequestInfoFromFile(), and CRemoteBlast::x_GetRequestInfoFromRID().
◆ m_Alignment
|
protected |
alignments for this query
Definition at line 267 of file blast_results.hpp.
Referenced by CSearchResults::GetSeqAlign(), CSearchResults::HasAlignments(), CSearchResults::SetSeqAlign(), CIgBlastResults::SetSeqAlign(), and CSearchResults::TrimSeqAlign().
◆ m_Aligns
|
private |
Alignments for a single or a pair of reads.
Definition at line 223 of file magicblast.hpp.
Referenced by CMagicBlastResults::GetSeqAlign(), CMagicBlastResults::SetSeqAlign(), CMagicBlastResults::SortAlignments(), and CMagicBlastResults::x_SetInfo().
◆ m_AncillaryData [1/2]
|
private |
Ancillary BLAST data.
Definition at line 205 of file bl2seq.hpp.
Referenced by CBl2Seq::GetAncillaryResults(), CBl2Seq::x_BuildAncillaryData(), and CBl2Seq::x_ResetInternalDs().
◆ m_AncillaryData [2/2]
|
protected |
non-alignment ancillary data for this query
Definition at line 279 of file blast_results.hpp.
Referenced by CSearchResults::GetAncillaryData().
◆ m_Annotation
|
private |
Definition at line 233 of file igblast.hpp.
Referenced by CIgBlastResults::GetIgAnnotation(), and CIgBlastResults::SetIgAnnotation().
◆ m_AnnotationInfo
|
private |
Definition at line 306 of file igblast.hpp.
Referenced by CIgBlast::x_AnnotateD(), CIgBlast::x_AnnotateDJ(), CIgBlast::x_AnnotateDomain(), CIgBlast::x_AnnotateJ(), CIgBlast::x_FillJDomain(), CIgBlast::x_FindDJAln(), and CIgBlast::x_ProcessDGeneResult().
◆ m_App
|
private |
Definition at line 108 of file blast_input_unit_test_aux.hpp.
Referenced by CAutoNcbiConfigFile::CAutoNcbiConfigFile(), and CAutoNcbiConfigFile::~CAutoNcbiConfigFile().
◆ m_Archive
|
private |
Archive of BLAST search and results.
Definition at line 737 of file remote_blast.hpp.
Referenced by CRemoteBlast::IsErrMsgArchive(), CRemoteBlast::LoadFromArchive(), CRemoteBlast::x_GetGSRR(), and CRemoteBlast::x_GetRequestInfoFromFile().
◆ m_AsciiMsa
|
private |
The raw multiple sequence alignment in ASCII read from the input file.
Definition at line 139 of file msa_pssm_input.hpp.
Referenced by CPsiBlastInputClustalW::x_CopyQueryToMsa(), CPsiBlastInputClustalW::x_ExtractAlignmentData(), CPsiBlastInputClustalW::x_ExtractQueryFromMsa(), CPsiBlastInputClustalW::x_ReadAsciiMsa(), and CPsiBlastInputClustalW::x_ValidateQueryInMsa().
◆ m_AuxFile
|
private |
The auxiliary RPS-BLAST file (.aux)
Definition at line 146 of file rps_aux.hpp.
Referenced by CBlastRPSInfo::x_Init().
◆ m_AuxFilename
| string CIgBlastOptions::m_AuxFilename |
Definition at line 74 of file igblast.hpp.
Referenced by CIgAnnotationInfo::CIgAnnotationInfo(), and CIgBlastArgs::ExtractAlgorithmOptions().
◆ m_AvailableDatabases
|
private |
BLAST databases available to search.
Definition at line 277 of file blast_services.hpp.
Referenced by CBlastServices::GetDatabaseInfo(), CBlastServices::GetOrganismSpecificRepeatsDatabases(), CBlastServices::x_FindDbInfoFromAvailableDatabases(), and CBlastServices::x_GetAvailableDatabases().
◆ m_AvgLength
|
private |
Average length of sequences in this set.
Definition at line 79 of file seqsrc_query_factory.cpp.
Referenced by CQueryFactoryInfo::GetAvgLength(), and CQueryFactoryInfo::SetAvgLength().
◆ m_batch_num_str
|
private |
Definition at line 148 of file local_blast.hpp.
Referenced by CLocalBlast::Run(), and CLocalBlast::SetBatchNumber().
◆ m_Bioseqs [1/3]
|
private |
Definition at line 67 of file objmgrfree_query_data.hpp.
Referenced by CObjMgrFree_QueryFactory::x_MakeLocalQueryData(), and CObjMgrFree_QueryFactory::x_MakeRemoteQueryData().
◆ m_Bioseqs [2/3]
|
protected |
Data member to cache the CBioseq_set.
Definition at line 129 of file query_data.hpp.
Referenced by CObjMgr_RemoteQueryData::GetBioseqSet(), and CObjMgrFree_RemoteQueryData::GetBioseqSet().
◆ m_Bioseqs [3/3]
|
private |
Contains pointers to the input data.
Definition at line 194 of file bioseq_extract_data_priv.hpp.
Referenced by CBlastQuerySourceBioseqSet::CBlastQuerySourceBioseqSet(), CBlastQuerySourceBioseqSet::GetBlastSequence(), CBlastQuerySourceBioseqSet::GetGeneticCodeId(), CBlastQuerySourceBioseqSet::GetLength(), CBlastQuerySourceBioseqSet::GetSegmentInfo(), CBlastQuerySourceBioseqSet::GetSeqId(), CBlastQuerySourceBioseqSet::GetSeqLoc(), CBlastQuerySourceBioseqSet::GetTitle(), and CBlastQuerySourceBioseqSet::Size().
◆ m_BioseqSet
|
private |
Definition at line 87 of file objmgrfree_query_data.cpp.
Referenced by CObjMgrFree_LocalQueryData::GetQueryInfo(), and CObjMgrFree_LocalQueryData::GetSequenceBlk().
◆ m_Blast
|
private |
The actual BLAST instance.
Definition at line 184 of file bl2seq.hpp.
Referenced by CBl2Seq::RunEx(), and CBl2Seq::x_InitCLocalBlast().
◆ m_BlastDb
|
private |
Definition at line 110 of file blast_input_unit_test_aux.hpp.
Referenced by CAutoNcbiConfigFile::RemoveBLASTDBEnvVar(), and CAutoNcbiConfigFile::~CAutoNcbiConfigFile().
◆ m_BtopSpliceSignals
|
private |
Should BTOP strings be formatted with splice signals.
Definition at line 131 of file magicblast.hpp.
Referenced by CMagicBlast::CMagicBlast(), CMagicBlast::x_BuildResultSet(), and CMagicBlast::x_BuildSeqAlignSet().
◆ m_CalculatedMasks
|
private |
this flag allows for lazy initialization of the masking locations
Definition at line 180 of file blast_objmgr_priv.hpp.
Referenced by CBlastQuerySourceOM::x_CalculateMasks().
◆ m_Candidates
|
private |
Number of target seqs to process with BLAST.
Definition at line 111 of file blastp_kmer_options.hpp.
◆ m_CBOH
|
private |
Options for new search.
Definition at line 728 of file remote_blast.hpp.
Referenced by CRemoteBlast::GetResultSet(), CRemoteBlast::GetSearchOptions(), CRemoteBlast::x_Init(), CRemoteBlast::x_QueryMaskingLocationsToNetwork(), and CRemoteBlast::x_SetAlgoOpts().
◆ m_CddData
|
private |
MSA of CDs and CD data.
Definition at line 457 of file cdd_pssm_input.hpp.
Referenced by CCddInputData::GetData(), CCddInputData::Process(), and CCddInputData::x_CreateMsa().
◆ m_CDomain
| int CIgAnnotation::m_CDomain[2] |
Definition at line 113 of file igblast.hpp.
Referenced by CIgAnnotation::CIgAnnotation(), and CBlastFormat::PrintOneResultSet().
◆ m_ChainType
| vector<string> CIgAnnotation::m_ChainType |
Definition at line 98 of file igblast.hpp.
Referenced by CBlastFormat::PrintOneResultSet(), CIgBlast::x_AnnotateDomain(), CIgBlast::x_FindDJ(), CBlastFormat::x_PrintIgTabularReport(), and CIgBlast::x_SetChainType().
◆ m_ChainTypeToShow
| string CIgAnnotation::m_ChainTypeToShow |
Definition at line 99 of file igblast.hpp.
Referenced by CBlastFormat::PrintOneResultSet(), CIgBlast::x_AnnotateDomain(), and CBlastFormat::x_PrintIgTabularReport().
◆ m_ChunkSize
|
private |
Size of the query chunks.
Definition at line 119 of file split_query.hpp.
Referenced by CQuerySplitter::GetChunkSize(), and CQuerySplitter::x_ComputeChunkRanges().
◆ m_ClientBioseqSet
|
private |
Queries, expressed as a CBioseq_set.
Definition at line 194 of file objmgrfree_query_data.cpp.
Referenced by CObjMgrFree_RemoteQueryData::GetBioseqSet(), and CObjMgrFree_RemoteQueryData::GetSeqLocs().
◆ m_ClientId [1/2]
|
private |
Client ID submitting requests throw this interface.
Definition at line 833 of file remote_blast.hpp.
Referenced by CRemoteBlast::GetClientId(), CRemoteBlast::GetSearchStrategy(), CRemoteBlast::SetClientId(), CRemoteBlast::x_GetRequestInfoFromRID(), CRemoteBlast::x_Init(), and CRemoteBlast::x_SendRequest().
◆ m_ClientId [2/2]
|
private |
Definition at line 262 of file search_strategy.hpp.
Referenced by CExportStrategy::GetSearchStrategy().
◆ m_Concordant
|
private |
True if results are concordant pair.
Definition at line 229 of file magicblast.hpp.
Referenced by CMagicBlastResults::IsConcordant(), and CMagicBlastResults::x_SetInfo().
◆ m_ContextsPerChunk
|
private |
Each element in this vector represents a chunk, and it contains the contexts numbers that correspond in the full concatenated query.
Definition at line 164 of file split_query_aux_priv.hpp.
Referenced by CContextTranslator::CContextTranslator(), CContextTranslator::GetAbsoluteContext(), CContextTranslator::GetContextInChunk(), and operator<<().
◆ m_CreatedBy
|
private |
Created-by attribution for this search.
Definition at line 788 of file remote_blast.hpp.
Referenced by CRemoteBlast::GetCreatedBy(), CRemoteBlast::x_GetRequestInfoFromFile(), and CRemoteBlast::x_GetRequestInfoFromRID().
◆ m_CurrentData
|
private |
Identifiers for sequences found in the current iteration.
Definition at line 134 of file psiblast_iteration.hpp.
Referenced by CPsiBlastIterationState::Advance(), CPsiBlastIterationState::GetPreviouslyFoundSeqIds(), and CPsiBlastIterationState::HasConverged().
◆ m_CustomInternalData
| string CIgBlastOptions::m_CustomInternalData |
Definition at line 76 of file igblast.hpp.
Referenced by CIgAnnotationInfo::CIgAnnotationInfo(), CIgBlastArgs::ExtractAlgorithmOptions(), CIgBlast::Run(), and CIgBlast::x_AnnotateDomain().
◆ m_D_penalty
| int CIgBlastOptions::m_D_penalty |
Definition at line 72 of file igblast.hpp.
Referenced by CIgBlastArgs::ExtractAlgorithmOptions(), CIgBlast::Run(), CIgBlast::x_FindDJAln(), CIgBlast::x_SetupDJSearch(), and CIgBlast::x_SetupNoOverlapDSearch().
◆ m_Data [1/10]
|
private |
Definition at line 178 of file search_strategy.hpp.
Referenced by CImportStrategy::FetchData(), CImportStrategy::GetDBFilteringID(), CImportStrategy::GetDBFilteringKey(), CImportStrategy::GetOptionsHandle(), CImportStrategy::GetPsiNumOfIterations(), CImportStrategy::GetQueryRange(), CImportStrategy::GetSubjectMaskingType(), and CImportStrategy::GetTask().
◆ m_Data [2/10]
|
private |
the pointer managed by this object
Definition at line 144 of file setup_factory.hpp.
Referenced by CStructWrapper< TData >::GetPointer(), CStructWrapper< TData >::operator*(), CStructWrapper< TData >::operator->(), and CStructWrapper< TData >::~CStructWrapper().
◆ m_Data [3/10]
|
private |
double** representation of a CNcbiMatrix
Definition at line 334 of file pssm_engine.cpp.
Referenced by SNcbiMatrix2DoubleMatrix::operator double **(), SNcbiMatrix2DoubleMatrix::SNcbiMatrix2DoubleMatrix(), and SNcbiMatrix2DoubleMatrix::~SNcbiMatrix2DoubleMatrix().
◆ m_Data [4/10]
|
private |
The data structure this class manages.
Definition at line 92 of file rps_aux.cpp.
Referenced by CBlastRPSAuxInfo::CBlastRPSAuxInfo(), CBlastRPSAuxInfo::operator()(), and CBlastRPSAuxInfo::x_DoDestroy().
◆ m_Data [5/10]
|
private |
Definition at line 175 of file rps_aux.cpp.
Referenced by CRpsAuxFile::CRpsAuxFile(), and CRpsAuxFile::operator()().
◆ m_Data [6/10]
|
private |
The data structure this class manages.
Definition at line 286 of file rps_aux.cpp.
Referenced by CRpsLookupTblFile::CRpsLookupTblFile(), and CRpsLookupTblFile::operator()().
◆ m_Data [7/10]
|
private |
The data structure this class manages.
Definition at line 333 of file rps_aux.cpp.
Referenced by CRpsPssmFile::CRpsPssmFile(), and CRpsPssmFile::operator()().
◆ m_Data [8/10]
|
private |
The data this class manages.
Definition at line 381 of file rps_aux.cpp.
Referenced by CRpsFreqsFile::CRpsFreqsFile(), and CRpsFreqsFile::operator()().
◆ m_Data [9/10]
|
private |
Header.
Definition at line 431 of file rps_aux.cpp.
Referenced by CRpsObsrFile::CRpsObsrFile(), and CRpsObsrFile::operator()().
◆ m_Data [10/10]
|
private |
The data this class manages.
Definition at line 481 of file rps_aux.cpp.
Referenced by CRpsFreqRatiosFile::CRpsFreqRatiosFile(), and CRpsFreqRatiosFile::operator()().
◆ m_Database
|
private |
BLAST database for the search class to use.
Definition at line 76 of file local_search.hpp.
Referenced by CLocalSeqSearch::Run(), and CLocalSeqSearch::SetSubject().
◆ m_DataSource
|
private |
Definition at line 119 of file seqinfosrc_bioseq.hpp.
Referenced by CBioseqSeqInfoSrc::GetId(), CBioseqSeqInfoSrc::GetLength(), and CBioseqSeqInfoSrc::Size().
◆ m_Db
| CRef<CLocalDbAdapter> CIgBlastOptions::m_Db[5] |
Definition at line 78 of file igblast.hpp.
Referenced by CIgBlastArgs::ExtractAlgorithmOptions(), CIgBlastnApp::CIgWorker::Main(), CIgBlastnApp::CIgFormatter::Main(), CIgBlast::Run(), CIgBlastnApp::Run(), CIgBlastpApp::Run(), and CIgBlast::x_AnnotateDomain().
◆ m_DbAdapter
|
private |
Definition at line 168 of file prelim_stage.hpp.
Referenced by CBlastPrelimSearch::x_BuildStdSegList().
◆ m_DbFilteringAlgorithmId [1/2]
The GI list (or none).
Definition at line 306 of file blast_options_builder.hpp.
Referenced by CBlastOptionsBuilder::GetDbFilteringAlgorithmId(), CBlastOptionsBuilder::HasDbFilteringAlgorithmId(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ m_DbFilteringAlgorithmId [2/2]
|
private |
filtering algorithm to use in the database
Definition at line 821 of file remote_blast.hpp.
Referenced by CRemoteBlast::GetDbFilteringAlgorithmId(), CRemoteBlast::GetSearchOptions(), CRemoteBlast::SetDbFilteringAlgorithmId(), and CRemoteBlast::x_Init().
◆ m_DbFilteringAlgorithmKey [1/2]
Definition at line 307 of file blast_options_builder.hpp.
Referenced by CBlastOptionsBuilder::GetDbFilteringAlgorithmKey(), CBlastOptionsBuilder::HasDbFilteringAlgorithmKey(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ m_DbFilteringAlgorithmKey [2/2]
|
private |
filtering algorithm key to use in the database
Definition at line 824 of file remote_blast.hpp.
Referenced by CRemoteBlast::GetDbFilteringAlgorithmKey(), CRemoteBlast::GetSearchOptions(), CRemoteBlast::SetDbFilteringAlgorithmKey(), and CRemoteBlast::x_Init().
◆ m_DbInfo [1/2]
|
private |
Object containing BLAST database description.
Definition at line 138 of file local_db_adapter.hpp.
Referenced by CLocalDbAdapter::GetFilteringAlgorithm(), CLocalDbAdapter::GetFilteringAlgorithmKey(), CLocalDbAdapter::GetSearchDatabase(), CLocalDbAdapter::IsProtein(), CLocalDbAdapter::MakeSeqInfoSrc(), and CLocalDbAdapter::MakeSeqSrc().
◆ m_DbInfo [2/2]
|
private |
Definition at line 169 of file prelim_stage.hpp.
Referenced by CBlastPrelimSearch::x_BuildStdSegList().
◆ m_DbInitialized
|
mutableprivate |
Definition at line 204 of file uniform_search.hpp.
Referenced by CSearchDatabase::GetSeqDb(), CSearchDatabase::SetSeqDb(), CSearchDatabase::x_InitializeDb(), and CSearchDatabase::x_TranslateFilteringAlgorithm().
◆ m_DbName [1/4]
|
private |
CDD database name.
Definition at line 447 of file cdd_pssm_input.hpp.
Referenced by CCddInputData::x_FillHitsData().
◆ m_DbName [2/4]
This is initialized ONLY if this object represents a BLAST database.
Definition at line 152 of file local_db_adapter.hpp.
Referenced by CLocalDbAdapter::GetDatabaseName(), and CLocalDbAdapter::IsBlastDb().
◆ m_DbName [3/4]
|
private |
database name
Definition at line 192 of file uniform_search.hpp.
Referenced by CSearchDatabase::GetDatabaseName(), CSearchDatabase::SetDatabaseName(), and CSearchDatabase::x_InitializeDb().
◆ m_DbName [4/4]
|
private |
Database name.
Definition at line 595 of file seqsrc_seqdb.cpp.
◆ m_DbOpts [1/2]
|
private |
Definition at line 97 of file blast_memento_priv.hpp.
Referenced by CBlastTracebackSearch::Run(), and CBlastTracebackSearch::RunSimple().
◆ m_DbOpts [2/2]
|
private |
Blast database settings.
Definition at line 384 of file blast_options_local_priv.hpp.
Referenced by CBlastOptionsLocal::CBlastOptionsLocal(), CBlastOptionsMemento::CBlastOptionsMemento(), CBlastOptionsLocal::DebugDump(), CBlastOptionsLocal::GetDbGeneticCode(), CBlastOptionsLocal::GetDbOpts(), CBlastOptionsLocal::operator==(), CBlastOptionsLocal::SetDbGeneticCode(), and CBlastOptionsLocal::x_DoDeepCopy().
◆ m_Dbs
|
private |
Databases.
Definition at line 773 of file remote_blast.hpp.
Referenced by CRemoteBlast::GetDatabases(), CRemoteBlast::IsDbSearch(), CRemoteBlast::x_GetRequestInfoFromRID(), CRemoteBlast::x_SetDatabase(), and CRemoteBlast::x_SetSubjectSequences().
◆ m_DBscanInfo
|
private |
Tracks information from database scanning phase.
Right now only used for the number of occurrences of a pattern in phiblast run.
Definition at line 134 of file traceback_stage.hpp.
Referenced by CBlastTracebackSearch::Run(), CBlastTracebackSearch::RunSimple(), and CBlastTracebackSearch::SetDBScanInfo().
◆ m_DbScanMode [1/3]
|
private |
Scan like a databsase (as opposed to pairwise)
Definition at line 185 of file bl2seq.hpp.
Referenced by CBl2Seq::x_InitCLocalBlast().
◆ m_DbScanMode [2/3]
|
private |
Specifies that bl2seq search run in database scan mode (not pairwise)
Definition at line 155 of file local_db_adapter.hpp.
Referenced by CLocalDbAdapter::IsDbScanMode(), and CLocalDbAdapter::MakeSeqSrc().
◆ m_DbScanMode [3/3]
|
private |
Database scanning mode (not pairwise)
Definition at line 75 of file seqsrc_multiseq.cpp.
Referenced by CMultiSeqInfo::CMultiSeqInfo().
◆ m_DefaultsMode [1/2]
|
protected |
Set to true when 'remote' options should ignore setters.
Definition at line 338 of file blast_options_handle.hpp.
◆ m_DefaultsMode [2/2]
|
private |
Definition at line 153 of file blast_options_cxx.cpp.
Referenced by CBlastOptionsRemote::GetDefaultsMode(), CBlastOptionsRemote::SetDefaultsMode(), CBlastOptionsRemote::SetValue(), and CBlastOptionsRemote::x_DoDeepCopy().
◆ m_DeleteFunction
|
private |
deallocation function for the pointer above
Definition at line 146 of file setup_factory.hpp.
Referenced by CStructWrapper< TData >::~CStructWrapper().
◆ m_DeltaBlastOpts
|
private |
Delta-Blast settings.
Definition at line 381 of file blast_options_local_priv.hpp.
Referenced by CBlastOptionsLocal::CBlastOptionsLocal(), CBlastOptionsLocal::DebugDump(), CBlastOptionsLocal::GetDomainInclusionThreshold(), CBlastOptionsLocal::operator==(), CBlastOptionsLocal::SetDomainInclusionThreshold(), and CBlastOptionsLocal::x_DoDeepCopy().
◆ m_DetectOverlap
| bool CIgBlastOptions::m_DetectOverlap |
Definition at line 89 of file igblast.hpp.
Referenced by CIgBlastArgs::ExtractAlgorithmOptions(), CIgBlast::Run(), CIgBlast::x_FindDJAln(), and CIgBlast::x_SetupDJSearch().
◆ m_DFrameFileName
| string CIgBlastOptions::m_DFrameFileName |
Definition at line 75 of file igblast.hpp.
Referenced by CIgAnnotationInfo::CIgAnnotationInfo(), and CIgBlastArgs::ExtractAlgorithmOptions().
◆ m_DframeStart
| int CIgAnnotation::m_DframeStart |
Definition at line 114 of file igblast.hpp.
Referenced by CIgAnnotation::CIgAnnotation().
◆ m_Diagnostics
| CRef<TBlastDiagnostics> SInternalData::m_Diagnostics |
Diagnostic output from preliminary and traceback stages.
Definition at line 332 of file setup_factory.hpp.
Referenced by BOOST_AUTO_TEST_CASE(), CBlastTracebackSearch::CBlastTracebackSearch(), CLocalBlast::GetDiagnostics(), CLocalBlast::GetNumExtensions(), CBl2Seq::RunEx(), CBlastPrelimSearch::SetNumberOfThreads(), and CBlastTracebackSearch::x_Init().
◆ m_DiagnosticsRequest [1/3]
|
private |
PSSM engine Diagnostics request.
Definition at line 472 of file cdd_pssm_input.hpp.
Referenced by CCddInputData::GetDiagnosticsRequest().
◆ m_DiagnosticsRequest [2/3]
|
private |
Diagnostics request structure.
Definition at line 147 of file msa_pssm_input.hpp.
Referenced by CPsiBlastInputClustalW::~CPsiBlastInputClustalW().
◆ m_DiagnosticsRequest [3/3]
|
private |
Diagnostics request structure.
Definition at line 247 of file psi_pssm_input.hpp.
Referenced by CPsiBlastInputData::CPsiBlastInputData(), and CPsiBlastInputData::GetDiagnosticsRequest().
◆ m_disk_cache_error_flag
|
private |
disk cache error flag
Definition at line 839 of file remote_blast.hpp.
Referenced by CRemoteBlast::ClearDiskCacheError(), CRemoteBlast::IsDiskCacheError(), CRemoteBlast::x_GetSearchResultsHTTP(), and CRemoteBlast::x_InitDiskCache().
◆ m_disk_cache_error_msg
|
private |
disk cache error message
Definition at line 841 of file remote_blast.hpp.
Referenced by CRemoteBlast::GetDiskCacheErrorMessahe(), CRemoteBlast::x_GetSearchResultsHTTP(), and CRemoteBlast::x_InitDiskCache().
◆ m_DJChainType
Definition at line 191 of file igblast.hpp.
Referenced by CIgAnnotationInfo::CIgAnnotationInfo(), and CIgAnnotationInfo::GetDJChainType().
◆ m_DomainChainType
Definition at line 189 of file igblast.hpp.
Referenced by CIgAnnotationInfo::CIgAnnotationInfo(), and CIgAnnotationInfo::GetDomainChainType().
◆ m_DomainData
|
private |
Definition at line 188 of file igblast.hpp.
Referenced by CIgAnnotationInfo::CIgAnnotationInfo(), and CIgAnnotationInfo::GetDomainInfo().
◆ m_DomainDb
|
private |
Reference to a BLAST conserved domain database object.
Definition at line 138 of file deltablast.hpp.
Referenced by CDeltaBlast::Run(), CDeltaBlast::x_FindDomainHits(), and CDeltaBlast::x_Validate().
◆ m_DomainIndex
Definition at line 187 of file igblast.hpp.
Referenced by CIgAnnotationInfo::CIgAnnotationInfo(), and CIgAnnotationInfo::GetDomainInfo().
◆ m_DomainInfo
| int CIgAnnotation::m_DomainInfo[12] |
Definition at line 105 of file igblast.hpp.
Referenced by CIgAnnotation::CIgAnnotation(), CBlastFormat::PrintOneResultSet(), CIgBlast::x_AnnotateDomain(), and CBlastFormat::x_ReverseQuery().
◆ m_DomainInfo_S
| int CIgAnnotation::m_DomainInfo_S[10] |
Definition at line 108 of file igblast.hpp.
Referenced by CIgAnnotation::CIgAnnotation(), CBlastFormat::PrintOneResultSet(), and CIgBlast::x_AnnotateDomain().
◆ m_DomainResults
|
private |
Conseved domain search (intermediate) results.
Definition at line 150 of file deltablast.hpp.
Referenced by CDeltaBlast::GetDomainResults(), and CDeltaBlast::Run().
◆ m_DomainSystem
| string CIgBlastOptions::m_DomainSystem |
Definition at line 68 of file igblast.hpp.
Referenced by CIgAnnotationInfo::CIgAnnotationInfo(), and CIgBlastArgs::ExtractAlgorithmOptions().
◆ m_EffLenOpts [1/2]
|
private |
Definition at line 99 of file blast_memento_priv.hpp.
Referenced by CBlastTracebackSearch::Run(), and CBlastTracebackSearch::RunSimple().
◆ m_EffLenOpts [2/2]
|
private |
Effective lengths options.
Definition at line 390 of file blast_options_local_priv.hpp.
Referenced by CBlastOptionsLocal::CBlastOptionsLocal(), CBlastOptionsMemento::CBlastOptionsMemento(), CEffectiveSearchSpacesMemento::CEffectiveSearchSpacesMemento(), CBlastOptionsLocal::DebugDump(), CBlastOptionsLocal::GetDbLength(), CBlastOptionsLocal::GetDbSeqNum(), CBlastOptionsLocal::GetEffectiveSearchSpace(), CBlastOptionsLocal::GetEffLenOpts(), CBlastOptionsLocal::operator==(), CBlastOptionsLocal::SetDbLength(), CBlastOptionsLocal::SetDbSeqNum(), CBlastOptionsLocal::SetEffectiveSearchSpace(), CBlastOptionsLocal::x_DoDeepCopy(), and CEffectiveSearchSpacesMemento::~CEffectiveSearchSpacesMemento().
◆ m_EffLenOrig
|
private |
Original effective length options.
Definition at line 144 of file blast_memento_priv.hpp.
Referenced by CEffectiveSearchSpacesMemento::CEffectiveSearchSpacesMemento(), and CEffectiveSearchSpacesMemento::~CEffectiveSearchSpacesMemento().
◆ m_EffLenReplace
|
private |
Effective length that will be replaced in the BLAST options object.
Definition at line 146 of file blast_memento_priv.hpp.
Referenced by CEffectiveSearchSpacesMemento::CEffectiveSearchSpacesMemento(), and CEffectiveSearchSpacesMemento::~CEffectiveSearchSpacesMemento().
◆ m_Encoding
|
private |
Encoding used in the data above.
Definition at line 97 of file bioseq_extract_data_priv.hpp.
Referenced by CBlastSeqVectorFromCSeq_data::SetCoding(), and CBlastSeqVectorFromCSeq_data::x_ComplementData().
◆ m_EntrezQuery [1/3]
The entreq query to use (or none).
Definition at line 291 of file blast_options_builder.hpp.
Referenced by CBlastOptionsBuilder::GetEntrezQuery(), CBlastOptionsBuilder::HaveEntrezQuery(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ m_EntrezQuery [2/3]
|
private |
Entrez Query, if any.
Definition at line 806 of file remote_blast.hpp.
Referenced by CRemoteBlast::GetSearchOptions(), and CRemoteBlast::SetEntrezQuery().
◆ m_EntrezQuery [3/3]
|
private |
Definition at line 307 of file igblast.hpp.
Referenced by CIgBlast::Run().
◆ m_EntrezQueryLimitation
|
private |
entrez query
Definition at line 194 of file uniform_search.hpp.
Referenced by CSearchDatabase::GetEntrezQueryLimitation(), and CSearchDatabase::SetEntrezQueryLimitation().
◆ m_ErrIgn
|
private |
Count of server glitches (communication errors) to ignore.
Definition at line 758 of file remote_blast.hpp.
Referenced by CRemoteBlast::x_CheckResults(), CRemoteBlast::x_CheckResultsDC(), and CRemoteBlast::x_Init().
◆ m_Errors
|
protected |
error/warning messages for this query
Definition at line 270 of file blast_results.hpp.
Referenced by CSearchResults::GetErrors(), CSearchResults::GetErrorStrings(), CSearchResults::GetWarningStrings(), CSearchResults::HasErrors(), and CSearchResults::HasWarnings().
◆ m_Errs
|
private |
List of errors encountered.
Definition at line 749 of file remote_blast.hpp.
Referenced by CRemoteBlast::GetErrors(), CRemoteBlast::GetErrorVector(), CRemoteBlast::LoadFromArchive(), CRemoteBlast::Submit(), CRemoteBlast::SubmitSync(), CRemoteBlast::x_CheckResults(), CRemoteBlast::x_CheckResultsDC(), CRemoteBlast::x_GetBlast4SearchRequestBody(), CRemoteBlast::x_GetState(), CRemoteBlast::x_SearchErrors(), and CRemoteBlast::x_SubmitSearch().
◆ m_Evalue
| double CCddInputData::CHit::m_Evalue |
E-value.
Definition at line 358 of file cdd_pssm_input.hpp.
◆ m_ExtendAlign3end
| bool CIgBlastOptions::m_ExtendAlign3end |
Definition at line 86 of file igblast.hpp.
Referenced by CIgBlastArgs::ExtractAlgorithmOptions(), and CIgBlast::Run().
◆ m_ExtendAlign5end
| bool CIgBlastOptions::m_ExtendAlign5end |
Definition at line 85 of file igblast.hpp.
Referenced by CIgBlastArgs::ExtractAlgorithmOptions(), and CIgBlast::Run().
◆ m_ExtnOpts [1/2]
|
private |
Definition at line 94 of file blast_memento_priv.hpp.
Referenced by CSetupFactory::CreateHspPipe(), CSetupFactory::CreateHspStream(), CSetupFactory::CreateHspWriter(), CSetupFactory::CreateScoreBlock(), CBlastTracebackSearch::Run(), and CBlastTracebackSearch::RunSimple().
◆ m_ExtnOpts [2/2]
|
private |
Hit extension settings.
Definition at line 372 of file blast_options_local_priv.hpp.
Referenced by CBlastOptionsLocal::CBlastOptionsLocal(), CBlastOptionsMemento::CBlastOptionsMemento(), CBlastOptionsLocal::DebugDump(), CBlastOptionsLocal::GetChaining(), CBlastOptionsLocal::GetCompositionBasedStats(), CBlastOptionsLocal::GetExtnOpts(), CBlastOptionsLocal::GetGapExtnAlgorithm(), CBlastOptionsLocal::GetGapTracebackAlgorithm(), CBlastOptionsLocal::GetGapXDropoff(), CBlastOptionsLocal::GetGapXDropoffFinal(), CBlastOptionsLocal::GetMaxMismatches(), CBlastOptionsLocal::GetMismatchWindow(), CBlastOptionsLocal::GetSmithWatermanMode(), CBlastOptionsLocal::GetUnifiedP(), CBlastOptionsLocal::operator==(), CBlastOptionsLocal::SetChaining(), CBlastOptionsLocal::SetCompositionBasedStats(), CBlastOptionsLocal::SetGapExtnAlgorithm(), CBlastOptionsLocal::SetGapTracebackAlgorithm(), CBlastOptionsLocal::SetGapXDropoff(), CBlastOptionsLocal::SetGapXDropoffFinal(), CBlastOptionsLocal::SetMaxMismatches(), CBlastOptionsLocal::SetMismatchWindow(), CBlastOptionsLocal::SetSmithWatermanMode(), CBlastOptionsLocal::SetUnifiedP(), CBlastOptionsLocal::Validate(), and CBlastOptionsLocal::x_DoDeepCopy().
◆ m_FilteringAlgoId
|
private |
Filtering algorithm ID used with these subjects, use -1 if not applicable.
Definition at line 121 of file seqinfosrc_seqdb.hpp.
Referenced by CSeqDbSeqInfoSrc::GetMasks(), and CSeqDbSeqInfoSrc::SetFilteringAlgorithmId().
◆ m_FilteringAlgorithmId
|
mutableprivate |
Definition at line 201 of file uniform_search.hpp.
Referenced by CSearchDatabase::GetFilteringAlgorithm(), CSearchDatabase::SetFilteringAlgorithm(), CSearchDatabase::x_TranslateFilteringAlgorithm(), and CSearchDatabase::x_ValidateMaskingAlgorithm().
◆ m_FilteringAlgorithmString
|
private |
filtering to apply to database sequences
Definition at line 200 of file uniform_search.hpp.
Referenced by CSearchDatabase::GetFilteringAlgorithmKey(), CSearchDatabase::SetFilteringAlgorithm(), and CSearchDatabase::x_TranslateFilteringAlgorithm().
◆ m_FilteringID
| int CImportStrategyData::m_FilteringID |
Filtering ID.
Definition at line 69 of file search_strategy.hpp.
◆ m_FilteringKey
| string CImportStrategyData::m_FilteringKey |
Filtering key.
Definition at line 80 of file search_strategy.hpp.
◆ m_FilterOpts
|
private |
original filtering options specified in m_OptsMemento
Definition at line 79 of file effsearchspace_calc.cpp.
◆ m_FilterString
|
private |
original filtering string specified in m_OptsMemento
Definition at line 77 of file effsearchspace_calc.cpp.
◆ m_FinalDbSeq [1/3]
The last OID to process (or none).
Definition at line 297 of file blast_options_builder.hpp.
Referenced by CBlastOptionsBuilder::GetFinalDbSeq(), CBlastOptionsBuilder::HaveFinalDbSeq(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ m_FinalDbSeq [2/3]
|
private |
Final database sequence.
Definition at line 812 of file remote_blast.hpp.
Referenced by CRemoteBlast::GetSearchOptions().
◆ m_FinalDbSeq [3/3]
|
private |
Ordinal id of the last sequence to search.
Definition at line 598 of file seqsrc_seqdb.cpp.
◆ m_FirstDbSeq [1/3]
The first OID to process (or none).
Definition at line 294 of file blast_options_builder.hpp.
Referenced by CBlastOptionsBuilder::GetFirstDbSeq(), CBlastOptionsBuilder::HaveFirstDbSeq(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ m_FirstDbSeq [2/3]
|
private |
First database sequence.
Definition at line 809 of file remote_blast.hpp.
Referenced by CRemoteBlast::GetSearchOptions().
◆ m_FirstDbSeq [3/3]
|
private |
Ordinal id of the first sequence to search.
Definition at line 597 of file seqsrc_seqdb.cpp.
◆ m_FirstInfo
|
private |
Alignment flags for the query.
Definition at line 232 of file magicblast.hpp.
Referenced by CMagicBlastResults::FirstAligned(), CMagicBlastResults::GetFirstInfo(), and CMagicBlastResults::x_SetInfo().
◆ m_FnInterrupt
| TInterruptFnPtr SInternalData::m_FnInterrupt |
The interrupt callback.
Definition at line 344 of file setup_factory.hpp.
Referenced by CBlastTracebackSearch::Run(), CBlastTracebackSearch::RunSimple(), CBlastPrelimSearch::SetInterruptCallback(), and SplitQuery_CreateChunkData().
◆ m_FocusV
| bool CIgBlastOptions::m_FocusV |
Definition at line 83 of file igblast.hpp.
Referenced by CIgBlastArgs::ExtractAlgorithmOptions(), and CIgBlast::x_SetupDbSearch().
◆ m_ForceMbIndex
|
private |
Should loading of the megablast BLAST DB index be required?
Definition at line 326 of file blast_options_builder.hpp.
Referenced by CBlastOptionsBuilder::x_ApplyInteractions(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ m_ForceMBIndex
|
private |
Definition at line 397 of file blast_options_local_priv.hpp.
Referenced by CBlastOptionsLocal::CBlastOptionsLocal(), CBlastOptionsLocal::GetForceIndex(), CBlastOptionsLocal::SetUseIndex(), and CBlastOptionsLocal::x_DoDeepCopy().
◆ m_FormatOpts
|
private |
Options relevant to the format application.
Definition at line 800 of file remote_blast.hpp.
Referenced by CRemoteBlast::GetPsiNumberOfIterations(), CRemoteBlast::GetSearchOptions(), CRemoteBlast::x_GetRequestInfoFromFile(), and CRemoteBlast::x_GetRequestInfoFromRID().
◆ m_Frame
|
private |
Frame to look for.
Definition at line 155 of file blast_aux.hpp.
Referenced by CFrameFinder::operator()().
◆ m_FrameInfo
| int CIgAnnotation::m_FrameInfo[3] |
Definition at line 103 of file igblast.hpp.
Referenced by CIgAnnotation::CIgAnnotation(), CBlastFormat::PrintOneResultSet(), CIgBlast::x_AnnotateDomain(), and CBlastFormat::x_ReverseQuery().
◆ m_FrameOffset
Definition at line 190 of file igblast.hpp.
Referenced by CIgAnnotationInfo::CIgAnnotationInfo(), and CIgAnnotationInfo::GetFrameOffset().
◆ m_Frames
|
private |
Frames for masked locations.
Definition at line 525 of file blast_setup.hpp.
Referenced by CBlastQueryFilteredFrames::AddSeqLoc(), and CBlastQueryFilteredFrames::ListFrames().
◆ m_FreqRatios
|
private |
Frequency ratios.
Definition at line 148 of file psi_pssm_input.hpp.
◆ m_FreqRatiosFile
|
private |
Frequency ratios file (.freq) used for composition based statistics and cobalt.
Definition at line 162 of file rps_aux.hpp.
Referenced by CBlastRPSInfo::x_Init().
◆ m_FreqsFile
|
private |
Weighted residue frequencies file (.wcounts) used by delta-blast.
Definition at line 154 of file rps_aux.hpp.
Referenced by CBlastRPSInfo::x_Init().
◆ m_Fwr4EndOffset
Definition at line 193 of file igblast.hpp.
Referenced by CIgAnnotationInfo::CIgAnnotationInfo(), and CIgAnnotationInfo::GetFwr4EndOffset().
◆ m_GapExistence [1/4]
|
private |
Gap existence for underlying scoring system.
Definition at line 482 of file cdd_pssm_input.hpp.
Referenced by CCddInputData::GetGapExistence().
◆ m_GapExistence [2/4]
|
private |
Gap existence parameter used.
Definition at line 151 of file msa_pssm_input.hpp.
◆ m_GapExistence [3/4]
|
private |
Gap existence penalty.
Definition at line 144 of file psi_pssm_input.hpp.
◆ m_GapExistence [4/4]
|
private |
Gap existence paramter used.
Definition at line 251 of file psi_pssm_input.hpp.
Referenced by CPsiBlastInputData::GetGapExistence().
◆ m_GapExtension [1/4]
|
private |
Gap extension for underlying scoring system.
Definition at line 485 of file cdd_pssm_input.hpp.
Referenced by CCddInputData::GetGapExtension().
◆ m_GapExtension [2/4]
|
private |
Gap extension parameter used.
Definition at line 153 of file msa_pssm_input.hpp.
◆ m_GapExtension [3/4]
|
private |
Gap extension penalty.
Definition at line 146 of file psi_pssm_input.hpp.
◆ m_GapExtension [4/4]
|
private |
Gap extension paramter used.
Definition at line 253 of file psi_pssm_input.hpp.
Referenced by CPsiBlastInputData::GetGapExtension().
◆ m_GappedKarlinBlk
|
private |
Gapped Karlin parameters for one query.
Definition at line 137 of file blast_results.hpp.
Referenced by CBlastAncillaryData::CBlastAncillaryData(), CBlastAncillaryData::do_copy(), and CBlastAncillaryData::~CBlastAncillaryData().
◆ m_GeneInfo
| int CIgAnnotation::m_GeneInfo[8] |
Definition at line 102 of file igblast.hpp.
Referenced by CIgAnnotation::CIgAnnotation(), CIgBlast::x_AnnotateV(), CBlastFormat::x_ReverseQuery(), and CIgBlast::x_SetAnnotation().
◆ m_GiList [1/3]
The GI list (or none).
Definition at line 300 of file blast_options_builder.hpp.
Referenced by CBlastOptionsBuilder::GetGiList(), CBlastOptionsBuilder::HaveGiList(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ m_GiList [2/3]
|
private |
GI list.
Definition at line 815 of file remote_blast.hpp.
Referenced by CRemoteBlast::GetSearchOptions(), and CRemoteBlast::SetGIList().
◆ m_GiList [3/3]
|
mutableprivate |
gi list
Definition at line 196 of file uniform_search.hpp.
Referenced by CSearchDatabase::GetGiList(), CSearchDatabase::GetGiListLimitation(), CSearchDatabase::SetGiList(), and CSearchDatabase::x_InitializeDb().
◆ m_GiListSet
|
private |
Definition at line 198 of file uniform_search.hpp.
Referenced by CSearchDatabase::SetGiList(), and CSearchDatabase::SetNegativeGiList().
◆ m_GumbelBlk
|
private |
Gumbel parameters for one query.
Definition at line 131 of file blast_results.hpp.
Referenced by CBlastAncillaryData::CBlastAncillaryData(), CBlastAncillaryData::do_copy(), and CBlastAncillaryData::~CBlastAncillaryData().
◆ m_handler
|
private |
Definition at line 264 of file blast_aux.hpp.
Referenced by CBlastAppDiagHandler::Post(), and CBlastAppDiagHandler::~CBlastAppDiagHandler().
◆ m_Hits
|
private |
RPS-BLAST hits in internal representation.
Definition at line 453 of file cdd_pssm_input.hpp.
Referenced by CCddInputData::Process(), CCddInputData::x_CreateMsa(), CCddInputData::x_FillHitsData(), CCddInputData::x_ProcessAlignments(), CCddInputData::x_RemoveMultipleCdHits(), CCddInputData::x_ValidateHits(), CCddInputData::x_ValidateMsa(), and CCddInputData::~CCddInputData().
◆ m_HitSaveOpts [1/2]
|
private |
Definition at line 95 of file blast_memento_priv.hpp.
Referenced by CSetupFactory::CreateHspPipe(), CSetupFactory::CreateHspWriter(), CBlastTracebackSearch::Run(), and CBlastTracebackSearch::RunSimple().
◆ m_HitSaveOpts [2/2]
|
private |
Hit saving settings.
Definition at line 375 of file blast_options_local_priv.hpp.
Referenced by CBlastOptionsLocal::CBlastOptionsLocal(), CBlastOptionsMemento::CBlastOptionsMemento(), CBlastOptionsLocal::DebugDump(), CBlastOptionsLocal::GetBestHitOverhang(), CBlastOptionsLocal::GetBestHitScoreEdge(), CBlastOptionsLocal::GetCullingLimit(), CBlastOptionsLocal::GetCutoffScore(), CBlastOptionsLocal::GetCutoffScoreCoeffs(), CBlastOptionsLocal::GetEvalueThreshold(), CBlastOptionsLocal::GetHitlistSize(), CBlastOptionsLocal::GetHitSaveOpts(), CBlastOptionsLocal::GetLongestIntronLength(), CBlastOptionsLocal::GetLowScorePerc(), CBlastOptionsLocal::GetMaskLevel(), CBlastOptionsLocal::GetMaxEditDistance(), CBlastOptionsLocal::GetMaxHspsPerSubject(), CBlastOptionsLocal::GetMaxNumHspPerSequence(), CBlastOptionsLocal::GetMinDiagSeparation(), CBlastOptionsLocal::GetPaired(), CBlastOptionsLocal::GetPercentIdentity(), CBlastOptionsLocal::GetQueryCovHspPerc(), CBlastOptionsLocal::GetSplice(), CBlastOptionsLocal::GetSubjectBestHit(), CBlastOptionsLocal::GetSumStatisticsMode(), CBlastOptionsLocal::operator==(), CBlastOptionsLocal::SetBestHitOverhang(), CBlastOptionsLocal::SetBestHitScoreEdge(), CBlastOptionsLocal::SetCullingLimit(), CBlastOptionsLocal::SetCutoffScore(), CBlastOptionsLocal::SetCutoffScoreCoeffs(), CBlastOptionsLocal::SetEvalueThreshold(), CBlastOptionsLocal::SetHitlistSize(), CBlastOptionsLocal::SetLongestIntronLength(), CBlastOptionsLocal::SetLowScorePerc(), CBlastOptionsLocal::SetMaskLevel(), CBlastOptionsLocal::SetMaxEditDistance(), CBlastOptionsLocal::SetMaxHspsPerSubject(), CBlastOptionsLocal::SetMaxNumHspPerSequence(), CBlastOptionsLocal::SetMinDiagSeparation(), CBlastOptionsLocal::SetPaired(), CBlastOptionsLocal::SetPercentIdentity(), CBlastOptionsLocal::SetQueryCovHspPerc(), CBlastOptionsLocal::SetSplice(), CBlastOptionsLocal::SetSubjectBestHit(), CBlastOptionsLocal::SetSumStatisticsMode(), CBlastOptionsLocal::Validate(), and CBlastOptionsLocal::x_DoDeepCopy().
◆ m_HspRangeMax
|
private |
How much culling to do.
Definition at line 288 of file blast_options_builder.hpp.
Referenced by CBlastOptionsBuilder::x_ApplyInteractions(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ m_HspStream
| CRef<TBlastHSPStream> SInternalData::m_HspStream |
HSP output of the preliminary stage goes here.
Definition at line 335 of file setup_factory.hpp.
Referenced by BOOST_AUTO_TEST_CASE(), CBlastPrelimSearch::Run(), CBlastTracebackSearch::Run(), CMagicBlast::Run(), CMagicBlast::RunEx(), CBlastTracebackSearch::RunSimple(), CBlastPrelimSearch::SetNumberOfThreads(), CBlastPrelimSearch::x_BuildStdSegList(), and CBlastTracebackSearch::x_Init().
◆ m_iAvgLength
|
private |
Average length of sequences in this set.
Definition at line 73 of file seqsrc_multiseq.cpp.
Referenced by CMultiSeqInfo::CMultiSeqInfo(), CMultiSeqInfo::GetAvgLength(), and CMultiSeqInfo::SetAvgLength().
◆ m_ibIsProt
|
private |
Internal fields.
Are these sequences protein or nucleotide?
Definition at line 70 of file seqsrc_multiseq.cpp.
Referenced by CMultiSeqInfo::CMultiSeqInfo(), and CMultiSeqInfo::GetIsProtein().
◆ m_IgDataPath
| string CIgBlastOptions::m_IgDataPath |
Definition at line 77 of file igblast.hpp.
Referenced by CIgAnnotationInfo::CIgAnnotationInfo(), and CIgBlastArgs::ExtractAlgorithmOptions().
◆ m_IgnoreQueryMasks
|
private |
Indicated that query masks have already been collected.
Definition at line 314 of file blast_options_builder.hpp.
Referenced by CBlastOptionsBuilder::GetSearchOptions(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ m_IgnoreUnsupportedOptions [1/2]
|
private |
Should this class quietly ignore unsupported options.
Definition at line 323 of file blast_options_builder.hpp.
Referenced by CBlastOptionsBuilder::SetIgnoreUnsupportedOptions(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ m_IgnoreUnsupportedOptions [2/2]
|
private |
ignore unsupported options when creating blast options builder object
Definition at line 183 of file search_strategy.hpp.
Referenced by CImportStrategy::FetchData().
◆ m_IgOptions
|
private |
Definition at line 305 of file igblast.hpp.
Referenced by CIgBlast::Run(), CIgBlast::x_AnnotateC(), CIgBlast::x_AnnotateD(), CIgBlast::x_AnnotateDJ(), CIgBlast::x_AnnotateDomain(), CIgBlast::x_AnnotateJ(), CIgBlast::x_AnnotateV(), CIgBlast::x_FindDJAln(), CIgBlast::x_ProcessDGeneResult(), CIgBlast::x_SetAnnotation(), CIgBlast::x_SetupCRegionSearch(), CIgBlast::x_SetupDbSearch(), CIgBlast::x_SetupDJSearch(), CIgBlast::x_SetupNoOverlapDSearch(), and CIgBlast::x_SetupVSearch().
◆ m_iMaxLength
|
private |
Length of the longest sequence in this set.
Definition at line 72 of file seqsrc_multiseq.cpp.
Referenced by CMultiSeqInfo::CMultiSeqInfo(), CMultiSeqInfo::GetMaxLength(), and CMultiSeqInfo::SetMaxLength().
◆ m_ImpalaScaleFactor
|
private |
Definition at line 151 of file psi_pssm_input.hpp.
◆ m_Impl [1/2]
|
private |
Implementation class.
Definition at line 119 of file psibl2seq.hpp.
Referenced by CPsiBl2Seq::CPsiBl2Seq(), CPsiBl2Seq::Run(), and CPsiBl2Seq::~CPsiBl2Seq().
◆ m_Impl [2/2]
|
private |
Implementation class.
Definition at line 130 of file psiblast.hpp.
Referenced by CPsiBlast::CPsiBlast(), CPsiBlast::GetPssm(), CPsiBlast::Run(), CPsiBlast::SetPssm(), and CPsiBlast::~CPsiBlast().
◆ m_InitWordOpts [1/2]
|
private |
Definition at line 93 of file blast_memento_priv.hpp.
◆ m_InitWordOpts [2/2]
|
private |
Word settings.
Definition at line 369 of file blast_options_local_priv.hpp.
Referenced by CBlastOptionsLocal::CBlastOptionsLocal(), CBlastOptionsMemento::CBlastOptionsMemento(), CBlastOptionsLocal::DebugDump(), CBlastOptionsLocal::GetGapTrigger(), CBlastOptionsLocal::GetInitWordOpts(), CBlastOptionsLocal::GetOffDiagonalRange(), CBlastOptionsLocal::GetWindowSize(), CBlastOptionsLocal::GetXDropoff(), CBlastOptionsLocal::operator==(), CBlastOptionsLocal::SetGapTrigger(), CBlastOptionsLocal::SetOffDiagonalRange(), CBlastOptionsLocal::SetWindowSize(), CBlastOptionsLocal::SetXDropoff(), CBlastOptionsLocal::Validate(), and CBlastOptionsLocal::x_DoDeepCopy().
◆ m_InternalData [1/7]
|
private |
Internal core data structures which are used in the preliminary and traceback stages of the search.
Definition at line 129 of file local_blast.hpp.
Referenced by CLocalBlast::GetDiagnostics(), CLocalBlast::GetNumExtensions(), CLocalBlast::Run(), and CBl2Seq::RunEx().
◆ m_InternalData [2/7]
|
private |
Internal data strctures.
Definition at line 125 of file magicblast.hpp.
Referenced by CMagicBlast::Run(), CMagicBlast::RunEx(), CMagicBlast::x_BuildResultSet(), CMagicBlast::x_BuildSeqAlignSet(), and CMagicBlast::x_Run().
◆ m_InternalData [3/7]
|
private |
Definition at line 164 of file prelim_stage.hpp.
Referenced by CBlastPrelimSearch::CBlastPrelimSearch(), CBlastPrelimSearch::CheckInternalData(), CBlastPrelimSearch::ComputeBlastHSPResults(), CBlastPrelimSearch::Run(), CBlastPrelimSearch::SetInterruptCallback(), CBlastPrelimSearch::SetNumberOfThreads(), CBlastPrelimSearch::x_BuildStdSegList(), CBlastPrelimSearch::x_Init(), and CBlastPrelimSearch::x_LaunchMultiThreadedSearch().
◆ m_InternalData [4/7]
|
private |
Fields and data from the preliminary search.
Definition at line 116 of file traceback_stage.hpp.
Referenced by CBlastTracebackSearch::CBlastTracebackSearch(), CBlastTracebackSearch::Run(), CBlastTracebackSearch::RunSimple(), and CBlastTracebackSearch::x_Init().
◆ m_InternalData [5/7]
| CRef<SInternalData> SBlastSetupData::m_InternalData |
Definition at line 109 of file blast_aux_priv.hpp.
◆ m_InternalData [6/7]
|
private |
Data structure containing all the needed C structures for the preliminary stage of the BLAST search.
Definition at line 95 of file prelim_search_runner.hpp.
◆ m_InternalData [7/7]
|
private |
Definition at line 154 of file prelim_search_runner.hpp.
Referenced by CPrelimSearchThread::CPrelimSearchThread(), CPrelimSearchThread::Main(), and CPrelimSearchThread::~CPrelimSearchThread().
◆ m_InterruptFnx
|
private |
Interrupt callback.
Definition at line 211 of file bl2seq.hpp.
Referenced by CBl2Seq::SetInterruptCallback(), and CBl2Seq::x_InitCLocalBlast().
◆ m_InterruptUserData
|
private |
Interrupt user datacallback.
Definition at line 213 of file bl2seq.hpp.
Referenced by CBl2Seq::SetInterruptCallback(), and CBl2Seq::x_InitCLocalBlast().
◆ m_iSeqDb
BLAST database object.
Definition at line 118 of file seqinfosrc_seqdb.hpp.
Referenced by CSeqDbSeqInfoSrc::CSeqDbSeqInfoSrc(), CSeqDbSeqInfoSrc::GetId(), CSeqDbSeqInfoSrc::GetLength(), CSeqDbSeqInfoSrc::GetMasks(), CSeqDbSeqInfoSrc::HasGiList(), and CSeqDbSeqInfoSrc::Size().
◆ m_IsLocal
|
private |
Definition at line 298 of file igblast.hpp.
Referenced by CIgBlast::Run().
◆ m_IsPhiBlast
|
private |
True if this object contains PHI-BLAST results.
Definition at line 481 of file blast_results.hpp.
Referenced by CSearchResultSet::SetFilteredQueryRegions(), and CSearchResultSet::x_Init().
◆ m_IsProt [1/2]
|
private |
True if the data contained in this object is protein.
Definition at line 191 of file bioseq_extract_data_priv.hpp.
Referenced by CBlastQuerySourceBioseqSet::GetGeneticCodeId(), CBlastQuerySourceBioseqSet::GetStrand(), and CBlastQuerySourceBioseqSet::x_BioseqSanityCheck().
◆ m_IsProt [2/2]
|
private |
Are these sequences protein or nucleotide?
Definition at line 75 of file seqsrc_query_factory.cpp.
Referenced by CQueryFactoryInfo::CQueryFactoryInfo(), and CQueryFactoryInfo::GetIsProtein().
◆ m_IsProtein [1/2]
| bool CIgBlastOptions::m_IsProtein |
Definition at line 66 of file igblast.hpp.
Referenced by CIgAnnotationInfo::CIgAnnotationInfo(), CIgBlastArgs::ExtractAlgorithmOptions(), CIgBlastnApp::CIgFormatter::Main(), CIgBlast::Run(), CIgBlastnApp::Run(), CIgBlastpApp::Run(), CIgBlast::x_AnnotateDomain(), and CIgBlast::x_SetupVSearch().
◆ m_IsProtein [2/2]
|
private |
Is this database protein?
Definition at line 596 of file seqsrc_seqdb.cpp.
◆ m_IsSet
|
private |
True if the value has been specified.
Definition at line 246 of file blast_options_builder.hpp.
◆ m_IterationsDone
|
private |
Number of iterations already done.
Definition at line 128 of file psiblast_iteration.hpp.
Referenced by CPsiBlastIterationState::Advance(), CPsiBlastIterationState::GetIterationNumber(), CPsiBlastIterationState::HasConverged(), and CPsiBlastIterationState::HasMoreIterations().
◆ m_iTotalLength
|
private |
Total length of sequences in this set.
Definition at line 74 of file seqsrc_multiseq.cpp.
Referenced by CMultiSeqInfo::CMultiSeqInfo(), and CMultiSeqInfo::GetTotLength().
◆ m_ivSeqBlkVec
|
private |
Vector of sequence blocks.
Definition at line 71 of file seqsrc_multiseq.cpp.
Referenced by CMultiSeqInfo::CMultiSeqInfo(), CMultiSeqInfo::GetNumSeqs(), CMultiSeqInfo::GetSeqBlk(), and CMultiSeqInfo::~CMultiSeqInfo().
◆ m_J_penalty
| int CIgBlastOptions::m_J_penalty |
Definition at line 73 of file igblast.hpp.
Referenced by CIgBlastArgs::ExtractAlgorithmOptions(), CIgBlast::Run(), CIgBlast::x_FindDJAln(), and CIgBlast::x_SetupDJSearch().
◆ m_JDomain
| int CIgAnnotation::m_JDomain[5] |
Definition at line 111 of file igblast.hpp.
Referenced by CIgAnnotation::CIgAnnotation(), CBlastFormat::PrintOneResultSet(), and CIgBlast::x_FillJDomain().
◆ m_JDomainInfo
Definition at line 192 of file igblast.hpp.
Referenced by CIgAnnotationInfo::CIgAnnotationInfo(), and CIgAnnotationInfo::GetJDomain().
◆ m_LastChunkForQueryCache
|
private |
Lists the last chunk where the query can be found.
Definition at line 248 of file split_query_aux_priv.hpp.
Referenced by CQueryDataPerChunk::CQueryDataPerChunk(), and CQueryDataPerChunk::GetLastChunk().
◆ m_LastInfo
|
private |
Alignment flags for the mate.
Definition at line 235 of file magicblast.hpp.
Referenced by CMagicBlastResults::GetLastInfo(), CMagicBlastResults::LastAligned(), and CMagicBlastResults::x_SetInfo().
◆ m_LengthAdjustment
|
private |
Length adjustment for boundary conditions.
Definition at line 150 of file blast_results.hpp.
Referenced by CBlastAncillaryData::CBlastAncillaryData().
◆ m_LocalBlast
|
private |
Local database search class.
Definition at line 73 of file local_search.hpp.
Referenced by CLocalSeqSearch::Run().
◆ m_LocalDb
|
private |
Definition at line 302 of file igblast.hpp.
Referenced by CIgBlast::Run().
◆ m_LocalDbAdapter [1/2]
|
private |
Local DB adaptor (if one was) passed to constructor.
Definition at line 138 of file local_blast.hpp.
Referenced by CLocalBlast::Run().
◆ m_LocalDbAdapter [2/2]
|
private |
Reference to a BLAST subject/database object.
Definition at line 116 of file magicblast.hpp.
Referenced by CMagicBlast::x_BuildResultSet(), CMagicBlast::x_BuildSeqAlignSet(), CMagicBlast::x_Run(), and CMagicBlast::x_Validate().
◆ m_Locality
|
private |
API Locality of resulting options.
Definition at line 320 of file blast_options_builder.hpp.
Referenced by CBlastOptionsBuilder::GetSearchOptions().
◆ m_LocalQueryData [1/2]
|
protected |
Definition at line 158 of file query_data.hpp.
Referenced by IQueryFactory::MakeLocalQueryData().
◆ m_LocalQueryData [2/2]
|
private |
Source of local query data.
Definition at line 115 of file split_query.hpp.
Referenced by operator<<(), CQuerySplitter::x_ComputeContextOffsets_NonTranslatedQueries(), CQuerySplitter::x_ComputeContextOffsets_TranslatedQueries(), CQuerySplitter::x_ComputeQueryContextsForChunks(), CQuerySplitter::x_ComputeQueryIndicesForChunks(), and CQuerySplitter::x_ExtractCScopesAndMasks().
◆ m_Lookup
|
private |
Definition at line 154 of file seedtop.hpp.
Referenced by CSeedTop::Run(), and CSeedTop::x_MakeLookupTable().
◆ m_LookupTable
| CRef<TLookupTableWrap> SInternalData::m_LookupTable |
Lookup table, usually only needed in the preliminary stage of the search, but for PHI-BLAST it's also needed in the traceback stage.
Definition at line 329 of file setup_factory.hpp.
Referenced by CBlastTracebackSearch::Run(), CBlastTracebackSearch::RunSimple(), and CBlastTracebackSearch::x_Init().
◆ m_LutFile
|
private |
The lookup table RPS-BLAST file (.loo)
Definition at line 150 of file rps_aux.hpp.
Referenced by CBlastRPSInfo::x_Init().
◆ m_LutOpts [1/2]
|
private |
Definition at line 92 of file blast_memento_priv.hpp.
Referenced by CSetupFactory::CreateLookupTable().
◆ m_LutOpts [2/2]
|
private |
Lookup table settings.
Definition at line 366 of file blast_options_local_priv.hpp.
Referenced by CBlastOptionsLocal::CBlastOptionsLocal(), CBlastOptionsMemento::CBlastOptionsMemento(), CBlastOptionsLocal::DebugDump(), CBlastOptionsLocal::GetLookupDbFilter(), CBlastOptionsLocal::GetLookupTableStride(), CBlastOptionsLocal::GetLookupTableType(), CBlastOptionsLocal::GetLutOpts(), CBlastOptionsLocal::GetMaxDbWordCount(), CBlastOptionsLocal::GetMBTemplateLength(), CBlastOptionsLocal::GetMBTemplateType(), CBlastOptionsLocal::GetPHIPattern(), CBlastOptionsLocal::GetWordSize(), CBlastOptionsLocal::GetWordThreshold(), CBlastOptionsLocal::operator==(), CBlastOptionsLocal::SetLookupDbFilter(), CBlastOptionsLocal::SetLookupTableStride(), CBlastOptionsLocal::SetLookupTableType(), CBlastOptionsLocal::SetMaxDbWordCount(), CBlastOptionsLocal::SetMBTemplateLength(), CBlastOptionsLocal::SetMBTemplateType(), CBlastOptionsLocal::SetPHIPattern(), CBlastOptionsLocal::SetWordSize(), CBlastOptionsLocal::SetWordThreshold(), CBlastOptionsLocal::Validate(), and CBlastOptionsLocal::x_DoDeepCopy().
◆ m_MaskAlgoId
|
private |
filtering algorithm ID to use when retrieving sequence data
Definition at line 600 of file seqsrc_seqdb.cpp.
◆ m_Masks [1/2]
|
protected |
this query's masked regions
Definition at line 273 of file blast_results.hpp.
Referenced by CSearchResults::GetMaskedQueryRegions(), and CSearchResults::SetMaskedQueryRegions().
◆ m_Masks [2/2]
| TSeqLocInfoVector SBlastSetupData::m_Masks |
Definition at line 111 of file blast_aux_priv.hpp.
◆ m_MasksForAllQueries
|
private |
Query masking information.
Definition at line 175 of file prelim_stage.hpp.
Referenced by CBlastPrelimSearch::GetFilteredQueryRegions(), and CBlastPrelimSearch::x_Init().
◆ m_MaskType [1/2]
|
private |
Definition at line 202 of file uniform_search.hpp.
Referenced by CSearchDatabase::GetFilteringAlgorithm(), CSearchDatabase::GetFilteringAlgorithmKey(), CSearchDatabase::GetMaskType(), CSearchDatabase::SetFilteringAlgorithm(), and CSearchDatabase::x_TranslateFilteringAlgorithm().
◆ m_MaskType [2/2]
|
private |
Definition at line 601 of file seqsrc_seqdb.cpp.
◆ m_MateId
Mate id if results are for paired reads.
Definition at line 220 of file magicblast.hpp.
Referenced by CMagicBlastResults::GetLastId(), and CMagicBlastResults::x_SetInfo().
◆ m_MatrixName [1/4]
|
private |
Scoring matrix name.
Definition at line 470 of file cdd_pssm_input.hpp.
Referenced by CCddInputData::GetMatrixName().
◆ m_MatrixName [2/4]
|
private |
Underlying matrix to use.
Definition at line 149 of file msa_pssm_input.hpp.
◆ m_MatrixName [3/4]
|
private |
Name of underlying scoring matrix.
Definition at line 142 of file psi_pssm_input.hpp.
◆ m_MatrixName [4/4]
|
private |
Underlying matrix to use.
Definition at line 249 of file psi_pssm_input.hpp.
Referenced by CPsiBlastInputData::CPsiBlastInputData(), and CPsiBlastInputData::GetMatrixName().
◆ m_MaxLength
|
private |
Length of the longest sequence in this set.
Definition at line 77 of file seqsrc_query_factory.cpp.
Referenced by CQueryFactoryInfo::CQueryFactoryInfo(), and CQueryFactoryInfo::GetMaxLength().
◆ m_MBIndexLoaded
|
private |
Database index has been loaded.
Definition at line 401 of file blast_options_local_priv.hpp.
Referenced by CBlastOptionsLocal::CBlastOptionsLocal(), CBlastOptionsLocal::GetMBIndexLoaded(), CBlastOptionsLocal::SetMBIndexLoaded(), and CBlastOptionsLocal::x_DoDeepCopy().
◆ m_MbIndexName
|
private |
Which megablast BLAST DB index name to load.
Definition at line 328 of file blast_options_builder.hpp.
Referenced by CBlastOptionsBuilder::x_ApplyInteractions(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ m_MBIndexName
|
private |
Megablast database index name.
Definition at line 404 of file blast_options_local_priv.hpp.
Referenced by CBlastOptionsLocal::GetIndexName(), CBlastOptionsLocal::SetUseIndex(), and CBlastOptionsLocal::x_DoDeepCopy().
◆ m_Messages [1/7]
|
private |
Stores any warnings emitted during query setup.
Definition at line 198 of file bl2seq.hpp.
Referenced by CBl2Seq::GetMessages(), CBl2Seq::RunEx(), and CBl2Seq::x_ResetInternalDs().
◆ m_messages
|
private |
Definition at line 265 of file blast_aux.hpp.
Referenced by CBlastAppDiagHandler::GetMessages(), CBlastAppDiagHandler::Post(), and CBlastAppDiagHandler::ResetMessages().
◆ m_Messages [2/7]
|
private |
Warnings and error messages.
Definition at line 145 of file local_blast.hpp.
Referenced by CLocalBlast::GetSearchMessages(), and CLocalBlast::Run().
◆ m_Messages [3/7]
|
private |
Warning and error messages.
Definition at line 128 of file magicblast.hpp.
Referenced by CMagicBlast::GetSearchMessages().
◆ m_Messages [4/7]
|
private |
Warnings and error messages.
Definition at line 172 of file prelim_stage.hpp.
Referenced by CBlastPrelimSearch::GetSearchMessages(), CBlastPrelimSearch::Run(), and CBlastPrelimSearch::x_Init().
◆ m_Messages [5/7]
|
protected |
Error/warning messages are stored here.
Definition at line 107 of file query_data.hpp.
Referenced by ILocalQueryData::GetMessages(), ILocalQueryData::GetQueryMessages(), CObjMgr_LocalQueryData::GetSequenceBlk(), and CObjMgrFree_LocalQueryData::GetSequenceBlk().
◆ m_Messages [6/7]
|
private |
Warnings and Errors.
Definition at line 122 of file traceback_stage.hpp.
Referenced by CBlastTracebackSearch::GetSearchMessages(), CBlastTracebackSearch::Run(), and CBlastTracebackSearch::x_Init().
◆ m_Messages [7/7]
| TSearchMessages SBlastSetupData::m_Messages |
Definition at line 112 of file blast_aux_priv.hpp.
◆ m_Min_D_match
| int CIgBlastOptions::m_Min_D_match |
Definition at line 70 of file igblast.hpp.
Referenced by CIgBlastArgs::ExtractAlgorithmOptions(), CIgBlast::x_FindDJAln(), CIgBlast::x_ProcessDGeneResult(), CIgBlast::x_SetupDJSearch(), and CIgBlast::x_SetupNoOverlapDSearch().
◆ m_MinEvalue
|
private |
Min e-value threshold for all hits to be included in PSSM computation.
This is needed mostly for experiments.
Definition at line 476 of file cdd_pssm_input.hpp.
Referenced by CCddInputData::Process(), and CCddInputData::SetMinCddEvalue().
◆ m_MinHits
|
private |
number of hits to initiate calculation of Jaccard distance in LSH
Definition at line 108 of file blastp_kmer_options.hpp.
◆ m_MinJLength
| int CIgBlastOptions::m_MinJLength |
Definition at line 88 of file igblast.hpp.
Referenced by CIgBlastArgs::ExtractAlgorithmOptions(), CIgBlast::Run(), and CIgBlast::x_SetAnnotation().
◆ m_MinLength
|
private |
Length of the longest sequence in this set.
Definition at line 78 of file seqsrc_query_factory.cpp.
Referenced by CQueryFactoryInfo::GetMinLength().
◆ m_MinusStrand
| bool CIgAnnotation::m_MinusStrand |
Definition at line 96 of file igblast.hpp.
Referenced by CIgBlast::x_AnnotateDomain().
◆ m_MinVLength
| int CIgBlastOptions::m_MinVLength |
Definition at line 87 of file igblast.hpp.
Referenced by CIgBlastArgs::ExtractAlgorithmOptions(), and CIgBlast::Run().
◆ m_MmappedFile
|
protected |
The data structure this class manages.
Definition at line 252 of file rps_aux.cpp.
Referenced by CRpsFreqRatiosFile::CRpsFreqRatiosFile(), CRpsFreqsFile::CRpsFreqsFile(), CRpsLookupTblFile::CRpsLookupTblFile(), CRpsMmappedFile::CRpsMmappedFile(), CRpsObsrFile::CRpsObsrFile(), and CRpsPssmFile::CRpsPssmFile().
◆ m_MolType
|
private |
molecule type
Definition at line 193 of file uniform_search.hpp.
Referenced by CSearchDatabase::GetMoleculeType(), and CSearchDatabase::SetMoleculeType().
◆ m_Msa [1/3]
|
private |
Pointer to MSA.
Definition at line 464 of file cdd_pssm_input.hpp.
Referenced by CCddInputData::x_CreateMsa(), CCddInputData::x_ValidateMsa(), and CCddInputData::~CCddInputData().
◆ m_Msa [2/3]
|
private |
Structure representing the multiple sequence alignment.
Definition at line 141 of file msa_pssm_input.hpp.
Referenced by CPsiBlastInputClustalW::Process(), CPsiBlastInputClustalW::x_CopyQueryToMsa(), CPsiBlastInputClustalW::x_ExtractAlignmentData(), and CPsiBlastInputClustalW::~CPsiBlastInputClustalW().
◆ m_Msa [3/3]
|
private |
Structure representing the multiple sequence alignment.
Definition at line 239 of file psi_pssm_input.hpp.
Referenced by CPsiBlastInputData::CPsiBlastInputData(), CPsiBlastInputData::GetData(), CPsiBlastInputData::Process(), CPsiBlastInputData::x_CopyQueryToMsa(), CPsiBlastInputData::x_ProcessDenseg(), and CPsiBlastInputData::~CPsiBlastInputData().
◆ m_MsaData [1/2]
| vector<PSICdMsaCellData> CCddInputData::CHitSegment::m_MsaData |
Data used for PSSM computation.
Definition at line 273 of file cdd_pssm_input.hpp.
◆ m_MsaData [2/2]
|
private |
MSA data.
Definition at line 462 of file cdd_pssm_input.hpp.
Referenced by CCddInputData::CHitSegment::FillData(), CCddInputData::CHitSegment::Validate(), CCddInputData::x_CreateMsa(), CCddInputData::CHitSegment::x_FillObservations(), and CCddInputData::CHitSegment::x_FillResidueCounts().
◆ m_MsaDimensions [1/3]
|
private |
MSA dimensions, used by PSSM engine.
Definition at line 459 of file cdd_pssm_input.hpp.
Referenced by CCddInputData::Process().
◆ m_MsaDimensions [2/3]
|
private |
Multiple sequence alignment dimensions.
Definition at line 143 of file msa_pssm_input.hpp.
Referenced by CPsiBlastInputClustalW::Process(), and CPsiBlastInputClustalW::x_ExtractQueryFromMsa().
◆ m_MsaDimensions [3/3]
|
private |
Multiple sequence alignment dimensions.
Definition at line 241 of file psi_pssm_input.hpp.
Referenced by CPsiBlastInputData::CPsiBlastInputData(), CPsiBlastInputData::GetNumAlignedSequences(), CPsiBlastInputData::GetQueryLength(), and CPsiBlastInputData::Process().
◆ m_MsaIdx
| int CCddInputData::CHit::m_MsaIdx |
Hit index in MSA table.
Definition at line 361 of file cdd_pssm_input.hpp.
◆ m_Mutex
|
private |
Mutex for writing to the queue.
Definition at line 73 of file hspstream_queue.hpp.
◆ m_NeedConfig
|
private |
Bitfield to track whether all necessary configuration is done.
Definition at line 767 of file remote_blast.hpp.
Referenced by CRemoteBlast::SetDatabase(), CRemoteBlast::SetQueries(), CRemoteBlast::SetSubjectSequences(), CRemoteBlast::x_CheckConfig(), and CRemoteBlast::x_Init().
◆ m_NeedsFilteringTranslation
|
mutableprivate |
Definition at line 203 of file uniform_search.hpp.
Referenced by CSearchDatabase::GetFilteringAlgorithm(), CSearchDatabase::SetFilteringAlgorithm(), and CSearchDatabase::x_TranslateFilteringAlgorithm().
◆ m_NegativeGiList [1/3]
The negative GI list (or none).
Definition at line 303 of file blast_options_builder.hpp.
Referenced by CBlastOptionsBuilder::GetNegativeGiList(), CBlastOptionsBuilder::HaveNegativeGiList(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ m_NegativeGiList [2/3]
|
private |
Negative GI list.
Definition at line 818 of file remote_blast.hpp.
Referenced by CRemoteBlast::GetSearchOptions(), and CRemoteBlast::SetNegativeGIList().
◆ m_NegativeGiList [3/3]
|
mutableprivate |
negative gi list
Definition at line 197 of file uniform_search.hpp.
Referenced by CSearchDatabase::GetNegativeGiList(), CSearchDatabase::GetNegativeGiListLimitation(), CSearchDatabase::SetNegativeGiList(), and CSearchDatabase::x_InitializeDb().
◆ m_NegativeTaxidList [1/2]
The negative tax id list (or none).
Definition at line 334 of file blast_options_builder.hpp.
Referenced by CBlastOptionsBuilder::GetNegativeTaxidList(), CBlastOptionsBuilder::HaveNegativeTaxidList(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ m_NegativeTaxidList [2/2]
Definition at line 843 of file remote_blast.hpp.
Referenced by CRemoteBlast::GetNegativeTaxidList(), and CRemoteBlast::GetSearchOptions().
◆ m_NumActualC
| int CIgBlastResults::m_NumActualC |
Definition at line 204 of file igblast.hpp.
Referenced by CIgBlast::s_AppendResults(), and CIgBlast::x_SetChainType().
◆ m_NumActualD
| int CIgBlastResults::m_NumActualD |
Definition at line 202 of file igblast.hpp.
Referenced by CIgBlast::s_AppendResults(), and CIgBlast::x_SetChainType().
◆ m_NumActualJ
| int CIgBlastResults::m_NumActualJ |
Definition at line 203 of file igblast.hpp.
Referenced by CIgBlast::s_AppendResults(), and CIgBlast::x_SetChainType().
◆ m_NumActualV
| int CIgBlastResults::m_NumActualV |
Definition at line 201 of file igblast.hpp.
Referenced by CIgBlast::s_AppendResults(), and CIgBlast::x_SetChainType().
◆ m_NumAlign
| int CIgBlastOptions::m_NumAlign[4] |
Definition at line 82 of file igblast.hpp.
Referenced by CIgBlastArgs::ExtractAlgorithmOptions(), CIgBlast::Run(), CIgBlast::x_AnnotateC(), CIgBlast::x_AnnotateD(), CIgBlast::x_AnnotateDJ(), CIgBlast::x_AnnotateJ(), CIgBlast::x_AnnotateV(), CIgBlast::x_SetupCRegionSearch(), CIgBlast::x_SetupDJSearch(), CIgBlast::x_SetupNoOverlapDSearch(), and CIgBlast::x_SetupVSearch().
◆ m_NumChunks
|
private |
Number of chunks, if this is 1, no splitting occurs.
Definition at line 109 of file split_query.hpp.
Referenced by CQuerySplitter::GetNumberOfChunks(), CQuerySplitter::GetQueryFactoryForChunk(), CQuerySplitter::Split(), CQuerySplitter::x_ComputeChunkRanges(), CQuerySplitter::x_ComputeContextOffsets_NonTranslatedQueries(), CQuerySplitter::x_ComputeContextOffsets_TranslatedQueries(), CQuerySplitter::x_ComputeQueryContextsForChunks(), CQuerySplitter::x_ComputeQueryIndicesForChunks(), CQuerySplitter::x_ExtractCScopesAndMasks(), and CSplitQueryTestFixture::x_ValidateQuerySeqLocsPerChunk().
◆ m_NumCols
|
private |
number of columns in the matrix (for deallocation)
Definition at line 336 of file pssm_engine.cpp.
Referenced by SNcbiMatrix2DoubleMatrix::~SNcbiMatrix2DoubleMatrix().
◆ m_NumPatOccurInDB
| int SDatabaseScanData::m_NumPatOccurInDB |
Number of times pattern found to occur in database (for phi-blast only).
Definition at line 363 of file setup_factory.hpp.
Referenced by CBlastTracebackSearch::CBlastTracebackSearch(), CBlastTracebackSearch::Run(), CBlastTracebackSearch::RunSimple(), and SDatabaseScanData::SDatabaseScanData().
◆ m_NumQueries
|
private |
Number of queries.
Definition at line 475 of file blast_results.hpp.
Referenced by CSearchResultSet::clear(), CSearchResultSet::GetNumQueries(), CSearchResultSet::GetResults(), CSearchResultSet::push_back(), and CSearchResultSet::x_Init().
◆ m_NumSeqs
|
private |
Number of sequences.
Definition at line 82 of file seqsrc_query_factory.cpp.
Referenced by CQueryFactoryInfo::CQueryFactoryInfo(), and CQueryFactoryInfo::GetNumSeqs().
◆ m_NumThreads [1/2]
|
protected |
Keep track of how many threads should be used.
Definition at line 181 of file setup_factory.hpp.
Referenced by CThreadable::GetNumberOfThreads(), CThreadable::IsMultiThreaded(), CBlastTracebackSearch::Run(), CBlastTracebackSearch::RunSimple(), and CThreadable::SetNumberOfThreads().
◆ m_NumThreads [2/2]
|
private |
Definition at line 299 of file igblast.hpp.
Referenced by CIgBlast::Run(), and CIgBlast::SetNumberOfThreads().
◆ m_ObjectStream
|
private |
Use to ready CBlast4_archive.
Definition at line 743 of file remote_blast.hpp.
Referenced by CRemoteBlast::LoadFromArchive(), and CRemoteBlast::x_Init().
◆ m_ObjectType
|
private |
Type of object CBlast4_archive as determined by CFormatGuess.
Definition at line 746 of file remote_blast.hpp.
Referenced by CRemoteBlast::x_Init().
◆ m_ObsrFile
|
private |
Number of independent observations file (.obsr) used by delta-blast.
Definition at line 158 of file rps_aux.hpp.
Referenced by CBlastRPSInfo::x_Init().
◆ m_OldStyleMBIndex
|
private |
Definition at line 398 of file blast_options_local_priv.hpp.
Referenced by CBlastOptionsLocal::GetIsOldStyleMBIndex(), and CBlastOptionsLocal::SetUseIndex().
◆ m_Options [1/10]
|
private |
Delta Blast options.
Definition at line 141 of file deltablast.hpp.
Referenced by CDeltaBlast::Run(), CDeltaBlast::x_FindDomainHits(), and CDeltaBlast::x_Validate().
◆ m_Options [2/10]
|
private |
Options to configure the search.
Definition at line 119 of file magicblast.hpp.
Referenced by CMagicBlast::x_BuildResultSet(), CMagicBlast::x_BuildSeqAlignSet(), CMagicBlast::x_Run(), and CMagicBlast::x_Validate().
◆ m_Options [3/10]
|
private |
Definition at line 165 of file prelim_stage.hpp.
Referenced by CBlastPrelimSearch::ComputeBlastHSPResults(), CBlastPrelimSearch::Run(), CBlastPrelimSearch::SetNumberOfThreads(), CBlastPrelimSearch::x_BuildStdSegList(), and CBlastPrelimSearch::x_LaunchMultiThreadedSearch().
◆ m_Options [4/10]
|
private |
The options with which this search is configured.
Definition at line 113 of file traceback_stage.hpp.
Referenced by CBlastTracebackSearch::Run().
◆ m_Options [5/10]
|
private |
Definition at line 304 of file igblast.hpp.
Referenced by CIgBlast::Run(), and CIgBlast::x_SetupVSearch().
◆ m_Options [6/10]
|
private |
Snapshopt of BLAST options.
Definition at line 142 of file blast_memento_priv.hpp.
Referenced by CEffectiveSearchSpacesMemento::~CEffectiveSearchSpacesMemento().
◆ m_Options [7/10]
|
protected |
BLAST algorithm options.
Definition at line 176 of file blast_objmgr_priv.hpp.
Referenced by CBlastQuerySourceOM::x_AutoDetectGeneticCodes(), and CBlastQuerySourceOM::x_CalculateMasks().
◆ m_Options [8/10]
|
private |
Definition at line 187 of file objmgr_query_data.cpp.
Referenced by CObjMgr_LocalQueryData::GetQueryInfo(), and CObjMgr_LocalQueryData::GetSequenceBlk().
◆ m_Options [9/10]
|
private |
Definition at line 86 of file objmgrfree_query_data.cpp.
Referenced by CObjMgrFree_LocalQueryData::GetQueryInfo(), and CObjMgrFree_LocalQueryData::GetSequenceBlk().
◆ m_Options [10/10]
|
private |
BLAST options.
Definition at line 107 of file split_query.hpp.
Referenced by CQuerySplitter::Split(), CQuerySplitter::x_ComputeChunkRanges(), CQuerySplitter::x_ComputeContextOffsets_NonTranslatedQueries(), CQuerySplitter::x_ComputeContextOffsets_TranslatedQueries(), CQuerySplitter::x_ComputeContextOffsetsForChunks(), CQuerySplitter::x_ComputeQueryContextsForChunks(), and CQuerySplitter::x_ComputeQueryIndicesForChunks().
◆ m_OptionsBuilder
|
private |
Definition at line 181 of file search_strategy.hpp.
Referenced by CImportStrategy::FetchData(), and CImportStrategy::GetOptionsBuilder().
◆ m_OptionsHandle
| CRef<blast::CBlastOptionsHandle> CImportStrategyData::m_OptionsHandle |
BLAST options.
Definition at line 66 of file search_strategy.hpp.
◆ m_Opts [1/5]
|
protected |
Data type this class controls access to.
Definition at line 335 of file blast_options_handle.hpp.
Referenced by CBlastOptionsHandle::ClearFilterOptions(), CBlastOptionsHandle::DoneDefaults(), CBlastOptionsHandle::GetComplexityAdjMode(), CBlastOptionsHandle::GetCullingLimit(), CBlastOptionsHandle::GetCutoffScore(), CBlastOptionsHandle::GetDbLength(), CBlastOptionsHandle::GetDbSeqNum(), CBlastOptionsHandle::GetEffectiveSearchSpace(), CBlastOptionsHandle::GetEvalueThreshold(), CBlastOptionsHandle::GetFilterString(), CBlastOptionsHandle::GetGappedMode(), CBlastOptionsHandle::GetGapTrigger(), CBlastOptionsHandle::GetGapXDropoff(), CBlastOptionsHandle::GetGapXDropoffFinal(), CBlastOptionsHandle::GetHitlistSize(), CBlastOptionsHandle::GetLowScorePerc(), CBlastOptionsHandle::GetMaskAtHash(), CBlastOptionsHandle::GetMaskLevel(), CBlastOptionsHandle::GetMaxHspsPerSubject(), CBlastOptionsHandle::GetMaxNumHspPerSequence(), CBlastOptionsHandle::GetMinDiagSeparation(), CBlastOptionsHandle::GetOffDiagonalRange(), CBlastOptionsHandle::GetOptions(), CBlastOptionsHandle::GetPercentIdentity(), CPHIBlastNuclOptionsHandle::GetPHIPattern(), CPHIBlastProtOptionsHandle::GetPHIPattern(), CBlastOptionsHandle::GetQueryCovHspPerc(), CBlastOptionsHandle::GetWindowSize(), CBlastOptionsHandle::SetComplexityAdjMode(), CBlastOptionsHandle::SetCullingLimit(), CBlastOptionsHandle::SetCutoffScore(), CBlastOptionsHandle::SetDbLength(), CBlastOptionsHandle::SetDbSeqNum(), CBlastNucleotideOptionsHandle::SetDefaults(), CBlastOptionsHandle::SetDefaults(), CMagicBlastOptionsHandle::SetDefaults(), CDeltaBlastOptionsHandle::SetDeltaBlastDefaults(), CMagicBlastOptionsHandle::SetEffectiveLengthsOptionsDefaults(), CBlastOptionsHandle::SetEffectiveSearchSpace(), CBlastOptionsHandle::SetEvalueThreshold(), CBlastOptionsHandle::SetFilterString(), CBlastAdvancedProteinOptionsHandle::SetGappedExtensionDefaults(), CBlastProteinOptionsHandle::SetGappedExtensionDefaults(), CBlastRPSOptionsHandle::SetGappedExtensionDefaults(), CBlastxOptionsHandle::SetGappedExtensionDefaults(), CDeltaBlastOptionsHandle::SetGappedExtensionDefaults(), CMagicBlastOptionsHandle::SetGappedExtensionDefaults(), CTBlastnOptionsHandle::SetGappedExtensionDefaults(), CTBlastxOptionsHandle::SetGappedExtensionDefaults(), CBlastOptionsHandle::SetGappedMode(), CBlastOptionsHandle::SetGapTrigger(), CBlastOptionsHandle::SetGapXDropoff(), CBlastOptionsHandle::SetGapXDropoffFinal(), CMagicBlastOptionsHandle::SetGenomeToGenomeDefaults(), CBlastOptionsHandle::SetHitlistSize(), CBlastRPSOptionsHandle::SetHitSavingOptionsDefaults(), CBlastxOptionsHandle::SetHitSavingOptionsDefaults(), CMagicBlastOptionsHandle::SetHitSavingOptionsDefaults(), CTBlastnOptionsHandle::SetHitSavingOptionsDefaults(), CTBlastxOptionsHandle::SetHitSavingOptionsDefaults(), CBlastNucleotideOptionsHandle::SetLookupTableDefaults(), CBlastProteinOptionsHandle::SetLookupTableDefaults(), CBlastRPSOptionsHandle::SetLookupTableDefaults(), CBlastxOptionsHandle::SetLookupTableDefaults(), CMagicBlastOptionsHandle::SetLookupTableDefaults(), CTBlastxOptionsHandle::SetLookupTableDefaults(), CBlastOptionsHandle::SetLowScorePerc(), CBlastOptionsHandle::SetMaskAtHash(), CBlastOptionsHandle::SetMaskLevel(), CBlastOptionsHandle::SetMaxHspsPerSubject(), CBlastOptionsHandle::SetMaxNumHspPerSequence(), CDiscNucleotideOptionsHandle::SetMBInitialWordOptionsDefaults(), CBlastNucleotideOptionsHandle::SetMBLookupTableDefaults(), CDiscNucleotideOptionsHandle::SetMBLookupTableDefaults(), CBlastNucleotideOptionsHandle::SetMBScoringOptionsDefaults(), CBlastOptionsHandle::SetMinDiagSeparation(), CBlastOptionsHandle::SetOffDiagonalRange(), CBlastOptionsHandle::SetOptions(), CBlastOptionsHandle::SetPercentIdentity(), CPHIBlastNuclOptionsHandle::SetPHIPattern(), CPHIBlastProtOptionsHandle::SetPHIPattern(), CPSIBlastOptionsHandle::SetPSIBlastDefaults(), CPSIBlastOptionsHandle::SetPSITblastnDefaults(), CBlastOptionsHandle::SetQueryCovHspPerc(), CBlastProteinOptionsHandle::SetQueryOptionDefaults(), CBlastRPSOptionsHandle::SetQueryOptionDefaults(), CBlastxOptionsHandle::SetQueryOptionDefaults(), CDeltaBlastOptionsHandle::SetQueryOptionDefaults(), CMagicBlastOptionsHandle::SetQueryOptionDefaults(), CPSIBlastOptionsHandle::SetQueryOptionDefaults(), CRPSTBlastnOptionsHandle::SetQueryOptionDefaults(), CTBlastxOptionsHandle::SetQueryOptionDefaults(), CMagicBlastOptionsHandle::SetRNAToGenomeDefaults(), CMagicBlastOptionsHandle::SetRNAToRNADefaults(), CBlastNucleotideOptionsHandle::SetScoringOptionsDefaults(), CBlastProteinOptionsHandle::SetScoringOptionsDefaults(), CBlastRPSOptionsHandle::SetScoringOptionsDefaults(), CMagicBlastOptionsHandle::SetScoringOptionsDefaults(), CTBlastxOptionsHandle::SetScoringOptionsDefaults(), CTBlastxOptionsHandle::SetSubjectSequenceOptionsDefaults(), CBlastNucleotideOptionsHandle::SetTraditionalBlastnDefaults(), CBlastNucleotideOptionsHandle::SetTraditionalMegablastDefaults(), CBlastNucleotideOptionsHandle::SetVecScreenDefaults(), CBlastOptionsHandle::SetWindowSize(), CBlastProteinOptionsHandle::SetWordSize(), and CBlastOptionsHandle::Validate().
◆ m_Opts [2/5]
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private |
Delta BLAST options for PSSM Engine.
Definition at line 468 of file cdd_pssm_input.hpp.
Referenced by CCddInputData::GetOptions(), and CCddInputData::Process().
◆ m_Opts [3/5]
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private |
◆ m_Opts [4/5]
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private |
Algorithm options.
Definition at line 145 of file msa_pssm_input.hpp.
◆ m_Opts [5/5]
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private |
Algorithm options.
Definition at line 245 of file psi_pssm_input.hpp.
Referenced by CPsiBlastInputData::CPsiBlastInputData(), CPsiBlastInputData::GetOptions(), CPsiBlastInputData::x_CountAndSelectQualifyingAlignments(), and CPsiBlastInputData::x_ExtractAlignmentData().
◆ m_OptsHandle [1/3]
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private |
Blast options.
Definition at line 183 of file bl2seq.hpp.
Referenced by CBl2Seq::CBl2Seq(), CBl2Seq::GetOptionsHandle(), CBl2Seq::SetOptionsHandle(), and CBl2Seq::x_InitCLocalBlast().
◆ m_OptsHandle [2/3]
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private |
Options to be used when instantiating the subject sequences.
Definition at line 144 of file local_db_adapter.hpp.
Referenced by CLocalDbAdapter::IsProtein(), CLocalDbAdapter::MakeSeqInfoSrc(), and CLocalDbAdapter::MakeSeqSrc().
◆ m_OptsHandle [3/3]
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private |
Options to use.
Definition at line 112 of file psiblast_impl.hpp.
Referenced by CPsiBlastImpl::Run(), CPsiBlastImpl::x_CreatePssmScoresFromFrequencyRatios(), and CPsiBlastImpl::x_Validate().
◆ m_OptsMemento [1/4]
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private |
Options from the preliminary search.
Definition at line 119 of file traceback_stage.hpp.
Referenced by CBlastTracebackSearch::Run(), CBlastTracebackSearch::RunSimple(), CBlastTracebackSearch::x_Init(), and CBlastTracebackSearch::~CBlastTracebackSearch().
◆ m_OptsMemento [2/4]
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private |
snapshopt of BLAST options
Definition at line 76 of file effsearchspace_calc.cpp.
◆ m_OptsMemento [3/4]
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private |
Pointer to memento which this class doesn't own.
Definition at line 98 of file prelim_search_runner.hpp.
◆ m_OptsMemento [4/4]
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private |
Definition at line 155 of file prelim_search_runner.hpp.
Referenced by CPrelimSearchThread::Main().
◆ m_Origin
| string CIgBlastOptions::m_Origin |
Definition at line 67 of file igblast.hpp.
Referenced by CIgAnnotationInfo::CIgAnnotationInfo(), CIgBlastArgs::ExtractAlgorithmOptions(), CIgBlastnApp::Run(), and CIgBlastpApp::Run().
◆ m_OwnTSeqLocVector
|
protected |
flag to determine if the member above should or not be deleted in the destructor
Definition at line 173 of file blast_objmgr_priv.hpp.
Referenced by CBlastQuerySourceOM::~CBlastQuerySourceOM().
◆ m_Paired
|
private |
True if results are for paired reads.
Definition at line 226 of file magicblast.hpp.
Referenced by CMagicBlastResults::IsPaired(), and CMagicBlastResults::x_SetInfo().
◆ m_Pattern
|
private |
Definition at line 153 of file seedtop.hpp.
Referenced by CSeedTop::x_MakeLookupTable(), and CSeedTop::x_ParsePattern().
◆ m_Pending
|
private |
Pending state: indicates that search still needs to be queued.
Definition at line 761 of file remote_blast.hpp.
Referenced by CRemoteBlast::x_CheckResults(), CRemoteBlast::x_CheckResultsDC(), CRemoteBlast::x_GetState(), CRemoteBlast::x_Init(), CRemoteBlast::x_PollUntilDone(), and CRemoteBlast::x_SubmitSearch().
◆ m_PerformCulling
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private |
Whether to perform culling.
Definition at line 285 of file blast_options_builder.hpp.
Referenced by CBlastOptionsBuilder::x_ApplyInteractions(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ m_PhiQueryInfo
|
protected |
PHI-BLAST information.
Definition at line 285 of file blast_results.hpp.
Referenced by CSearchResults::CSearchResults(), CSearchResults::GetPhiQueryInfo(), and CSearchResults::~CSearchResults().
◆ m_PrelimSearch [1/2]
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private |
Object which runs the preliminary stage of the search.
Definition at line 132 of file local_blast.hpp.
Referenced by CLocalBlast::Run(), and CLocalBlast::SetInterruptCallback().
◆ m_PrelimSearch [2/2]
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private |
Object that runs BLAST search.
Definition at line 122 of file magicblast.hpp.
Referenced by CMagicBlast::x_BuildResultSet(), and CMagicBlast::x_Run().
◆ m_PreviousData
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private |
Identifiers for sequences found in the previous iteration.
Definition at line 131 of file psiblast_iteration.hpp.
Referenced by CPsiBlastIterationState::Advance(), and CPsiBlastIterationState::HasConverged().
◆ m_Program [1/8]
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private |
Program value for blast4 protocol.
Definition at line 279 of file blast_options_builder.hpp.
Referenced by CBlastOptionsBuilder::GetSearchOptions().
◆ m_Program [2/8]
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private |
BLAST program.
Definition at line 85 of file effsearchspace_calc.hpp.
Referenced by CEffectiveSearchSpaceCalculator::CEffectiveSearchSpaceCalculator(), and CEffectiveSearchSpaceCalculator::GetEffSearchSpace().
◆ m_Program [3/8]
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private |
Program value used when submitting this search.
Definition at line 782 of file remote_blast.hpp.
Referenced by CRemoteBlast::GetMasks(), CRemoteBlast::GetProgram(), CRemoteBlast::x_GetRequestInfoFromFile(), CRemoteBlast::x_GetRequestInfoFromRID(), CRemoteBlast::x_Init(), CRemoteBlast::x_QueryMaskingLocationsToNetwork(), and CRemoteBlast::x_SetDatabase().
◆ m_Program [4/8]
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staticprivate |
Definition at line 152 of file seedtop.hpp.
Referenced by CSeedTop::x_MakeLookupTable(), and CSeedTop::x_MakeScoreBlk().
◆ m_Program [5/8]
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private |
BLAST program variable.
Definition at line 183 of file blast_objmgr_priv.hpp.
Referenced by CBlastQuerySourceOM::GetMaskedRegions(), and CBlastQuerySourceOM::x_AutoDetectGeneticCodes().
◆ m_Program [6/8]
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private |
Blast program.
Definition at line 393 of file blast_options_local_priv.hpp.
Referenced by CBlastOptionsLocal::CBlastOptionsLocal(), CBlastOptionsLocal::DebugDump(), CBlastOptionsLocal::GetProgram(), CBlastOptionsLocal::GetProgramType(), CBlastOptionsLocal::operator==(), CBlastOptionsLocal::SetProgram(), CBlastOptionsLocal::SetSubjectBestHit(), CBlastOptionsLocal::Validate(), and CBlastOptionsLocal::x_DoDeepCopy().
◆ m_Program [7/8]
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private |
The type of search being done.
Definition at line 514 of file blast_setup.hpp.
Referenced by CBlastQueryFilteredFrames::AddSeqLoc(), CBlastQueryFilteredFrames::GetNumFrames(), CBlastQueryFilteredFrames::QueryHasMultipleFrames(), CBlastQueryFilteredFrames::x_NeedsTrans(), and CBlastQueryFilteredFrames::x_VerifyFrame().
◆ m_Program [8/8]
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private |
BLAST program type.
Definition at line 238 of file split_query_aux_priv.hpp.
Referenced by CQueryDataPerChunk::x_ContextInChunkToQueryIndex().
◆ m_ProgramOpts
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private |
Options relevant to the search application.
Definition at line 797 of file remote_blast.hpp.
Referenced by CRemoteBlast::GetSearchOptions(), CRemoteBlast::x_GetRequestInfoFromFile(), and CRemoteBlast::x_GetRequestInfoFromRID().
◆ m_ProgramType
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private |
Definition at line 90 of file blast_memento_priv.hpp.
Referenced by CSetupFactory::CreateHspStream(), CSetupFactory::CreateHspWriter(), CSetupFactory::CreateLookupTable(), CSetupFactory::CreateScoreBlock(), CBlastTracebackSearch::Run(), CBlastTracebackSearch::RunSimple(), and CBlastTracebackSearch::x_Init().
◆ m_ProgressMonitor
| CRef<CSBlastProgress> SInternalData::m_ProgressMonitor |
The user data structure to aid in progress monitoring.
Definition at line 347 of file setup_factory.hpp.
Referenced by CPrelimSearchThread::CPrelimSearchThread(), CBlastTracebackSearch::Run(), CBlastTracebackSearch::RunSimple(), CBlastPrelimSearch::SetInterruptCallback(), and SplitQuery_CreateChunkData().
◆ m_PsiBlast
Search class.
Definition at line 104 of file local_search.hpp.
◆ m_PSIBlastOpts [1/2]
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private |
Definition at line 96 of file blast_memento_priv.hpp.
Referenced by CBlastTracebackSearch::Run(), and CBlastTracebackSearch::RunSimple().
◆ m_PSIBlastOpts [2/2]
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private |
PSI-Blast settings.
Definition at line 378 of file blast_options_local_priv.hpp.
Referenced by CBlastOptionsLocal::CBlastOptionsLocal(), CBlastOptionsMemento::CBlastOptionsMemento(), CBlastOptionsLocal::DebugDump(), CBlastOptionsLocal::GetIgnoreMsaMaster(), CBlastOptionsLocal::GetInclusionThreshold(), CBlastOptionsLocal::GetPseudoCount(), CBlastOptionsLocal::GetPSIBlastOpts(), CBlastOptionsLocal::operator==(), CBlastOptionsLocal::SetIgnoreMsaMaster(), CBlastOptionsLocal::SetInclusionThreshold(), CBlastOptionsLocal::SetPseudoCount(), and CBlastOptionsLocal::x_DoDeepCopy().
◆ m_PsiGappedKarlinBlk
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private |
PSI-BLAST gapped Karlin parameters for one query (if applicable)
Definition at line 143 of file blast_results.hpp.
Referenced by CBlastAncillaryData::CBlastAncillaryData(), CBlastAncillaryData::do_copy(), and CBlastAncillaryData::~CBlastAncillaryData().
◆ m_PsiNumOfIterations
| unsigned int CImportStrategyData::m_PsiNumOfIterations |
Definition at line 77 of file search_strategy.hpp.
◆ m_PsiUngappedKarlinBlk
|
private |
PSI-BLAST ungapped Karlin parameters for one query (if applicable)
Definition at line 140 of file blast_results.hpp.
Referenced by CBlastAncillaryData::CBlastAncillaryData(), CBlastAncillaryData::do_copy(), and CBlastAncillaryData::~CBlastAncillaryData().
◆ m_Pssm [1/4]
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private |
PSSMs computed for each query.
Definition at line 147 of file deltablast.hpp.
Referenced by CDeltaBlast::GetPssm(), and CDeltaBlast::Run().
◆ m_Pssm [2/4]
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private |
Search queries.
Definition at line 107 of file local_search.hpp.
Referenced by CLocalPssmSearch::Run(), and CLocalPssmSearch::SetQuery().
◆ m_Pssm [3/4]
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private |
Search queries.
Definition at line 117 of file remote_search.hpp.
Referenced by CRemotePssmSearch::SetQuery(), and CRemotePssmSearch::x_RemoteBlast().
◆ m_Pssm [4/4]
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private |
PSSM to be used as query.
Definition at line 103 of file psiblast_impl.hpp.
Referenced by CPsiBlastImpl::GetPssm(), CPsiBlastImpl::Run(), CPsiBlastImpl::SetPssm(), CPsiBlastImpl::x_CreatePssmScoresFromFrequencyRatios(), CPsiBlastImpl::x_ExtractQueryFromPssm(), and CPsiBlastImpl::x_Validate().
◆ m_PssmFile
|
private |
The PSSM RPS-BLAST file (.rps)
Definition at line 148 of file rps_aux.hpp.
Referenced by CBlastRPSInfo::x_Init().
◆ m_PssmInput
|
private |
Handle to strategy to process raw PSSM input data.
Definition at line 137 of file pssm_engine.hpp.
Referenced by CPssmEngine::Run(), CPssmEngine::x_CreatePssmFromMsa(), CPssmEngine::x_GetGapExistence(), CPssmEngine::x_GetGapExtension(), CPssmEngine::x_GetMatrixName(), CPssmEngine::x_GetQuery(), and CPssmEngine::x_GetQueryLength().
◆ m_PssmInputCdd
|
private |
Pointer to strategy to process raw PSSM input data Note: Only one m_PssmInput* should be non-NULL.
Definition at line 145 of file pssm_engine.hpp.
Referenced by CPssmEngine::Run(), and CPssmEngine::x_CreatePssmFromCDD().
◆ m_PssmInputFreqRatios
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private |
Pointer to input data to create PSSM from frequency ratios.
Definition at line 139 of file pssm_engine.hpp.
Referenced by CPssmEngine::Run(), CPssmEngine::x_CreatePssmFromFreqRatios(), CPssmEngine::x_GetGapExistence(), CPssmEngine::x_GetGapExtension(), CPssmEngine::x_GetMatrixName(), CPssmEngine::x_GetQuery(), and CPssmEngine::x_GetQueryLength().
◆ m_Ptr [1/31]
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private |
Definition at line 309 of file blast_aux.hpp.
Referenced by CBLAST_SequenceBlk::DebugDump().
◆ m_Ptr [2/31]
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private |
Definition at line 311 of file blast_aux.hpp.
Referenced by CBlastQueryInfo::DebugDump().
◆ m_Ptr [3/31]
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private |
Definition at line 312 of file blast_aux.hpp.
Referenced by CQuerySetUpOptions::DebugDump().
◆ m_Ptr [4/31]
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private |
Definition at line 314 of file blast_aux.hpp.
Referenced by CLookupTableOptions::DebugDump().
◆ m_Ptr [5/31]
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private |
Definition at line 315 of file blast_aux.hpp.
Referenced by CLookupTableWrap::DebugDump().
◆ m_Ptr [6/31]
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private |
Definition at line 318 of file blast_aux.hpp.
Referenced by CBlastInitialWordOptions::DebugDump().
◆ m_Ptr [7/31]
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private |
Definition at line 320 of file blast_aux.hpp.
Referenced by CBlastInitialWordParameters::DebugDump().
◆ m_Ptr [8/31]
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private |
Definition at line 322 of file blast_aux.hpp.
Referenced by CBlast_ExtendWord::DebugDump().
◆ m_Ptr [9/31]
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private |
Definition at line 323 of file blast_aux.hpp.
Referenced by CBlastExtensionOptions::DebugDump().
◆ m_Ptr [10/31]
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private |
Definition at line 324 of file blast_aux.hpp.
Referenced by CBlastExtensionParameters::DebugDump().
◆ m_Ptr [11/31]
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private |
Definition at line 326 of file blast_aux.hpp.
Referenced by CBlastHitSavingOptions::DebugDump().
◆ m_Ptr [12/31]
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private |
Definition at line 328 of file blast_aux.hpp.
Referenced by CBlastHitSavingParameters::DebugDump().
◆ m_Ptr [13/31]
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private |
Definition at line 330 of file blast_aux.hpp.
Referenced by CPSIBlastOptions::DebugDump().
◆ m_Ptr [14/31]
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private |
Definition at line 331 of file blast_aux.hpp.
Referenced by CBlastDatabaseOptions::DebugDump().
◆ m_Ptr [15/31]
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private |
Definition at line 333 of file blast_aux.hpp.
Referenced by CBlastScoreBlk::DebugDump().
◆ m_Ptr [16/31]
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private |
Definition at line 334 of file blast_aux.hpp.
Referenced by CBlastScoringOptions::DebugDump().
◆ m_Ptr [17/31]
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private |
Definition at line 335 of file blast_aux.hpp.
Referenced by CBlastScoringParameters::DebugDump().
◆ m_Ptr [18/31]
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private |
Definition at line 338 of file blast_aux.hpp.
Referenced by CBlastEffectiveLengthsOptions::DebugDump().
◆ m_Ptr [19/31]
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private |
Definition at line 340 of file blast_aux.hpp.
Referenced by CBlastEffectiveLengthsParameters::DebugDump().
◆ m_Ptr [20/31]
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private |
Definition at line 342 of file blast_aux.hpp.
Referenced by CBlastGapAlignStruct::DebugDump().
◆ m_Ptr [21/31]
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private |
Definition at line 343 of file blast_aux.hpp.
Referenced by CBlastHSPResults::DebugDump().
◆ m_Ptr [22/31]
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private |
Definition at line 345 of file blast_aux.hpp.
Referenced by CPSIMsa::DebugDump().
◆ m_Ptr [23/31]
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private |
Definition at line 346 of file blast_aux.hpp.
Referenced by CPSIMatrix::DebugDump().
◆ m_Ptr [24/31]
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private |
Definition at line 347 of file blast_aux.hpp.
Referenced by CPSIDiagnosticsRequest::DebugDump().
◆ m_Ptr [25/31]
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private |
Definition at line 348 of file blast_aux.hpp.
Referenced by CPSIDiagnosticsResponse::DebugDump().
◆ m_Ptr [26/31]
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private |
Definition at line 350 of file blast_aux.hpp.
Referenced by CBlastSeqSrc::DebugDump().
◆ m_Ptr [27/31]
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private |
Definition at line 351 of file blast_aux.hpp.
Referenced by CBlastSeqSrcIterator::DebugDump().
◆ m_Ptr [28/31]
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private |
Definition at line 352 of file blast_aux.hpp.
Referenced by CBlast_Message::DebugDump().
◆ m_Ptr [29/31]
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private |
Definition at line 354 of file blast_aux.hpp.
Referenced by CBlastMaskLoc::DebugDump().
◆ m_Ptr [30/31]
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private |
Definition at line 355 of file blast_aux.hpp.
Referenced by CBlastSeqLoc::DebugDump().
◆ m_Ptr [31/31]
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private |
Definition at line 357 of file blast_aux.hpp.
Referenced by CSBlastProgress::DebugDump().
◆ m_QSR
|
private |
Request object for new search.
Definition at line 731 of file remote_blast.hpp.
Referenced by CRemoteBlast::SetDatabase(), CRemoteBlast::SetQueries(), CRemoteBlast::SetQueryMasks(), CRemoteBlast::SetSubjectSequences(), CRemoteBlast::x_GetBlast4SearchRequestBody(), CRemoteBlast::x_Init(), CRemoteBlast::x_SetAlgoOpts(), CRemoteBlast::x_SetMaskingLocationsForQueries(), and CRemoteBlast::x_SetOneParam().
◆ m_Queries [1/7]
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private |
Queries.
Definition at line 132 of file deltablast.hpp.
Referenced by CDeltaBlast::Run(), CDeltaBlast::x_FindDomainHits(), and CDeltaBlast::x_Validate().
◆ m_Queries [2/7]
|
private |
Queries.
Definition at line 113 of file magicblast.hpp.
Referenced by CMagicBlast::x_BuildResultSet(), CMagicBlast::x_BuildSeqAlignSet(), CMagicBlast::x_Run(), and CMagicBlast::x_Validate().
◆ m_Queries [3/7]
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private |
Queries associated with this search.
Definition at line 791 of file remote_blast.hpp.
Referenced by CRemoteBlast::GetQueries(), CRemoteBlast::SetQueries(), CRemoteBlast::x_GetRequestInfoFromFile(), and CRemoteBlast::x_GetRequestInfoFromRID().
◆ m_Queries [4/7]
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private |
Search queries.
Definition at line 78 of file remote_search.hpp.
Referenced by CRemoteSeqSearch::SetQueryFactory(), and CRemoteSeqSearch::x_RemoteBlast().
◆ m_Queries [5/7]
| BLAST_SequenceBlk* SInternalData::m_Queries |
The query sequence data, these fields are "borrowed" from the query factory (which owns them)
Definition at line 320 of file setup_factory.hpp.
Referenced by CBlastPrelimSearch::Run(), CBlastTracebackSearch::Run(), CBlastTracebackSearch::RunSimple(), SInternalData::SInternalData(), and CBlastTracebackSearch::x_Init().
◆ m_Queries [6/7]
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private |
Adaptee in adapter design pattern.
Definition at line 185 of file objmgr_query_data.cpp.
Referenced by CObjMgr_LocalQueryData::GetSequenceBlk().
◆ m_Queries [7/7]
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private |
Queries, if input representation is TSeqLocVector, or NULL.
Definition at line 280 of file objmgr_query_data.cpp.
Referenced by CObjMgr_RemoteQueryData::GetBioseqSet(), and CObjMgr_RemoteQueryData::GetSeqLocs().
◆ m_Query [1/5]
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private |
Pointer to query sequence.
Definition at line 137 of file msa_pssm_input.hpp.
Referenced by CPsiBlastInputClustalW::x_CopyQueryToMsa(), CPsiBlastInputClustalW::x_ExtractAlignmentData(), CPsiBlastInputClustalW::x_ExtractQueryForPssm(), CPsiBlastInputClustalW::x_ExtractQueryFromMsa(), and CPsiBlastInputClustalW::x_ValidateQueryInMsa().
◆ m_Query [2/5]
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private |
Query sequence data.
Definition at line 138 of file psi_pssm_input.hpp.
◆ m_Query [3/5]
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private |
Pointer to query sequence.
Definition at line 233 of file psi_pssm_input.hpp.
Referenced by CPsiBlastInputData::CPsiBlastInputData(), CPsiBlastInputData::GetQuery(), CPsiBlastInputData::Process(), CPsiBlastInputData::x_CopyQueryToMsa(), CPsiBlastInputData::x_ExtractQueryForPssm(), CPsiBlastInputData::x_ProcessDenseg(), and CPsiBlastInputData::~CPsiBlastInputData().
◆ m_Query [4/5]
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private |
Definition at line 300 of file igblast.hpp.
Referenced by CIgBlast::x_ConvertResultType(), CIgBlast::x_SetupCRegionSearch(), CIgBlast::x_SetupDbSearch(), CIgBlast::x_SetupDJSearch(), CIgBlast::x_SetupNoOverlapDSearch(), and CIgBlast::x_SetupVSearch().
◆ m_Query [5/5]
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private |
Query sequence (either extracted from PSSM or provided in constructor)
Definition at line 106 of file psiblast_impl.hpp.
Referenced by CPsiBlastImpl::Run(), CPsiBlastImpl::x_ExtractQueryFromPssm(), and CPsiBlastImpl::x_Validate().
◆ m_QueryBioseq [1/3]
|
private |
Query as Bioseq.
Definition at line 479 of file cdd_pssm_input.hpp.
Referenced by CCddInputData::GetQueryForPssm(), and CCddInputData::x_ExtractQueryForPssm().
◆ m_QueryBioseq [2/3]
|
private |
Query as CBioseq for PSSM.
Definition at line 157 of file msa_pssm_input.hpp.
Referenced by CPsiBlastInputClustalW::x_ExtractQueryForPssm().
◆ m_QueryBioseq [3/3]
|
private |
Query as CBioseq for PSSM.
Definition at line 255 of file psi_pssm_input.hpp.
Referenced by CPsiBlastInputData::GetQueryForPssm(), and CPsiBlastInputData::x_ExtractQueryForPssm().
◆ m_QueryChunkFactories
|
private |
Vector of query factories, each element corresponds to a chunk.
Definition at line 113 of file split_query.hpp.
Referenced by CQuerySplitter::GetQueryFactoryForChunk(), CQuerySplitter::Split(), CQuerySplitter::x_ComputeContextOffsets_NonTranslatedQueries(), and CQuerySplitter::x_ComputeContextOffsets_TranslatedQueries().
◆ m_QueryData
|
private |
Query sequence.
Definition at line 441 of file cdd_pssm_input.hpp.
Referenced by CCddInputData::CCddInputData(), CCddInputData::GetQuery(), CCddInputData::GetQueryLength(), CCddInputData::Process(), CCddInputData::x_CreateMsa(), CCddInputData::x_ExtractQueryForPssm(), and CCddInputData::x_ValidateMsa().
◆ m_QueryFactory [1/6]
|
private |
source of query sequence(s)
Definition at line 84 of file effsearchspace_calc.hpp.
Referenced by CEffectiveSearchSpaceCalculator::CEffectiveSearchSpaceCalculator().
◆ m_QueryFactory [2/6]
|
private |
Query factory from which to obtain the query sequence data.
Definition at line 122 of file local_blast.hpp.
Referenced by CLocalBlast::Run().
◆ m_QueryFactory [3/6]
|
private |
Factory which provides the query data to be populated in m_Queries.
Definition at line 79 of file local_search.hpp.
Referenced by CLocalSeqSearch::Run(), and CLocalSeqSearch::SetQueryFactory().
◆ m_QueryFactory [4/6]
|
private |
Query factory is retained to ensure the lifetime of the data (queries) produced by it.
Definition at line 163 of file prelim_stage.hpp.
Referenced by CBlastPrelimSearch::Run(), CBlastPrelimSearch::SetNumberOfThreads(), and CBlastPrelimSearch::x_BuildStdSegList().
◆ m_QueryFactory [5/6]
|
private |
The query to search for.
Definition at line 110 of file traceback_stage.hpp.
Referenced by CBlastTracebackSearch::Run().
◆ m_QueryFactory [6/6]
|
private |
The original, unsplit query factory.
Definition at line 105 of file split_query.hpp.
Referenced by CQuerySplitter::Split(), and CQuerySplitter::x_ExtractCScopesAndMasks().
◆ m_QueryId [1/2]
|
protected |
this query's id
Definition at line 264 of file blast_results.hpp.
Referenced by CSearchResults::GetSeqId().
◆ m_QueryId [2/2]
Query id.
Definition at line 217 of file magicblast.hpp.
Referenced by CMagicBlastResults::GetQueryId(), and CMagicBlastResults::x_SetInfo().
◆ m_QueryIndicesPerChunk
|
private |
Each element in this vector represents a chunk, and it contains the query indices that correspond in the full concatenated query.
Definition at line 242 of file split_query_aux_priv.hpp.
Referenced by CQueryDataPerChunk::CQueryDataPerChunk(), CQueryDataPerChunk::GetLastChunk(), and CQueryDataPerChunk::GetQueryLength().
◆ m_QueryInfo [1/3]
|
private |
struct to store eff. search spaces
Definition at line 86 of file effsearchspace_calc.hpp.
Referenced by CEffectiveSearchSpaceCalculator::CEffectiveSearchSpaceCalculator(), CEffectiveSearchSpaceCalculator::GetEffSearchSpace(), CEffectiveSearchSpaceCalculator::GetEffSearchSpaceForContext(), and CEffectiveSearchSpaceCalculator::GetQueryInfo().
◆ m_QueryInfo [2/3]
|
protected |
Data member to cache the BlastQueryInfo.
Definition at line 104 of file query_data.hpp.
Referenced by CObjMgr_LocalQueryData::GetQueryInfo(), and CObjMgrFree_LocalQueryData::GetQueryInfo().
◆ m_QueryInfo [3/3]
| BlastQueryInfo* SInternalData::m_QueryInfo |
The query information structure.
Definition at line 322 of file setup_factory.hpp.
Referenced by CBlastPrelimSearch::ComputeBlastHSPResults(), CPrelimSearchThread::CPrelimSearchThread(), CBlastTracebackSearch::Run(), CBlastTracebackSearch::RunSimple(), SInternalData::SInternalData(), SplitQuery_SetEffectiveSearchSpace(), CMagicBlast::x_BuildResultSet(), CMagicBlast::x_BuildSeqAlignSet(), CBlastTracebackSearch::x_Init(), and CPrelimSearchThread::~CPrelimSearchThread().
◆ m_QueryLength
|
private |
Length of query sequence data.
Definition at line 140 of file psi_pssm_input.hpp.
◆ m_QueryLengths
|
private |
Lengths of the queries.
Definition at line 245 of file split_query_aux_priv.hpp.
Referenced by CQueryDataPerChunk::CQueryDataPerChunk(), and CQueryDataPerChunk::GetQueryLength().
◆ m_QueryMaskingLocations
|
private |
Masking locations for queries.
Definition at line 803 of file remote_blast.hpp.
Referenced by CRemoteBlast::x_Init(), CRemoteBlast::x_QueryMaskingLocationsToNetwork(), and CRemoteBlast::x_SetMaskingLocationsForQueries().
◆ m_QueryMasks [1/2]
The query masking locations.
Definition at line 311 of file blast_options_builder.hpp.
Referenced by CBlastOptionsBuilder::GetQueryMasks(), CBlastOptionsBuilder::GetSearchOptions(), CBlastOptionsBuilder::HaveQueryMasks(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ m_QueryMasks [2/2]
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private |
Stores the masked query regions, for convenience and usage in CBl2Seq.
Definition at line 484 of file blast_results.hpp.
Referenced by CSearchResultSet::GetFilteredQueryRegions(), and CSearchResultSet::SetFilteredQueryRegions().
◆ m_QueryOpts [1/2]
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private |
Definition at line 91 of file blast_memento_priv.hpp.
Referenced by CFilteringMemento::CFilteringMemento(), CSetupFactory::CreateLookupTable(), and CSetupFactory::CreateScoreBlock().
◆ m_QueryOpts [2/2]
|
private |
Query sequence settings.
Definition at line 363 of file blast_options_local_priv.hpp.
Referenced by CBlastOptionsLocal::CBlastOptionsLocal(), CBlastOptionsMemento::CBlastOptionsMemento(), CBlastOptionsLocal::DebugDump(), CBlastOptionsLocal::GetDustFiltering(), CBlastOptionsLocal::GetDustFilteringLevel(), CBlastOptionsLocal::GetDustFilteringLinker(), CBlastOptionsLocal::GetDustFilteringWindow(), CBlastOptionsLocal::GetFilterString(), CBlastOptionsLocal::GetMaskAtHash(), CBlastOptionsLocal::GetQueryGeneticCode(), CBlastOptionsLocal::GetQueryOpts(), CBlastOptionsLocal::GetReadMaxFractionAmbiguous(), CBlastOptionsLocal::GetReadMinDimerEntropy(), CBlastOptionsLocal::GetReadQualityFiltering(), CBlastOptionsLocal::GetRepeatFiltering(), CBlastOptionsLocal::GetRepeatFilteringDB(), CBlastOptionsLocal::GetSegFiltering(), CBlastOptionsLocal::GetSegFilteringHicut(), CBlastOptionsLocal::GetSegFilteringLocut(), CBlastOptionsLocal::GetSegFilteringWindow(), CBlastOptionsLocal::GetStrandOption(), CBlastOptionsLocal::GetWindowMaskerDatabase(), CBlastOptionsLocal::GetWindowMaskerTaxId(), CBlastOptionsLocal::operator==(), CBlastOptionsLocal::SetDustFiltering(), CBlastOptionsLocal::SetDustFilteringLevel(), CBlastOptionsLocal::SetDustFilteringLinker(), CBlastOptionsLocal::SetDustFilteringWindow(), CBlastOptionsLocal::SetFilterString(), CBlastOptionsLocal::SetMaskAtHash(), CBlastOptionsLocal::SetQueryGeneticCode(), CBlastOptionsLocal::SetReadMaxFractionAmbiguous(), CBlastOptionsLocal::SetReadMinDimerEntropy(), CBlastOptionsLocal::SetReadQualityFiltering(), CBlastOptionsLocal::SetRepeatFiltering(), CBlastOptionsLocal::SetRepeatFilteringDB(), CBlastOptionsLocal::SetSegFiltering(), CBlastOptionsLocal::SetSegFilteringHicut(), CBlastOptionsLocal::SetSegFilteringLocut(), CBlastOptionsLocal::SetSegFilteringWindow(), CBlastOptionsLocal::SetStrandOption(), CBlastOptionsLocal::SetWindowMaskerDatabase(), CBlastOptionsLocal::SetWindowMaskerTaxId(), and CBlastOptionsLocal::x_DoDeepCopy().
◆ m_QueryRange [1/3]
|
private |
The range to restrict the query sequence(s)
Definition at line 317 of file blast_options_builder.hpp.
Referenced by CBlastOptionsBuilder::x_ProcessOneOption().
◆ m_QueryRange [2/3]
| TRange CCddInputData::CHitSegment::m_QueryRange |
Segment range on query.
Definition at line 267 of file cdd_pssm_input.hpp.
Referenced by CCddInputData::CHitSegment::GetLength(), and CCddInputData::CHit::Subtract().
◆ m_QueryRange [3/3]
| TSeqRange CImportStrategyData::m_QueryRange |
Range of query.
Definition at line 72 of file search_strategy.hpp.
◆ m_QuerySource [1/3]
|
private |
Definition at line 188 of file objmgr_query_data.cpp.
Referenced by CObjMgr_LocalQueryData::CObjMgr_LocalQueryData(), CObjMgr_LocalQueryData::GetNumQueries(), CObjMgr_LocalQueryData::GetQueryInfo(), CObjMgr_LocalQueryData::GetSeq_loc(), CObjMgr_LocalQueryData::GetSeqLength(), and CObjMgr_LocalQueryData::GetSequenceBlk().
◆ m_QuerySource [2/3]
|
private |
Definition at line 89 of file objmgrfree_query_data.cpp.
Referenced by CObjMgrFree_LocalQueryData::CObjMgrFree_LocalQueryData(), CObjMgrFree_LocalQueryData::GetNumQueries(), CObjMgrFree_LocalQueryData::GetQueryInfo(), CObjMgrFree_LocalQueryData::GetSeq_loc(), CObjMgrFree_LocalQueryData::GetSeqLength(), and CObjMgrFree_LocalQueryData::GetSequenceBlk().
◆ m_QuerySource [3/3]
|
private |
local query data obtained from the query factory
Definition at line 81 of file seqsrc_query_factory.cpp.
Referenced by CQueryFactoryInfo::CQueryFactoryInfo(), and CQueryFactoryInfo::~CQueryFactoryInfo().
◆ m_QuerySplitter
| CRef<CQuerySplitter> SBlastSetupData::m_QuerySplitter |
Definition at line 110 of file blast_aux_priv.hpp.
◆ m_QueryTitle [1/2]
|
private |
Query title (for PSSM)
Definition at line 443 of file cdd_pssm_input.hpp.
Referenced by CCddInputData::x_ExtractQueryForPssm().
◆ m_QueryTitle [2/2]
|
private |
Title of query.
Definition at line 235 of file psi_pssm_input.hpp.
Referenced by CPsiBlastInputData::CPsiBlastInputData(), and CPsiBlastInputData::x_ExtractQueryForPssm().
◆ m_QueryVector [1/4]
|
private |
◆ m_QueryVector [2/4]
|
protected |
Reference to input CBlastQueryVector (or empty if not used)
Definition at line 166 of file blast_objmgr_priv.hpp.
Referenced by CBlastQuerySourceOM::GetBlastSequence(), CBlastQuerySourceOM::GetGeneticCodeId(), CBlastQuerySourceOM::GetLength(), CBlastQuerySourceOM::GetMask(), CBlastQuerySourceOM::GetMaskedRegions(), CBlastQuerySourceOM::GetSeqId(), CBlastQuerySourceOM::GetSeqLoc(), CBlastQuerySourceOM::GetStrand(), CBlastQuerySourceOM::GetTitle(), CBlastQuerySourceOM::Size(), CBlastQuerySourceOM::x_AutoDetectGeneticCodes(), and CBlastQuerySourceOM::x_CalculateMasks().
◆ m_QueryVector [3/4]
|
private |
Definition at line 186 of file objmgr_query_data.cpp.
Referenced by CObjMgr_LocalQueryData::GetSequenceBlk().
◆ m_QueryVector [4/4]
|
private |
Queries, if input representation is a CBlastQueryVector, or NULL.
Definition at line 283 of file objmgr_query_data.cpp.
Referenced by CObjMgr_RemoteQueryData::GetBioseqSet(), and CObjMgr_RemoteQueryData::GetSeqLocs().
◆ m_QueueSearchRequest
|
private |
Definition at line 261 of file search_strategy.hpp.
Referenced by CExportStrategy::GetSearchStrategy(), CExportStrategy::x_AddParameterToProgramOptions(), CExportStrategy::x_AddPsiNumOfIterationsToFormatOptions(), CExportStrategy::x_Process_BlastOptions(), CExportStrategy::x_Process_Pssm(), CExportStrategy::x_Process_Query(), CExportStrategy::x_Process_SearchDb(), and CExportStrategy::x_Process_Subject().
◆ m_ReadFile
|
private |
true if a CBlast4_archive should be read in.
Definition at line 740 of file remote_blast.hpp.
Referenced by CRemoteBlast::GetResultSet(), CRemoteBlast::x_GetGSRR(), CRemoteBlast::x_GetRequestInfo(), and CRemoteBlast::x_Init().
◆ m_RefCounter
|
staticprivate |
Definition at line 244 of file blast_aux.hpp.
Referenced by CAutomaticGenCodeSingleton::CAutomaticGenCodeSingleton(), and CAutomaticGenCodeSingleton::~CAutomaticGenCodeSingleton().
◆ m_Registry
|
private |
Definition at line 109 of file blast_input_unit_test_aux.hpp.
Referenced by CAutoNcbiConfigFile::CAutoNcbiConfigFile(), CAutoNcbiConfigFile::RemoveBLASTDBEnvVar(), CAutoNcbiConfigFile::SetNucleotideBlastDbDataLoader(), CAutoNcbiConfigFile::SetProteinBlastDbDataLoader(), and CAutoNcbiConfigFile::~CAutoNcbiConfigFile().
◆ m_RemoteBlast [1/2]
|
private |
Remote search management object.
Definition at line 75 of file remote_search.hpp.
Referenced by CRemoteSeqSearch::Run(), and CRemoteSeqSearch::x_RemoteBlast().
◆ m_RemoteBlast [2/2]
|
private |
Remote search management object.
Definition at line 114 of file remote_search.hpp.
Referenced by CRemotePssmSearch::Run(), CRemotePssmSearch::SetOptions(), and CRemotePssmSearch::x_RemoteBlast().
◆ m_RemoteDb
|
private |
Definition at line 303 of file igblast.hpp.
Referenced by CIgBlast::Run().
◆ m_RemoteQueryData
|
protected |
Definition at line 159 of file query_data.hpp.
Referenced by IQueryFactory::MakeRemoteQueryData().
◆ m_Reply
|
private |
Results of BLAST search.
Definition at line 734 of file remote_blast.hpp.
Referenced by CRemoteBlast::x_CheckResults(), CRemoteBlast::x_CheckResultsDC(), and CRemoteBlast::x_GetGSRR().
◆ m_ReqOpts
|
private |
Definition at line 151 of file blast_options_cxx.cpp.
Referenced by CBlastOptionsRemote::CBlastOptionsRemote(), CBlastOptionsRemote::GetBlast4AlgoOpts(), CBlastOptionsRemote::x_AttachValue(), CBlastOptionsRemote::x_DoDeepCopy(), and CBlastOptionsRemote::x_ResetValue().
◆ m_Request
|
private |
Definition at line 179 of file search_strategy.hpp.
Referenced by CImportStrategy::FetchData(), CImportStrategy::GetAlgoOptions(), CImportStrategy::GetCreatedBy(), CImportStrategy::GetProgram(), CImportStrategy::GetProgramOptions(), CImportStrategy::GetQueries(), CImportStrategy::GetService(), CImportStrategy::GetSubject(), and CImportStrategy::GetWebFormatOptions().
◆ m_Results [1/5]
|
private |
CLocalBlast results.
Definition at line 208 of file bl2seq.hpp.
Referenced by CBl2Seq::GetFilteredQueryRegions(), CBl2Seq::GetFilteredSubjectRegions(), CBl2Seq::Run(), CBl2Seq::RunEx(), CBl2Seq::x_BuildAncillaryData(), and CBl2Seq::x_ResetInternalDs().
◆ m_Results [2/5]
|
private |
Vector of results.
Definition at line 478 of file blast_results.hpp.
Referenced by CSearchResultSet::begin(), CSearchResultSet::clear(), CSearchResultSet::end(), CSearchResultSet::GetNumResults(), CSearchResultSet::GetResults(), CSearchResultSet::operator[](), CSearchResultSet::push_back(), CSearchResultSet::SetFilteredQueryRegions(), CSearchResultSet::SetRID(), and CSearchResultSet::x_Init().
◆ m_Results [3/5]
|
private |
Pssm-protein search results.
Definition at line 153 of file deltablast.hpp.
Referenced by CDeltaBlast::Run().
◆ m_Results [4/5]
|
private |
Definition at line 296 of file magicblast.hpp.
Referenced by CMagicBlastResultSet::begin(), CMagicBlastResultSet::clear(), CMagicBlastResultSet::end(), CMagicBlastResultSet::push_back(), CMagicBlastResultSet::reserve(), and CMagicBlastResultSet::size().
◆ m_Results [5/5]
|
private |
Holds a reference to the results.
Definition at line 115 of file psiblast_impl.hpp.
Referenced by CPsiBlastImpl::Run().
◆ m_resultsQueue
|
private |
Queue in a form of a linked list of HSP lists.
Definition at line 70 of file hspstream_queue.hpp.
◆ m_ResultType [1/3]
|
private |
Type of results stored in this object.
Definition at line 472 of file blast_results.hpp.
Referenced by CSearchResultSet::GetResults(), CSearchResultSet::GetResultType(), CSearchResultSet::operator[](), CSearchResultSet::SetFilteredQueryRegions(), and CSearchResultSet::x_Init().
◆ m_ResultType [2/3]
|
private |
Determines if BLAST database search or BLAST 2 sequences style of results should be produced.
Definition at line 130 of file traceback_stage.hpp.
Referenced by CBlastTracebackSearch::Run(), and CBlastTracebackSearch::SetResultType().
◆ m_ResultType [3/3]
|
private |
Specifies how the results should be produced.
Definition at line 118 of file psiblast_impl.hpp.
Referenced by CPsiBlastImpl::Run(), and CPsiBlastImpl::SetResultType().
◆ m_RID [1/3]
|
protected |
The RID, if applicable (otherwise it's empty)
Definition at line 282 of file blast_results.hpp.
Referenced by CSearchResults::GetRID(), and CSearchResults::SetRID().
◆ m_RID [2/3]
|
private |
Request ID of submitted or pre-existing search.
Definition at line 755 of file remote_blast.hpp.
Referenced by CRemoteBlast::GetPsiNumberOfIterations(), CRemoteBlast::GetRID(), CRemoteBlast::GetTitle(), CRemoteBlast::x_GetPsiIterationsFromServer(), CRemoteBlast::x_GetRequestInfoFromRID(), CRemoteBlast::x_GetSearchResults(), CRemoteBlast::x_GetSearchResultsHTTP(), CRemoteBlast::x_GetSearchStatsOnly(), CRemoteBlast::x_GetState(), CRemoteBlast::x_GetStringFromSearchInfoReply(), CRemoteBlast::x_GetSubjects(), CRemoteBlast::x_Init(), and CRemoteBlast::x_SubmitSearch().
◆ m_RID [3/3]
|
private |
Definition at line 309 of file igblast.hpp.
Referenced by CIgBlast::CIgBlast(), CIgBlast::GetRid(), and CIgBlast::Run().
◆ m_RpsData
| CRef<CBlastRPSInfo> SInternalData::m_RpsData |
The RPS-BLAST related data.
Definition at line 341 of file setup_factory.hpp.
Referenced by CBlastTracebackSearch::Run(), CBlastTracebackSearch::RunSimple(), and CBlastTracebackSearch::x_Init().
◆ m_RpsInfo
|
private |
Pointer which contains pointers to data managed by the data members above.
Definition at line 167 of file rps_aux.hpp.
Referenced by CBlastRPSInfo::GetGapExtensionCost(), CBlastRPSInfo::GetGapOpeningCost(), CBlastRPSInfo::GetMatrixName(), CBlastRPSInfo::GetScalingFactor(), CBlastRPSInfo::operator()(), and CBlastRPSInfo::x_Init().
◆ m_RpsOptions
|
private |
RPS Blast options.
Definition at line 144 of file deltablast.hpp.
Referenced by CDeltaBlast::x_FindDomainHits().
◆ m_save
|
private |
Definition at line 266 of file blast_aux.hpp.
Referenced by CBlastAppDiagHandler::DoNotSaveMessages(), and CBlastAppDiagHandler::Post().
◆ m_Scope [1/3]
|
private |
Scope where to retrieve the sequences in the aligment from.
Definition at line 237 of file psi_pssm_input.hpp.
Referenced by CPsiBlastInputData::CPsiBlastInputData(), and CPsiBlastInputData::x_ProcessDenseg().
◆ m_Scope [2/3]
Definition at line 308 of file igblast.hpp.
Referenced by CIgBlast::x_AnnotateC(), CIgBlast::x_ExtendAlign3end(), CIgBlast::x_ExtendAlign5end(), CIgBlast::x_FillJDomain(), and CIgBlast::x_FindDJAln().
◆ m_scope
Definition at line 424 of file igblast.hpp.
Referenced by ScorePositionSort::operator()(), and ScorePositionSort::ScorePositionSort().
◆ m_Scope [3/3]
|
private |
Definition at line 563 of file blast_objmgr_tools.cpp.
Referenced by CBlastSeqVectorOM::x_SetStrand().
◆ m_Scopes
|
private |
Definition at line 121 of file split_query.hpp.
Referenced by CQuerySplitter::x_ComputeQueryIndicesForChunks(), and CQuerySplitter::x_ExtractCScopesAndMasks().
◆ m_ScopeSrc
|
private |
◆ m_ScoreBlk [1/3]
|
private |
Blast score block structure.
Definition at line 141 of file pssm_engine.hpp.
Referenced by CPssmEngine::SetUngappedStatisticalParams(), CPssmEngine::x_CreatePssmFromCDD(), CPssmEngine::x_CreatePssmFromFreqRatios(), CPssmEngine::x_CreatePssmFromMsa(), and CPssmEngine::x_InitializeScoreBlock().
◆ m_ScoreBlk [2/3]
|
private |
Definition at line 155 of file seedtop.hpp.
Referenced by CSeedTop::x_MakeLookupTable(), and CSeedTop::x_MakeScoreBlk().
◆ m_ScoreBlk [3/3]
| CRef<TBlastScoreBlk> SInternalData::m_ScoreBlk |
BLAST score block structure.
Definition at line 325 of file setup_factory.hpp.
Referenced by CBlastPrelimSearch::CheckInternalData(), CBlastTracebackSearch::Run(), CPsiBlastImpl::Run(), CBlastTracebackSearch::RunSimple(), SplitQuery_SetEffectiveSearchSpace(), CBlastPrelimSearch::x_BuildStdSegList(), and CBlastTracebackSearch::x_Init().
◆ m_ScoringOpts [1/2]
|
private |
Definition at line 98 of file blast_memento_priv.hpp.
Referenced by CSetupFactory::CreateHspPipe(), CSetupFactory::CreateHspWriter(), CSetupFactory::CreateScoreBlock(), CBlastTracebackSearch::Run(), and CBlastTracebackSearch::RunSimple().
◆ m_ScoringOpts [2/2]
|
private |
Scoring options.
Definition at line 387 of file blast_options_local_priv.hpp.
Referenced by CBlastOptionsLocal::CBlastOptionsLocal(), CBlastOptionsMemento::CBlastOptionsMemento(), CBlastOptionsLocal::DebugDump(), CBlastOptionsLocal::GetComplexityAdjMode(), CBlastOptionsLocal::GetFrameShiftPenalty(), CBlastOptionsLocal::GetGapExtensionCost(), CBlastOptionsLocal::GetGapOpeningCost(), CBlastOptionsLocal::GetGappedMode(), CBlastOptionsLocal::GetMatchReward(), CBlastOptionsLocal::GetMatrixName(), CBlastOptionsLocal::GetMismatchPenalty(), CBlastOptionsLocal::GetOutOfFrameMode(), CBlastOptionsLocal::GetScoringOpts(), CBlastOptionsLocal::operator==(), CBlastOptionsLocal::SetComplexityAdjMode(), CBlastOptionsLocal::SetFrameShiftPenalty(), CBlastOptionsLocal::SetGapExtensionCost(), CBlastOptionsLocal::SetGapOpeningCost(), CBlastOptionsLocal::SetGappedMode(), CBlastOptionsLocal::SetMatchReward(), CBlastOptionsLocal::SetMatrixName(), CBlastOptionsLocal::SetMismatchPenalty(), CBlastOptionsLocal::SetOutOfFrameMode(), CBlastOptionsLocal::Validate(), and CBlastOptionsLocal::x_DoDeepCopy().
◆ m_SearchOpts [1/4]
|
private |
Search options.
Definition at line 70 of file local_search.hpp.
Referenced by CLocalSeqSearch::Run(), and CLocalSeqSearch::SetOptions().
◆ m_SearchOpts [2/4]
|
private |
Search configuration.
Definition at line 101 of file local_search.hpp.
Referenced by CLocalPssmSearch::Run(), and CLocalPssmSearch::SetOptions().
◆ m_SearchOpts [3/4]
|
private |
Search configuration.
Definition at line 72 of file remote_search.hpp.
Referenced by CRemoteSeqSearch::SetOptions(), and CRemoteSeqSearch::x_RemoteBlast().
◆ m_SearchOpts [4/4]
|
private |
Search configuration.
Definition at line 111 of file remote_search.hpp.
Referenced by CRemotePssmSearch::SetOptions(), and CRemotePssmSearch::x_RemoteBlast().
◆ m_SearchSpace
|
private |
Search space used when calculating e-values for one query.
Definition at line 147 of file blast_results.hpp.
Referenced by CBlastAncillaryData::CBlastAncillaryData(), and CBlastAncillaryData::do_copy().
◆ m_SegmentList
|
private |
List of hit segments.
Definition at line 365 of file cdd_pssm_input.hpp.
Referenced by CCddInputData::CHit::CHit(), and CCddInputData::CHit::GetSegments().
◆ m_Sema
|
private |
Semaphore fore reading from the queue.
Definition at line 74 of file hspstream_queue.hpp.
◆ m_SeqalignSet
|
private |
RPS-BLAST hits for the query.
Definition at line 450 of file cdd_pssm_input.hpp.
Referenced by CCddInputData::x_ExtractQueryForPssm(), and CCddInputData::x_ProcessAlignments().
◆ m_SeqAlignSet
|
private |
Pairwise alignment result of a BLAST search.
Definition at line 243 of file psi_pssm_input.hpp.
Referenced by CPsiBlastInputData::CPsiBlastInputData(), CPsiBlastInputData::x_CountAndSelectQualifyingAlignments(), CPsiBlastInputData::x_ExtractAlignmentData(), and CPsiBlastInputData::x_ExtractQueryForPssm().
◆ m_SeqBlk
|
protected |
Data member to cache the BLAST_SequenceBlk.
Definition at line 102 of file query_data.hpp.
Referenced by ILocalQueryData::FlushSequenceData(), CObjMgr_LocalQueryData::GetSequenceBlk(), and CObjMgrFree_LocalQueryData::GetSequenceBlk().
◆ m_SeqBlkVector
|
private |
Vector of sequence blocks.
Definition at line 76 of file seqsrc_query_factory.cpp.
Referenced by CQueryFactoryInfo::CQueryFactoryInfo(), CQueryFactoryInfo::GetSeqBlk(), and CQueryFactoryInfo::~CQueryFactoryInfo().
◆ m_SeqDb
Definition at line 205 of file uniform_search.hpp.
Referenced by CSearchDatabase::GetSeqDb(), CSearchDatabase::SetSeqDb(), CSearchDatabase::x_InitializeDb(), CSearchDatabase::x_TranslateFilteringAlgorithm(), and CSearchDatabase::x_ValidateMaskingAlgorithm().
◆ m_SeqEntry
|
private |
CSeq_entry obtained from the multiple sequence alignment.
Definition at line 155 of file msa_pssm_input.hpp.
Referenced by CPsiBlastInputClustalW::x_ExtractQueryForPssm(), and CPsiBlastInputClustalW::x_ReadAsciiMsa().
◆ m_SeqInfoSrc [1/3]
|
private |
User-specified IBlastSeqInfoSrc implementation (may be used for non-standard databases, etc.)
Definition at line 142 of file local_blast.hpp.
Referenced by CLocalBlast::Run().
◆ m_SeqInfoSrc [2/3]
|
private |
Pointer to the IBlastSeqInfoSrc.
Definition at line 135 of file local_db_adapter.hpp.
Referenced by CLocalDbAdapter::MakeSeqInfoSrc().
◆ m_SeqInfoSrc [3/3]
|
private |
Pointer to the IBlastSeqInfoSrc object to use to generate the Seq-aligns.
Definition at line 126 of file traceback_stage.hpp.
Referenced by CBlastTracebackSearch::Run().
◆ m_SeqLoc
Definition at line 562 of file blast_objmgr_tools.cpp.
Referenced by CBlastSeqVectorOM::CBlastSeqVectorOM(), CBlastSeqVectorOM::x_FixStrand(), and CBlastSeqVectorOM::x_SetStrand().
◆ m_SeqLocs
|
protected |
Data member to cache the TSeqLocs.
Definition at line 131 of file query_data.hpp.
Referenced by CObjMgr_RemoteQueryData::GetSeqLocs(), and CObjMgrFree_RemoteQueryData::GetSeqLocs().
◆ m_Seqlocs
|
private |
Frame and BlastSeqLoc* data.
Definition at line 520 of file blast_setup.hpp.
Referenced by CBlastQueryFilteredFrames::AddSeqLoc(), CBlastQueryFilteredFrames::ListFrames(), CBlastQueryFilteredFrames::operator[](), CBlastQueryFilteredFrames::Release(), CBlastQueryFilteredFrames::UseProteinCoords(), and CBlastQueryFilteredFrames::~CBlastQueryFilteredFrames().
◆ m_SeqlocTails
|
private |
Frame and tail of BlastSeqLoc* linked list (to speed up appending)
Definition at line 522 of file blast_setup.hpp.
Referenced by CBlastQueryFilteredFrames::AddSeqLoc(), and CBlastQueryFilteredFrames::Release().
◆ m_SeqSrc [1/2]
|
private |
Pointer to the BlastSeqSrc this object owns and manages.
Definition at line 132 of file local_db_adapter.hpp.
Referenced by CLocalDbAdapter::IsProtein(), CLocalDbAdapter::MakeSeqSrc(), CLocalDbAdapter::ResetBlastSeqSrcIteration(), and CLocalDbAdapter::~CLocalDbAdapter().
◆ m_SeqSrc [2/2]
| CRef<TBlastSeqSrc> SInternalData::m_SeqSrc |
The source of subject sequence data.
Definition at line 338 of file setup_factory.hpp.
Referenced by CBlastPrelimSearch::CBlastPrelimSearch(), CPrelimSearchThread::CPrelimSearchThread(), CLocalBlast::Run(), CBlastPrelimSearch::Run(), CBlastTracebackSearch::Run(), CBlastTracebackSearch::RunSimple(), SplitQuery_CreateChunkData(), SplitQuery_SetEffectiveSearchSpace(), and CBlastPrelimSearch::x_LaunchMultiThreadedSearch().
◆ m_SequenceData
|
private |
Container for the actual sequence data.
Definition at line 95 of file bioseq_extract_data_priv.hpp.
Referenced by CBlastSeqVectorFromCSeq_data::GetCompressedPlusStrand(), CBlastSeqVectorFromCSeq_data::operator[](), CBlastSeqVectorFromCSeq_data::SetCoding(), CBlastSeqVectorFromCSeq_data::x_ComplementData(), and CBlastSeqVectorFromCSeq_data::x_Size().
◆ m_SequenceType
| string CIgBlastOptions::m_SequenceType |
Definition at line 69 of file igblast.hpp.
Referenced by CIgBlastArgs::ExtractAlgorithmOptions(), and CIgBlastnApp::Run().
◆ m_SeqVec
|
private |
Vector of subject sequence locations to get information from.
Definition at line 105 of file seqinfosrc_seqvec.hpp.
Referenced by CSeqVecSeqInfoSrc::GetId(), CSeqVecSeqInfoSrc::GetLength(), CSeqVecSeqInfoSrc::GetMasks(), CSeqVecSeqInfoSrc::GetSeqLoc(), and CSeqVecSeqInfoSrc::Size().
◆ m_SeqVector
|
private |
Definition at line 564 of file blast_objmgr_tools.cpp.
Referenced by CBlastSeqVectorOM::GetCompressedPlusStrand(), CBlastSeqVectorOM::GetStrandData(), CBlastSeqVectorOM::operator[](), CBlastSeqVectorOM::SetCoding(), CBlastSeqVectorOM::x_SetStrand(), and CBlastSeqVectorOM::x_Size().
◆ m_Service [1/3]
|
private |
Service value for blast4 protocol.
Definition at line 282 of file blast_options_builder.hpp.
Referenced by CBlastOptionsBuilder::GetSearchOptions().
◆ m_Service [2/3]
|
private |
Service value used when submitting this search.
Definition at line 785 of file remote_blast.hpp.
Referenced by CRemoteBlast::GetMasks(), CRemoteBlast::GetResultSet(), CRemoteBlast::GetService(), CRemoteBlast::x_GetRequestInfoFromFile(), CRemoteBlast::x_GetRequestInfoFromRID(), CRemoteBlast::x_Init(), CRemoteBlast::x_QueryMaskingLocationsToNetwork(), and CRemoteBlast::x_SetDatabase().
◆ m_Service [3/3]
|
private |
Definition at line 180 of file search_strategy.hpp.
◆ m_SplitBlk
|
private |
Split query block structure.
Definition at line 111 of file split_query.hpp.
Referenced by CQuerySplitter::GetQueryFactoryForChunk(), CQuerySplitter::Split(), CQuerySplitter::x_ComputeChunkRanges(), CQuerySplitter::x_ComputeContextOffsets_NonTranslatedQueries(), CQuerySplitter::x_ComputeContextOffsets_TranslatedQueries(), CQuerySplitter::x_ComputeQueryContextsForChunks(), CQuerySplitter::x_ComputeQueryIndicesForChunks(), and CSplitQueryTestFixture::x_TestCContextTranslator().
◆ m_SplitQueriesInChunk
|
private |
Vector of split queries.
Definition at line 125 of file split_query.hpp.
Referenced by operator<<(), CQuerySplitter::Split(), CQuerySplitter::x_ComputeQueryIndicesForChunks(), and CSplitQueryTestFixture::x_ValidateQuerySeqLocsPerChunk().
◆ m_SplitQueryBlk
|
private |
The structure this object manages.
Definition at line 119 of file split_query_blk.hpp.
Referenced by CSplitQueryBlk::AddContextOffsetToChunk(), CSplitQueryBlk::AddContextToChunk(), CSplitQueryBlk::AddQueryToChunk(), CSplitQueryBlk::GetChunkBounds(), CSplitQueryBlk::GetChunkOverlapSize(), CSplitQueryBlk::GetContextOffsets(), CSplitQueryBlk::GetCStruct(), CSplitQueryBlk::GetNumChunks(), CSplitQueryBlk::GetNumQueriesForChunk(), CSplitQueryBlk::GetQueryContexts(), CSplitQueryBlk::GetQueryIndices(), CSplitQueryBlk::SetChunkBounds(), CSplitQueryBlk::SetChunkOverlapSize(), and CSplitQueryBlk::~CSplitQueryBlk().
◆ m_SSeqLocVector
|
private |
Definition at line 79 of file objmgr_query_data.hpp.
Referenced by CObjMgr_QueryFactory::CObjMgr_QueryFactory(), CObjMgr_QueryFactory::ExtractScopes(), CObjMgr_QueryFactory::ExtractUserSpecifiedMasks(), CObjMgr_QueryFactory::GetTSeqLocVector(), CObjMgr_QueryFactory::x_MakeLocalQueryData(), and CObjMgr_QueryFactory::x_MakeRemoteQueryData().
◆ m_StartingChunks
|
private |
Definition at line 166 of file split_query_aux_priv.hpp.
Referenced by CContextTranslator::CContextTranslator(), and operator<<().
◆ m_Strand
|
protected |
Maintains the state of the strand currently saved by the implementation of this class.
Definition at line 253 of file blast_setup.hpp.
Referenced by CBlastSeqVectorOM::CBlastSeqVectorOM(), IBlastSeqVector::GetStrand(), IBlastSeqVector::SetMinusStrand(), IBlastSeqVector::SetPlusStrand(), and CBlastSeqVectorOM::x_SetStrand().
◆ m_Subject [1/8]
|
private |
Reference to a BLAST subject/database object.
Definition at line 135 of file deltablast.hpp.
Referenced by CDeltaBlast::Run(), and CDeltaBlast::x_Validate().
◆ m_Subject [2/8]
|
private |
Subject database.
Definition at line 110 of file local_search.hpp.
Referenced by CLocalPssmSearch::Run(), and CLocalPssmSearch::SetSubject().
◆ m_Subject [3/8]
|
private |
Reference to a BLAST subject/database object.
Definition at line 116 of file psibl2seq.hpp.
Referenced by CPsiBl2Seq::CPsiBl2Seq(), and CPsiBl2Seq::x_InitSubject().
◆ m_Subject [4/8]
|
private |
Reference to a BLAST subject/database object.
Definition at line 127 of file psiblast.hpp.
Referenced by CPsiBlast::CPsiBlast().
◆ m_Subject [5/8]
|
private |
Search subject.
Definition at line 81 of file remote_search.hpp.
Referenced by CRemoteSeqSearch::SetSubject(), and CRemoteSeqSearch::x_RemoteBlast().
◆ m_Subject [6/8]
|
private |
Search subject.
Definition at line 120 of file remote_search.hpp.
Referenced by CRemotePssmSearch::SetSubject(), and CRemotePssmSearch::x_RemoteBlast().
◆ m_Subject [7/8]
|
private |
Definition at line 301 of file igblast.hpp.
Referenced by CIgBlast::Run().
◆ m_Subject [8/8]
|
private |
PSI-BLAST subject abstraction.
Definition at line 109 of file psiblast_impl.hpp.
Referenced by CPsiBlastImpl::Run(), and CPsiBlastImpl::x_Validate().
◆ m_SubjectFactory
|
private |
IQueryFactory containing the subject sequences.
Definition at line 141 of file local_db_adapter.hpp.
Referenced by CLocalDbAdapter::CLocalDbAdapter(), CLocalDbAdapter::MakeSeqInfoSrc(), and CLocalDbAdapter::MakeSeqSrc().
◆ m_SubjectId
Seq_id of hit subject.
Definition at line 355 of file cdd_pssm_input.hpp.
◆ m_SubjectMaskingType [1/3]
|
private |
Definition at line 308 of file blast_options_builder.hpp.
Referenced by CBlastOptionsBuilder::GetSubjectMaskingType(), CBlastOptionsBuilder::HasSubjectMaskingType(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ m_SubjectMaskingType [2/3]
|
private |
Definition at line 826 of file remote_blast.hpp.
Referenced by CRemoteBlast::GetSubjectMaskingType(), CRemoteBlast::SetDbFilteringAlgorithmId(), and CRemoteBlast::SetDbFilteringAlgorithmKey().
◆ m_SubjectMaskingType [3/3]
| ESubjectMaskingType CImportStrategyData::m_SubjectMaskingType |
Subject Masking Type.
Definition at line 83 of file search_strategy.hpp.
◆ m_SubjectMasks
|
protected |
the matching subjects masks
Definition at line 276 of file blast_results.hpp.
Referenced by CSearchResults::GetSubjectMasks(), and CSearchResults::SetSubjectMasks().
◆ m_SubjectRange
| TRange CCddInputData::CHitSegment::m_SubjectRange |
Segment range on subject.
Definition at line 270 of file cdd_pssm_input.hpp.
◆ m_Subjects
|
private |
This is initialized ONLY if the m_SubjectFactory is of type CObjMgr_QueryFactory, case in which it's not empty.
This is needed to handle delta sequences as input and it uses the object manager APIs
Definition at line 149 of file local_db_adapter.hpp.
Referenced by CLocalDbAdapter::CLocalDbAdapter(), CLocalDbAdapter::MakeSeqInfoSrc(), and CLocalDbAdapter::MakeSeqSrc().
◆ m_SubjectSeqLocs
|
private |
This field is populated when dealing with a remote bl2seq search (e.g.
: when formatting an RID using blast_formatter)
Definition at line 779 of file remote_blast.hpp.
Referenced by CRemoteBlast::GetSubjectSeqLocs(), CRemoteBlast::IsDbSearch(), CRemoteBlast::x_GetSubjects(), and CRemoteBlast::x_HasRetrievedSubjects().
◆ m_SubjectSequences
|
private |
Subject Sequences.
Definition at line 776 of file remote_blast.hpp.
Referenced by CRemoteBlast::GetSubjectSequences(), CRemoteBlast::IsDbSearch(), CRemoteBlast::x_GetRequestInfoFromFile(), CRemoteBlast::x_GetSubjects(), CRemoteBlast::x_HasRetrievedSubjects(), CRemoteBlast::x_SetDatabase(), and CRemoteBlast::x_SetSubjectSequences().
◆ m_SumOfSequenceLengths
|
private |
Definition at line 111 of file query_data.hpp.
Referenced by ILocalQueryData::GetSumOfSequenceLengths().
◆ m_Target2Find
|
private |
Definition at line 582 of file blast_options_builder.cpp.
Referenced by SBlast4ParamFinder::operator()().
◆ m_Task [1/2]
|
private |
Task used when the search was submitted (recovered via CBlastOptionsBuilder)
Definition at line 830 of file remote_blast.hpp.
Referenced by CRemoteBlast::GetResultSet(), CRemoteBlast::GetSearchOptions(), and CRemoteBlast::GetTask().
◆ m_Task [2/2]
| string CImportStrategyData::m_Task |
Task, such as megablast, blastn, blastp, etc.
Definition at line 75 of file search_strategy.hpp.
◆ m_TaxidList [1/2]
The tax id list (or none).
Definition at line 331 of file blast_options_builder.hpp.
Referenced by CBlastOptionsBuilder::GetTaxidList(), CBlastOptionsBuilder::HaveTaxidList(), and CBlastOptionsBuilder::x_ProcessOneOption().
◆ m_TaxidList [2/2]
Definition at line 842 of file remote_blast.hpp.
Referenced by CRemoteBlast::GetSearchOptions(), and CRemoteBlast::GetTaxidList().
◆ m_TbackSearch
|
private |
Object which runs the traceback stage of the search.
Definition at line 135 of file local_blast.hpp.
Referenced by CLocalBlast::Run().
◆ m_Thresh
|
private |
Jaccard distance cutoff.
Definition at line 105 of file blastp_kmer_options.hpp.
◆ m_TopGeneIds
| vector<string> CIgAnnotation::m_TopGeneIds |
Definition at line 97 of file igblast.hpp.
Referenced by CIgAnnotation::CIgAnnotation(), and CIgBlast::x_AnnotateV().
◆ m_TotalNumIterationsToDo
|
private |
Number of iterations to perform.
Definition at line 125 of file psiblast_iteration.hpp.
Referenced by CPsiBlastIterationState::HasMoreIterations().
◆ m_TotalQueryLength
|
private |
Length of the concatenated query.
Definition at line 117 of file split_query.hpp.
Referenced by CQuerySplitter::x_ComputeChunkRanges().
◆ m_tQueries
|
private |
query sequence(s)
Definition at line 181 of file bl2seq.hpp.
Referenced by CBl2Seq::GetQueries(), CBl2Seq::GetQuery(), CBl2Seq::SetQueries(), CBl2Seq::SetQuery(), CBl2Seq::x_Init(), and CBl2Seq::x_InitCLocalBlast().
◆ m_Translate
| bool CIgBlastOptions::m_Translate |
Definition at line 84 of file igblast.hpp.
Referenced by CIgBlastArgs::ExtractAlgorithmOptions().
◆ m_TranslateCoords
|
private |
True if this object's masked regions store DNA coordinates that will later be translated into protein coordinates.
Definition at line 529 of file blast_setup.hpp.
Referenced by CBlastQueryFilteredFrames::CBlastQueryFilteredFrames(), and CBlastQueryFilteredFrames::UseProteinCoords().
◆ m_TSeqLocVector
|
protected |
Reference to input TSeqLocVector (or NULL if not used)
Definition at line 169 of file blast_objmgr_priv.hpp.
Referenced by CBlastQuerySourceOM::GetBlastSequence(), CBlastQuerySourceOM::GetGeneticCodeId(), CBlastQuerySourceOM::GetLength(), CBlastQuerySourceOM::GetMask(), CBlastQuerySourceOM::GetMaskedRegions(), CBlastQuerySourceOM::GetSeqId(), CBlastQuerySourceOM::GetSeqLoc(), CBlastQuerySourceOM::GetStrand(), CBlastQuerySourceOM::GetTitle(), CBlastQuerySourceOM::Size(), CBlastQuerySourceOM::x_AutoDetectGeneticCodes(), CBlastQuerySourceOM::x_CalculateMasks(), and CBlastQuerySourceOM::~CBlastQuerySourceOM().
◆ m_tSubjects
|
private |
sequence(s) to BLAST against
Definition at line 182 of file bl2seq.hpp.
Referenced by CBl2Seq::GetSubject(), CBl2Seq::GetSubjects(), CBl2Seq::SetSubject(), CBl2Seq::SetSubjects(), CBl2Seq::x_Init(), and CBl2Seq::x_InitCLocalBlast().
◆ m_UngappedKarlinBlk
|
private |
Ungapped Karlin parameters for one query.
Definition at line 134 of file blast_results.hpp.
Referenced by CBlastAncillaryData::CBlastAncillaryData(), CBlastAncillaryData::do_copy(), and CBlastAncillaryData::~CBlastAncillaryData().
◆ m_Units
|
private |
Definition at line 156 of file seedtop.hpp.
Referenced by CSeedTop::Run(), CSeedTop::x_GetPatternRanges(), and CSeedTop::x_ParsePattern().
◆ m_use_disk_cache
|
private |
Use disk cache for retrieving results default: false.
Definition at line 837 of file remote_blast.hpp.
Referenced by CRemoteBlast::CheckDone(), CRemoteBlast::DisableDiskCacheUse(), CRemoteBlast::EnableDiskCacheUse(), CRemoteBlast::IsDiskCacheActive(), CRemoteBlast::x_GetSearchResultsHTTP(), CRemoteBlast::x_InitDiskCache(), and CRemoteBlast::x_PollUntilDone().
◆ m_UseMBIndex
|
private |
Use megablast database index.
Definition at line 396 of file blast_options_local_priv.hpp.
Referenced by CBlastOptionsLocal::CBlastOptionsLocal(), CBlastOptionsLocal::GetUseIndex(), CBlastOptionsLocal::SetUseIndex(), CBlastOptionsLocal::Validate(), and CBlastOptionsLocal::x_DoDeepCopy().
◆ m_UserSpecifiedMasks
|
private |
Vector of masking locations.
Definition at line 123 of file split_query.hpp.
Referenced by CQuerySplitter::x_ComputeQueryIndicesForChunks(), and CQuerySplitter::x_ExtractCScopesAndMasks().
◆ m_V_penalty
| int CIgBlastOptions::m_V_penalty |
Definition at line 71 of file igblast.hpp.
Referenced by CIgBlastArgs::ExtractAlgorithmOptions(), CIgBlastnApp::Run(), and CIgBlast::x_SetupVSearch().
◆ m_Value
|
private |
The value itself, valid only if m_IsSet is true.
Definition at line 249 of file blast_options_builder.hpp.
◆ m_Verbose [1/2]
|
private |
Verbosity mode: whether to produce debugging info on stdout.
Definition at line 764 of file remote_blast.hpp.
Referenced by CRemoteBlast::GetResultSet(), CRemoteBlast::SetVerbose(), CRemoteBlast::x_GetRequestInfoFromRID(), CRemoteBlast::x_GetSubjects(), CRemoteBlast::x_Init(), CRemoteBlast::x_PollUntilDone(), and CRemoteBlast::x_SendRequest().
◆ m_Verbose [2/2]
|
private |
Display verbose output to stdout?
Definition at line 281 of file blast_services.hpp.
Referenced by CBlastServices::GetTaxIdWithWindowMaskerSupport().
◆ m_Warn
|
private |
List of warnings encountered.
Definition at line 752 of file remote_blast.hpp.
Referenced by CRemoteBlast::GetWarnings(), CRemoteBlast::GetWarningVector(), CRemoteBlast::x_QueryMaskingLocationsToNetwork(), and CRemoteBlast::x_SearchErrors().
◆ m_Warnings [1/3]
|
private |
Warnings produced by the search.
Definition at line 82 of file local_search.hpp.
◆ m_Warnings [2/3]
|
private |
Warnings produced by the search.
Definition at line 84 of file remote_search.hpp.
Referenced by CRemoteSeqSearch::Run().
◆ m_Warnings [3/3]
|
private |
Warnings produced by the search.
Definition at line 123 of file remote_search.hpp.
Referenced by CRemotePssmSearch::Run().
◆ m_WFreqsData
|
private |
Buffer for residue frequencies from CDs.
Definition at line 277 of file cdd_pssm_input.hpp.
◆ m_WindowMaskedTaxIds
|
private |
Taxonomy IDs for which there's windowmasker masking data at NCBI.
Definition at line 279 of file blast_services.hpp.
Referenced by CBlastServices::GetTaxIdWithWindowMaskerSupport().
◆ m_writingDone
|
private |
Has writing to the queue finished?
Definition at line 72 of file hspstream_queue.hpp.
◆ mask_algo_id
| int SSeqDB_SeqSrc_Data::mask_algo_id |
Algorithm ID and type for mask data fetching.
Definition at line 94 of file seqsrc_seqdb.cpp.
Referenced by SSeqDB_SeqSrc_Data::clone().
◆ mask_type
| ESubjectMaskingType SSeqDB_SeqSrc_Data::mask_type |
Definition at line 95 of file seqsrc_seqdb.cpp.
Referenced by SSeqDB_SeqSrc_Data::clone().
◆ max_allowed_j_deletion
|
static |
Definition at line 57 of file igblast.cpp.
Referenced by CIgBlast::x_FindDJAln().
◆ max_allowed_V_end_to_J_end
|
static |
Definition at line 61 of file igblast.cpp.
Referenced by CIgBlast::x_SetupDJSearch(), and CIgBlast::x_SetupNoOverlapDSearch().
◆ max_allowed_VD_distance
|
static |
Definition at line 56 of file igblast.cpp.
Referenced by CIgBlast::x_FindDJAln(), and CIgBlast::x_ProcessDGeneResult().
◆ max_allowed_VJ_distance_with_D
|
static |
Definition at line 54 of file igblast.cpp.
Referenced by CIgBlast::x_FindDJAln().
◆ max_allowed_VJ_distance_without_D
|
static |
Definition at line 55 of file igblast.cpp.
Referenced by CIgBlast::x_FindDJAln().
◆ max_J_length
|
static |
Definition at line 60 of file igblast.cpp.
◆ max_v_j_overlap
|
static |
Definition at line 62 of file igblast.cpp.
Referenced by CIgBlast::x_SetupDJSearch().
◆ mi_pDiagnostics
|
private |
Return search statistics data.
Definition at line 202 of file bl2seq.hpp.
Referenced by CBl2Seq::GetDiagnostics(), CBl2Seq::RunEx(), CBl2Seq::x_Init(), and CBl2Seq::x_ResetInternalDs().
◆ min_J_position_diff
|
private |
Definition at line 425 of file igblast.hpp.
Referenced by ScorePositionSort::s_CompareSeqAlignByScoreAndPosition().
◆ mtx_
|
private |
mutex used for thread sync
Definition at line 471 of file blast_dbindex.cpp.
Referenced by CIndexedDb_New::EndSearchIndication(), and CIndexedDb_New::UpdateIndex().
◆ multiple_threads_
|
private |
flag indicating that multithreading is in effect
Definition at line 474 of file blast_dbindex.cpp.
Referenced by CIndexedDb_New::SetMultipleThreads().
◆ n_oids
| SIZE_TYPE CIndexedDb_New::SVolumeDescriptor::n_oids |
Number of sequences in the volume.
Definition at line 345 of file blast_dbindex.cpp.
Referenced by CIndexedDb_New::GetNextUnusedOID(), and CIndexedDb_New::UpdateIndex().
◆ n_threads_
|
private |
number of search threads running
Definition at line 476 of file blast_dbindex.cpp.
Referenced by CIndexedDb_New::SetMultipleThreads(), CIndexedDb_New::SetNumThreads(), and CIndexedDb_New::UpdateIndex().
◆ name
| std::string CIndexedDb_New::SVolumeDescriptor::name |
Fully qualified name of the volume.
Definition at line 346 of file blast_dbindex.cpp.
◆ NCBI4NA_TO_BLASTNA
Translates between ncbi4na and blastna.
The first four elements of this array match ncbi2na.
Definition at line 37 of file blast_encoding.c.
Referenced by BLAST_PackDNA(), GetSequenceSingleNucleotideStrand(), s_GetSeq4na(), s_GetSeq4naChunkSeq(), s_GetSeq4naChunkSeq_PartialFetching(), and CSequenceDataTester::x_CompareSequenceData().
◆ NCBI4NA_TO_IUPACNA
|
extern |
Translates between ncbi4na and iupacna.
Definition at line 80 of file blast_encoding.c.
Referenced by VDBSRC_Convert4naToString().
◆ NCBISTDAA_TO_AMINOACID
|
extern |
Translates between ncbieaa and ncbistdaa.
Definition at line 115 of file blast_encoding.c.
Referenced by TestUtil::GetResidue(), CBlastFormatUtil::PrintAsciiPssm(), CPsiBlastInputClustalW::x_ExtractAlignmentData(), CSeedTop::x_GetPatternRanges(), and CPsiBlastInputClustalW::x_ValidateQueryInMsa().
◆ program [1/2]
| EBlastProgramType SMultiSeqSrcNewArgs::program |
BLAST program.
Definition at line 464 of file seqsrc_multiseq.cpp.
Referenced by s_MultiSeqSrcNew().
◆ program [2/2]
| EBlastProgramType SQueryFactorySrcNewArgs::program |
BLAST program.
Definition at line 442 of file seqsrc_query_factory.cpp.
Referenced by s_QueryFactorySrcNew().
◆ queries_
|
private |
query data (from BLAST)
Definition at line 472 of file blast_dbindex.cpp.
Referenced by CIndexedDb_New::DoPreSearch(), and CIndexedDb_New::UpdateIndex().
◆ query_factory
| CRef<IQueryFactory> SQueryFactorySrcNewArgs::query_factory |
The query factory.
Definition at line 440 of file seqsrc_query_factory.cpp.
Referenced by s_QueryFactorySrcNew().
◆ ref_count
| int CIndexedDb_New::SVolResults::ref_count |
How many threads still need the result set.
Definition at line 384 of file blast_dbindex.cpp.
Referenced by CIndexedDb_New::UpdateIndex().
◆ reliable_J_match_factor
|
private |
Definition at line 426 of file igblast.hpp.
Referenced by ScorePositionSort::s_CompareSeqAlignByScoreAndPosition().
◆ res
| TVolResults CIndexedDb_New::SVolResults::res |
Seed set or null.
Definition at line 383 of file blast_dbindex.cpp.
Referenced by CIndexedDb_New::UpdateIndex().
◆ results_
|
private |
Set of result sets, one per loaded index.
Definition at line 235 of file blast_dbindex.cpp.
Referenced by CIndexedDb_Old::CheckOid(), CIndexedDb_Old::GetResults(), and CIndexedDb_Old::PreSearch().
◆ results_holder_
|
private |
reference counted seed set holders
Definition at line 470 of file blast_dbindex.cpp.
Referenced by CIndexedDb_New::CheckOid(), CIndexedDb_New::CIndexedDb_New(), CIndexedDb_New::EndSearchIndication(), CIndexedDb_New::GetResults(), and CIndexedDb_New::UpdateIndex().
◆ RunSearchFn
|
static |
Global pointer to the appropriate callback to run indexed search, based on whether or not index search is enabled.
Definition at line 133 of file blast_dbindex.cpp.
Referenced by ClearDbIndexCallbacks(), GetDbIndexRunSearchFn(), and SetUpDbIndexCallbacks().
◆ seq_ranges
| CSeqDB::TSequenceRanges SSeqDB_SeqSrc_Data::seq_ranges |
Ranges of the sequence to include (for masking).
Definition at line 102 of file seqsrc_seqdb.cpp.
◆ seq_vector
| TSeqLocVector SMultiSeqSrcNewArgs::seq_vector |
Vector of sequences.
Definition at line 463 of file seqsrc_multiseq.cpp.
Referenced by s_MultiSeqSrcNew().
◆ seqdb
| CRef<CSeqDBExpert> SSeqDB_SeqSrc_Data::seqdb |
SeqDB object.
Definition at line 91 of file seqsrc_seqdb.cpp.
Referenced by SSeqDB_SeqSrc_Data::clone(), SSeqDB_SeqSrc_Data::operator*(), and SSeqDB_SeqSrc_Data::operator->().
◆ seqmap_
|
private |
For each element of indices_ with index i seqmap_[i] contains one plus the last oid of that database index.
Definition at line 236 of file blast_dbindex.cpp.
Referenced by CIndexedDb_Old::CheckOid(), CIndexedDb_Old::GetResults(), CIndexedDb_Old::LocateIndex(), and CIndexedDb_Old::PreSearch().
◆ SetNumThreadsFn
|
static |
Global pointer to the appropriate callback to set the number of threads.
Definition at line 123 of file blast_dbindex.cpp.
Referenced by ClearDbIndexCallbacks(), GetDbIndexSetNumThreadsFn(), and SetUpDbIndexCallbacks().
◆ SetQueryInfoFn
|
static |
Global pointer to the appropriate callback to set query info, based on whether or not index search is enabled.
Definition at line 128 of file blast_dbindex.cpp.
Referenced by ClearDbIndexCallbacks(), GetDbIndexSetQueryInfoFn(), and SetUpDbIndexCallbacks().
◆ SetUsingThreadsFn
|
static |
Global pointer to the appropriate callback to set the state of concurrency.
Definition at line 120 of file blast_dbindex.cpp.
Referenced by ClearDbIndexCallbacks(), GetDbIndexSetUsingThreadsFn(), and SetUpDbIndexCallbacks().
◆ sopt_
|
private |
common search parameters
Definition at line 473 of file blast_dbindex.cpp.
Referenced by CIndexedDb_New::DoPreSearch(), and CIndexedDb_New::UpdateIndex().
◆ start_oid
| SIZE_TYPE CIndexedDb_New::SVolumeDescriptor::start_oid |
OId of the first sequence of the volume.
Definition at line 344 of file blast_dbindex.cpp.
Referenced by CIndexedDb_New::GetNextUnusedOID(), and CIndexedDb_New::UpdateIndex().
◆ subj_seqs
| TSeqLocVector SQueryFactorySrcNewArgs::subj_seqs |
The subject sequences.
Definition at line 441 of file seqsrc_query_factory.cpp.
Referenced by s_QueryFactorySrcNew().
◆ USING_NCBI_SCOPE [1/2]
| USING_NCBI_SCOPE |
Definition at line 47 of file seqsrc_seqdb.cpp.
◆ USING_NCBI_SCOPE [2/2]
| USING_NCBI_SCOPE |
Definition at line 46 of file blast_input_unit_test_aux.hpp.
◆ valid
| bool CImportStrategyData::valid |
Has the struct been properly filled in?
Definition at line 63 of file search_strategy.hpp.
◆ volumes_
|
private |
index volume descriptors
Definition at line 469 of file blast_dbindex.cpp.
Referenced by CIndexedDb_New::AddIndexInfo(), CIndexedDb_New::CheckOid(), CIndexedDb_New::CIndexedDb_New(), CIndexedDb_New::EndSearchIndication(), CIndexedDb_New::FindVolume(), CIndexedDb_New::GetNextUnusedOID(), CIndexedDb_New::GetResults(), CIndexedDb_New::MinIndexWordSize(), CIndexedDb_New::TraceVolumes(), and CIndexedDb_New::UpdateIndex().
Friends
◆ ::CBlastFilterTest [1/2]
|
friend |
Definition at line 218 of file bl2seq.hpp.
◆ ::CBlastFilterTest [2/2]
|
friend |
Definition at line 150 of file local_blast.hpp.
◆ ::CPssmCddInputTest
|
friend |
Definition at line 494 of file cdd_pssm_input.hpp.
◆ ::CPssmCreateTestFixture [1/2]
|
friend |
unit test class
Definition at line 310 of file psi_pssm_input.hpp.
◆ ::CPssmCreateTestFixture [2/2]
|
friend |
unit test class
Definition at line 247 of file pssm_engine.hpp.
◆ ::CSplitQueryTestFixture
|
friend |
Declare unit test class as a friend.
Definition at line 153 of file split_query.hpp.
◆ CBl2Seq
|
friend |
Definition at line 151 of file local_blast.hpp.
◆ CBlastOptions [1/2]
|
friend |
Definition at line 79 of file blast_memento_priv.hpp.
◆ CBlastOptions [2/2]
|
friend |
Definition at line 406 of file blast_options_local_priv.hpp.
◆ CBlastOptionsMemento
|
friend |
Friend class which allows extraction of this class' data members for internal use in the C++ API APIs.
Definition at line 410 of file blast_options_local_priv.hpp.
◆ CBlastPrelimSearch
|
friend |
Definition at line 84 of file blast_memento_priv.hpp.
◆ CBlastTracebackSearch [1/2]
|
friend |
Friend declaration so that this class can access the CSeqDB object to enable partial subject sequence fetching.
Definition at line 125 of file seqinfosrc_seqdb.hpp.
◆ CBlastTracebackSearch [2/2]
|
friend |
Definition at line 85 of file blast_memento_priv.hpp.
◆ CEffectiveSearchSpaceCalculator
|
friend |
Definition at line 87 of file blast_memento_priv.hpp.
◆ CEffectiveSearchSpacesMemento
|
friend |
Definition at line 411 of file blast_options_local_priv.hpp.
◆ CFilteringMemento
|
friend |
Definition at line 86 of file blast_memento_priv.hpp.
◆ CPrelimSearchRunner
|
friend |
Definition at line 83 of file blast_memento_priv.hpp.
◆ CSetupFactory
|
friend |
Definition at line 82 of file blast_memento_priv.hpp.
◆ operator<
|
friend |
Volumes are compared by their starting ordinal ids.
Definition at line 350 of file blast_dbindex.cpp.
◆ operator<< [1/4]
|
friend |
Print this object so that its contents can be directly used to update split_query.ini (for unit testing)
- Parameters
-
out stream to print this object [in|out] rhs object to print [in]
Definition at line 286 of file split_query_aux_priv.cpp.
◆ operator<< [2/4]
|
friend |
Print this object so that its contents can be directly used to update split_query.ini (for unit testing)
- Parameters
-
out stream to print this object [in|out] rhs object to print [in]
Definition at line 65 of file split_query_cxx.cpp.
◆ operator<< [3/4]
|
friend |
Print this object so that its contents can be directly used to update split_query.ini (for unit testing)
- Parameters
-
out stream to print this object [in|out] rhs object to print [in]
Definition at line 219 of file split_query_blk.cpp.
◆ operator<< [4/4]
|
friend |
This is only used for debug tracing.
Print out information about the volume.
Definition at line 359 of file blast_dbindex.cpp.
