CBioseq Class Reference

Search Toolkit Book for CBioseq

#include <objects/seq/Bioseq.hpp>

Inheritance diagram for CBioseq:

Collaboration diagram for CBioseq:

Public Types
enum	ELabelType { eType , eContent , eBoth }
Public Types inherited from CBioseq_Base
enum class	E_memberIndex {   e__allMandatory = 0 , e_id , e_descr , e_inst ,   e_annot }
typedef list< CRef< CSeq_id > >	TId
typedef CSeq_descr	TDescr
typedef CSeq_inst	TInst
typedef list< CRef< CSeq_annot > >	TAnnot
typedef Tparent::CMemberIndex< E_memberIndex, 5 >	TmemberIndex
Public Types inherited from CObject
enum	EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
	Control filling of newly allocated memory. More...
typedef CObjectCounterLocker	TLockerType
	Default locker type for CRef. More...
typedef atomic< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...
typedef Uint8	TCount
	Alias for value type of counter. More...

Public Member Functions
	CBioseq (void)
	~CBioseq (void)
CSeq_entry *	GetParentEntry (void) const
CConstRef< CBioseq_set >	GetParentSet (void) const
CConstRef< CSeqdesc >	GetClosestDescriptor (CSeqdesc::E_Choice choice, int *level=NULL) const
	CBioseq (const CSeq_loc &loc, const string &str_id=kEmptyStr)
void	GetLabel (string *label, ELabelType type, bool worst=false) const
const CSeq_id *	GetFirstId () const
const CSeq_id *	GetNonLocalId () const
	Find a non-local ID if present, consulting assembly details if all IDs for the overall sequence are local. More...
const CSeq_id *	GetLocalId () const
	Find a local ID if present. More...
bool	IsNa (void) const
bool	IsAa (void) const
TTaxId	GetTaxId () const
	Determine the tax-id for this bioseq. More...
bool	IsSetLength (void) const
TSeqPos	GetLength (void) const
void	PackAsDeltaSeq (bool gaps_ok=false)
	Convert a raw nucleotide sequence with occasional ambiguities or gaps into a tighter (but somewhat more complex) delta-seq representation. More...
Public Member Functions inherited from CBioseq_Base
	CBioseq_Base (void)
virtual	~CBioseq_Base (void)
	DECLARE_INTERNAL_TYPE_INFO ()
bool	IsSetId (void) const
	equivalent identifiers Check if a value has been assigned to Id data member. More...
bool	CanGetId (void) const
	Check if it is safe to call GetId method. More...
void	ResetId (void)
	Reset Id data member. More...
const TId &	GetId (void) const
	Get the Id member data. More...
TId &	SetId (void)
	Assign a value to Id data member. More...
bool	IsSetDescr (void) const
	descriptors Check if a value has been assigned to Descr data member. More...
bool	CanGetDescr (void) const
	Check if it is safe to call GetDescr method. More...
void	ResetDescr (void)
	Reset Descr data member. More...
const TDescr &	GetDescr (void) const
	Get the Descr member data. More...
void	SetDescr (TDescr &value)
	Assign a value to Descr data member. More...
TDescr &	SetDescr (void)
	Assign a value to Descr data member. More...
bool	IsSetInst (void) const
	the sequence data Check if a value has been assigned to Inst data member. More...
bool	CanGetInst (void) const
	Check if it is safe to call GetInst method. More...
void	ResetInst (void)
	Reset Inst data member. More...
const TInst &	GetInst (void) const
	Get the Inst member data. More...
void	SetInst (TInst &value)
	Assign a value to Inst data member. More...
TInst &	SetInst (void)
	Assign a value to Inst data member. More...
bool	IsSetAnnot (void) const
	Check if a value has been assigned to Annot data member. More...
bool	CanGetAnnot (void) const
	Check if it is safe to call GetAnnot method. More...
void	ResetAnnot (void)
	Reset Annot data member. More...
const TAnnot &	GetAnnot (void) const
	Get the Annot member data. More...
TAnnot &	SetAnnot (void)
	Assign a value to Annot data member. More...
virtual void	Reset (void)
	Reset the whole object. More...
Public Member Functions inherited from CSerialObject
	CSerialObject (void)
virtual	~CSerialObject (void)
virtual const CTypeInfo *	GetThisTypeInfo (void) const =0
virtual void	Assign (const CSerialObject &source, ESerialRecursionMode how=eRecursive)
	Set object to copy of another one. More...
virtual bool	Equals (const CSerialObject &object, ESerialRecursionMode how=eRecursive) const
	Check if both objects contain the same values. More...
virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. More...
void	ThrowUnassigned (TMemberIndex index) const
void	ThrowUnassigned (TMemberIndex index, const char *file_name, int file_line) const
bool	HasNamespaceName (void) const
	Check if object data type has namespace name. More...
const string &	GetNamespaceName (void) const
	Get namespace name. More...
bool	HasNamespacePrefix (void) const
	Check if data type has namespace prefix. More...
const string &	GetNamespacePrefix (void) const
	Get namespace prefix. More...
Public Member Functions inherited from CObject
	CObject (void)
	Constructor. More...
	CObject (const CObject &src)
	Copy constructor. More...
virtual	~CObject (void)
	Destructor. More...
CObject &	operator= (const CObject &src) THROWS_NONE
	Assignment operator. More...
bool	CanBeDeleted (void) const THROWS_NONE
	Check if object can be deleted. More...
bool	IsAllocatedInPool (void) const THROWS_NONE
	Check if object is allocated in memory pool (not system heap) More...
bool	Referenced (void) const THROWS_NONE
	Check if object is referenced. More...
bool	ReferencedOnlyOnce (void) const THROWS_NONE
	Check if object is referenced only once. More...
void	AddReference (void) const
	Add reference to object. More...
void	RemoveReference (void) const
	Remove reference to object. More...
void	ReleaseReference (void) const
	Remove reference without deleting object. More...
virtual void	DoNotDeleteThisObject (void)
	Mark this object as not allocated in heap – do not delete this object. More...
virtual void	DoDeleteThisObject (void)
	Mark this object as allocated in heap – object can be deleted. More...
void *	operator new (size_t size)
	Define new operator for memory allocation. More...
void *	operator new[] (size_t size)
	Define new[] operator for 'array' memory allocation. More...
void	operator delete (void *ptr)
	Define delete operator for memory deallocation. More...
void	operator delete[] (void *ptr)
	Define delete[] operator for memory deallocation. More...
void *	operator new (size_t size, void *place)
	Define new operator. More...
void	operator delete (void *ptr, void *place)
	Define delete operator. More...
void *	operator new (size_t size, CObjectMemoryPool *place)
	Define new operator using memory pool. More...
void	operator delete (void *ptr, CObjectMemoryPool *place)
	Define delete operator. More...
Public Member Functions inherited from CDebugDumpable
	CDebugDumpable (void)
virtual	~CDebugDumpable (void)
void	DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const
void	DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const
void	DumpToConsole (void) const
Public Member Functions inherited from CSerialUserOp
virtual	~CSerialUserOp ()

Protected Member Functions
virtual void	UserOp_Assign (const CSerialUserOp &source)
	Will be called after copying the datatool-generated members. More...
virtual bool	UserOp_Equals (const CSerialUserOp &object) const
	Will be called after comparing the datatool-generated members. More...
Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Private Types
typedef CBioseq_Base	Tparent

Private Member Functions
	CBioseq (const CBioseq &value)
CBioseq &	operator= (const CBioseq &value)
void	SetParentEntry (CSeq_entry *entry)

Static Private Member Functions
static void	x_SeqLoc_To_DeltaExt (const CSeq_loc &loc, CDelta_ext &ext)

Private Attributes
CSeq_entry *	m_ParentEntry

Static Private Attributes
static int	sm_ConstructedId = 0

Friends
class	CSeq_entry

Additional Inherited Members
Static Public Member Functions inherited from CSerialObject
static void	SetVerifyDataThread (ESerialVerifyData verify)
static void	SetVerifyDataGlobal (ESerialVerifyData verify)
static string	UnassignedString (void)
static CStringUTF8	UnassignedStringUTF8 (void)
static char	UnassignedByte (void)
Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (void)
	Define method to throw null pointer exception. More...
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (const type_info &type)
static EAllocFillMode	GetAllocFillMode (void)
static void	SetAllocFillMode (EAllocFillMode mode)
static void	SetAllocFillMode (const string &value)
	Set mode from configuration parameter value. More...
Static Public Member Functions inherited from CDebugDumpable
static void	EnableDebugDump (bool on)
Static Public Attributes inherited from CSerialObject
static const char *	ms_UnassignedStr = "<*unassigned*>"
static const char	ms_UnassignedByte = char(0xcd)
Static Public Attributes inherited from CObject
static const TCount	eCounterBitsCanBeDeleted = 1 << 0
	Define possible object states. More...
static const TCount	eCounterBitsInPlainHeap = 1 << 1
	Heap signature was found. More...
static const TCount	eCounterBitsPlaceMask
	Mask for 'in heap' state flags. More...
static const int	eCounterStep = 1 << 2
	Skip over the "in heap" bits. More...
static const TCount	eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
	Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...
static const TCount	eCounterStateMask
	Valid object, and object in heap. More...

Detailed Description

Definition at line 62 of file Bioseq.hpp.

Member Typedef Documentation

Tparent

typedef CBioseq_Base CBioseq::Tparent

private

Definition at line 64 of file Bioseq.hpp.

Member Enumeration Documentation

ELabelType

enum CBioseq::ELabelType

Enumerator
eType
eContent
eBoth

Definition at line 101 of file Bioseq.hpp.

Constructor & Destructor Documentation

CBioseq() [1/3]

CBioseq::CBioseq ( void  )

inline

Definition at line 162 of file Bioseq.hpp.

~CBioseq()

CBioseq::~CBioseq

(

void

)

Definition at line 84 of file Bioseq.cpp.

CBioseq() [2/3]

CBioseq::CBioseq ( const CSeq_loc &  loc, const string &  str_id = kEmptyStr  )

explicit

Definition at line 151 of file Bioseq.cpp.

References CSeq_inst_Base::eMol_other, CSeq_inst_Base::eRepr_const, NStr::IntToString(), CSeq_inst_Base::SetExt(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSeq_id_Base::SetLocal(), CSeq_inst_Base::SetMol(), CSeq_inst_Base::SetRepr(), CObject_id_Base::SetStr(), sm_ConstructedId, and x_SeqLoc_To_DeltaExt().

CBioseq() [3/3]

CBioseq::CBioseq ( const CBioseq &  value )

private

Member Function Documentation

GetClosestDescriptor()

CConstRef< CSeqdesc > CBioseq::GetClosestDescriptor	(	CSeqdesc::E_Choice	choice,
		int *	level = NULL
	)		const

Definition at line 212 of file Seq_entry.cpp.

References CSeq_descr_Base::Get(), CSeq_entry::GetDescr(), GetParentEntry(), CSeq_entry::GetParentEntry(), CSeq_entry::IsSetDescr(), ITERATE, NULL, and CSeqdesc_Base::Which().

Referenced by CFlatFileGenerator::Generate(), GetTitle(), CMacroFunction_MakeBoldXrefs::s_HasBarcodeDbXref(), CMacroFunction_GetSeqdesc::TheFunction(), CValidError_bioseq::ValidateMolInfoContext(), CValidError_bioseqset::ValidateNucProtSet(), CAsn2FastaApp::x_GetFastaOstream(), and CValidError_bioseq::x_ReportSuspiciousUseOfComplete().

GetFirstId()

const CSeq_id * CBioseq::GetFirstId

(

void

)

const

Definition at line 271 of file Bioseq.cpp.

References ctll::empty(), and CBioseq_Base::GetId().

Referenced by BOOST_AUTO_TEST_CASE(), CCachedSequence::CCachedSequence(), CFlatFileTextItem::CFlatFileTextItem(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CdBlaster::FillOutSeqLoc(), CViewGraphic::InitView(), CVcfTableView::InitView(), CTblastnNode::Main(), CMakeBadSpecificHostTable::MakeTable(), CSequesterSets::OnAccept(), CSelectFeatureDlg::OnButtonSaveFile(), CReorderSequencesDlg::ReadBioseq(), CSegregateSetsBase::ReadBioseq(), CPsiBlastApp::Run(), CLocalFinderApp::Run(), CVDBTblastnApp::Run(), s_AddSeqDataToPssm(), s_CreateQueryMap(), s_GetFastaDefline(), s_GetSequenceId(), SimpleSeqLocFromBioseq(), CSegregateSetsBase::TakeFromSet(), CTestAction::TestOID(), CVdbFastaExtractor::Write(), CAnnotGetter::x_AddAnnotations(), CAlnReader::x_AddMods(), CFastaReader::x_AddMods(), CSraInputSource::x_GetNextSeq_loc(), CAgpConverter::x_InitializeCopyOfTemplate(), CMakeProfileDBApp::x_MakeVol(), CBlastFormatterApp::x_QueryBioseqToSSeqLoc(), CBlastFormatterVdbApp::x_QueryBioseqToSSeqLoc(), CASN1InputSourceOMF::x_ReadOneSeq(), CDeltaBlastTestFixture::x_ReadSeqEntriesFromFile(), CTblastnApp::x_RunMTBySplitDB(), CSplitDataLoader::x_SplitSeq(), CPrimeCacheApplication::x_StripSeqEntry(), and CValidError_graph::x_ValidateGraphValues().

GetLabel()

void CBioseq::GetLabel	(	string *	label,
		ELabelType	type,
		bool	worst = false
	)		const

Definition at line 202 of file Bioseq.cpp.

References CSeq_id::Assign(), CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_Other, eContent, ctll::empty(), eType, FindBestChoice(), CEnumeratedTypeValues::FindName(), CBioseq_Base::GetId(), CBioseq_Base::GetInst(), GetLength(), CSeq_id::GetTextseq_Id(), NStr::IntToString(), CTextseq_id_Base::IsSetAccession(), IsSetLength(), ITERATE, label, CTextseq_id_Base::ResetName(), string, CSeq_id_Base::Which(), and CSeq_id::WorstRank().

Referenced by CValidError_bioseq::CheckForPubOnBioseq(), CValidErrorFormat::GetBioseqLabel(), CCorrectGenesDialog::GetCommand(), CBioseqHandler::GetLabel(), CSeq_entry::GetLabel(), CEditSequence::GetSeqTitle(), CPaintAlignment::GetSeqTitle(), s_CheckDataStatus(), CValidError_bioseq::ValidateSegRef(), and CValidError_bioseq::ValidateSeqDescContext().

GetLength()

TSeqPos CBioseq::GetLength

(

void

)

const

Definition at line 360 of file Bioseq.cpp.

References CBioseq_Base::GetInst(), and CSeq_inst_Base::GetLength().

Referenced by CGapsEditor::AddBioseqAsLiteral(), AddFeat(), AddProteinFeature(), CBuildDatabase::AddSequences(), AddToDeltaSeq(), AdjustSingleFeature(), CForeignContaminationScreenReportReader::AnnotateOrRemove(), BOOST_AUTO_TEST_CASE(), CheckGene(), CCmdAddCDS::Execute(), CCmdCreateCDS::Execute(), CBlastDBExtractor::ExtractFasta(), CdBlaster::FillOutSeqLoc(), FindGene(), fta_parse_tpa_tsa_block(), GapsToDelta(), GetLabel(), CBulkLocationPanel::GetLocForBioseq(), GetProtRefAnnot(), GetRetranslateCDSCommand(), GetSeqData(), GetSeqLen(), GetSPSegLocInfo(), IfOnlyStopCodon(), CBlastFormatUtil::InsertSubjectScores(), CConvertBadCdsAndRnaToMiscFeat::IsExtendableRight(), IsExtendableRight(), CConvertBadCdsAndRnaToMiscFeat::IsNonExtendable(), IsNonExtendable(), MakeEntryForDeltaConversion(), CScoreSeqCoverage::MakeScore(), CScoreUniqSeqCoverage::MakeScore(), OneTerminalTranslationExceptionTest(), CRemoveSequencesDlg::OnSelect(), CLengthSubpanel::OnSelectButton(), QSbuf_To_Single_Qscore_SeqGraph(), RetranslateCdregion(), RetranslateCDS(), RetrieveGi555WithTimeOut(), RetrieveLargeChromosomeWithTimeOut(), RetrieveLargeNuclSequence(), RetrieveLargeProteinWithTimeOut(), RetrievePartsOfLargeChromosome(), RevComp(), CUpdateSeq_Input::s_ConvertDeltaToRawBioseq(), s_ReadAndTestQueryFromString_CFastaReader(), SeqToDelta(), CLengthSubpanel::SetClusters(), SimpleSeqLocFromBioseq(), Split_Qscore_SeqGraph_By_DeltaSeq(), SrchSegLength(), TestOneGapSeq(), TestUTRPair(), CValidError_bioseq::ValidateDelta(), CValidError_bioseq::ValidateNsAndGaps(), CQualScoreWriter::Write(), CSequenceUpdater::x_AdjustProteinFeature(), CSequenceEditingEventHandler::x_CacheSelectedLocations(), CLocation_constraint::x_DoesLocationMatchDistanceConstraint(), CAdjustFeaturesForGaps::x_DoOne(), CNewCleanup_imp::x_ExtendFeatureToCoverSequence(), CNewCleanup_imp::x_ExtendProteinFeatureOnProteinSeq(), CAsn2FastaApp::x_GetFastaOstream(), CEditObjectSeq_feat::x_HandleCdsProduct(), CAgpConverter::x_InitializeAndCheckCopyOfTemplate(), CVectorTrimPanel::x_RetranslateCDS(), CQualScoreWriter::x_WriteHeader(), and CForeignContaminationScreenReportReader::xCheckLen().

GetLocalId()

const CSeq_id * CBioseq::GetLocalId

(

)

const

Find a local ID if present.

Definition at line 336 of file Bioseq.cpp.

References FindBestChoice(), CBioseq_Base::GetId(), CSeq_id_Base::IsLocal(), NULL, and s_BestLocalRank().

Referenced by BOOST_AUTO_TEST_CASE(), CLocalIDField::GetVals(), CLocalIDField::IsEmpty(), CEditingActionDescLocalId::Modify(), and seqsubmit_split::SIdCompare::xGetId().

GetNonLocalId()

const CSeq_id * CBioseq::GetNonLocalId

(

)

const

Find a non-local ID if present, consulting assembly details if all IDs for the overall sequence are local.

Definition at line 292 of file Bioseq.cpp.

References CSeq_hist_Base::CanGetAssembly(), CSeq_inst_Base::CanGetHist(), Empty(), FindBestChoice(), CSeq_hist_Base::GetAssembly(), CSeq_inst_Base::GetHist(), CBioseq_Base::GetId(), CBioseq_Base::GetInst(), CSeq_id_Base::IsLocal(), ITERATE, CSeq_id::Match(), NULL, and s_BestNonLocalRank().

Referenced by s_UseFastaReaderDeflines().

GetParentEntry()

CSeq_entry * CBioseq::GetParentEntry ( void  ) const

inline

Definition at line 174 of file Bioseq.hpp.

References m_ParentEntry.

Referenced by Convert_Bioseq_Seq_entry(), sequpd::FixCollidingIDs_Bioseq(), get_parent_seqset(), CValidError_imp::GetAncestor(), GetClosestDescriptor(), GetParentSet(), s_GetTaxId(), sx_FindBestId(), CDeflineProcess::UnindexedProcess(), CValidError_bioseq::ValidateGBBlock(), CValidError_bioseq::ValidateModifDescriptors(), CValidError_bioseq::ValidateMolInfoContext(), CValidError_bioseq::ValidateMoltypeDescriptors(), CValidError_bioseq::ValidateOrgContext(), CValidError_bioseq::ValidateSeqDescContext(), CValidError_bioseq::ValidateSeqFeatContext(), CValidError_bioseq::ValidateSeqParts(), CValidError_bioseq::ValidateUpdateDateContext(), CSeqMasterIndex::x_Initialize(), CValidError_bioseq::x_ReportSuspiciousUseOfComplete(), CValidError_bioseq::x_ValidateCompletness(), and CValidError_bioseq::x_ValidateTitle().

GetParentSet()

CConstRef< CBioseq_set > CBioseq::GetParentSet

(

void

)

const

Definition at line 312 of file Bioseq_set.cpp.

References GetParentEntry(), CSeq_entry::GetParentEntry(), CSeq_entry_Base::GetSet(), and CSeq_entry_Base::IsSet().

Referenced by CCleanup::AddPartialToProteinTitle(), CSourceModParser::ApplyAllMods(), CDescrCache::CDescrCache(), CollectNucProtBioseqs(), and s_SetDBLinkDesc().

GetTaxId()

TTaxId CBioseq::GetTaxId

(

void

)

const

Determine the tax-id for this bioseq.

Definition at line 177 of file Bioseq.cpp.

References Get(), CBioseq_Base::GetDescr(), CSeqdesc_Base::GetOrg(), CBioSource_Base::GetOrg(), CSeqdesc_Base::GetSource(), COrg_ref::GetTaxId(), CSeqdesc_Base::IsOrg(), CBioseq_Base::IsSetDescr(), CBioSource_Base::IsSetOrg(), CSeqdesc_Base::IsSource(), ITERATE, and ZERO_TAX_ID.

Referenced by BOOST_AUTO_TEST_CASE(), CSeqEntrySource::GetNext(), and CTestAction::TestOID().

IsAa()

bool CBioseq::IsAa

(

void

)

const

Definition at line 350 of file Bioseq.cpp.

References CBioseq_Base::GetInst(), and CSeq_inst::IsAa().

Referenced by CValidError_imp::AddBioseqWithNoPub(), CCleanup::AddMissingMolInfo(), CWriteDB_Impl::AddSequence(), CBuildDatabase::AddSequences(), CFeatGapInfo::AdjustProteinSeq(), CSourceModParser::ApplyAllMods(), CClearKeywords::ApplyToCSeq_entry(), CSeqTranslator::ChangeDeltaProteinToRawProtein(), CFeatureTableReader::ChangeDeltaProteinToRawProtein(), CNewCleanup_imp::CreateMissingMolInfo(), CCmdAddSeqEntry::Execute(), objects::CFixSuspectProductName::FixSuspectProductNames(), CApplyRNAITSDlg::GetCommand(), CGuiObjectInfoBioseq::GetIcon(), CBioseqHandler::GetLabel(), CDUpdater::GetOneBioseqFromSeqEntry(), CGuiObjectInfoBioseq::GetSubtype(), GetTitle(), CReadBlastApp::hasGenomicLocation(), CReadBlastApp::less_seq(), LoadFileForSubmission(), CLocation_constraint::Match(), CCDSTranslationPanel::OnImportCdsProteinHyperlinkClicked(), CNewCleanup_imp::RemoveBadProteinTitle(), CReadBlastApp::RemoveProblems(), CNewCleanup_imp::ResynchPeptidePartials(), CProsplignProcess::SeqEntryProcess(), SetCompleteness(), CMacroFunction_AddDBLink::TheFunction(), CMacroFunction_ApplyCDS::TheFunction(), CMacroFunction_ApplyRNA::TheFunction(), CMacroFunction_ApplyGene::TheFunction(), CValidError_bioseq::ValidateBioseqContext(), CValidError_bioseq::ValidateInst(), CValidError_bioseq::ValidateMolInfoContext(), CValidError_bioseq::ValidateMoltypeDescriptors(), CValidError_bioseqset::ValidateNucProtSet(), CValidError_bioseq::ValidateRawConst(), CValidError_bioseq::ValidateSegRef(), CValidError_bioseq::ValidateSeqDescContext(), CValidError_feat::ValidateSeqFeatContext(), CValidError_bioseq::ValidateSeqIds(), CValidError_bioseq::ValidateSeqLen(), CSequenceEditingEventHandler::x_CacheSelectedLocations(), CLocation_constraint::x_DoesBioseqMatchSequenceType(), CWriteDB_Impl::x_GetFastaReaderDeflines(), and CMacroFunction_UpdateProteinSeqs::x_ReadUpdateSeqs().

IsNa()

bool CBioseq::IsNa

(

void

)

const

Definition at line 345 of file Bioseq.cpp.

References CBioseq_Base::GetInst(), and CSeq_inst::IsNa().

Referenced by CFeatModApply::Apply(), CSourceModParser::ApplyAllMods(), CSourceModParser::ApplyMods(), CClearKeywords::ApplyToCSeq_entry(), CFastaReader::CheckDataLine(), FindNucInSeqEntry(), CApplyRNAITSDlg::GetCommand(), CGuiObjectInfoBioseq::GetIcon(), CBioseqHandler::GetLabel(), CMaskFastaReader::GetNextSequence(), CBioseq_set::GetNucFromNucProtSet(), CGuiObjectInfoBioseq::GetSubtype(), CValidError_bioseq::IsHistAssemblyMissing(), CFeatureTableReader::MoveRegionsToProteins(), CFastaReader::ParseDataLine(), CTable2AsnStructuredCommentsReader::ProcessComments(), CReorderSequencesDlg::ReadBioseq(), CSegregateSetsBase::ReadBioseq(), NMacroUtil::RemoveEmptyDescriptors(), RestoreModelFromInternalGnomonFeature(), RestoreModelFromPublicMrnaFeature(), RevComp(), s_AutoDefUserObjectFromBioseq(), s_CollectCollidingIDs_Entry(), CUpdateSeq_Input::s_ConvertDeltaToRawBioseq(), CUpdateSeq_Input::s_ConvertDeltaToRawEntry(), CUpdateSeq_Input::s_FixCollidingIDs_Entry(), s_HasUnprocessedCdregions(), CAgpwriteProcess::SeqEntryProcess(), CProsplignProcess::SeqEntryProcess(), CMacroFunction_SetStructCommDb::TheFunction(), CMacroFunction_Autodef::TheFunction(), CMacroFunction_RemoveAllFeatures::TheFunction(), CValidError_bioseqset::ValidateBioseqSet(), CValidError_bioseq::ValidateCompleteGenome(), CValidError_bioseq::ValidateDelta(), CValidError_graph::ValidateGraphsOnBioseq(), CValidError_bioseq::ValidateInst(), CValidError_bioseq::ValidateMolInfoContext(), CValidError_bioseqset::ValidateNucProtSet(), CValidError_bioseq::ValidateRawConst(), CValidError_bioseq::ValidateSeqDescContext(), CValidError_bioseq::ValidateSeqIds(), CConversionApp::Write(), CSequenceUpdater::x_AdjustProteinFeature(), CLocation_constraint::x_DoesBioseqMatchSequenceType(), CSubmissionWizard::x_ExtractDescriptorsFromSeqEntry(), CShowBlastDefline::x_InitDefline(), CSequenceUpdater::x_UpdateProteinID(), CValidError_bioseq::x_ValidateCompletness(), and CFeatureTableReader::xConvertSeqIntoSeqSet().

IsSetLength()

bool CBioseq::IsSetLength

(

void

)

const

Definition at line 355 of file Bioseq.cpp.

References CBioseq_Base::GetInst(), and CSeq_inst_Base::IsSetLength().

Referenced by CForeignContaminationScreenReportReader::AnnotateOrRemove(), GetLabel(), CBlastFormatUtil::InsertSubjectScores(), CScoreSeqCoverage::MakeScore(), CScoreUniqSeqCoverage::MakeScore(), CRemoveSequencesDlg::OnSelect(), CLengthSubpanel::OnSelectButton(), RetrievePartsOfLargeChromosome(), CAgpConverter::x_InitializeAndCheckCopyOfTemplate(), CQualScoreWriter::x_WriteHeader(), and CForeignContaminationScreenReportReader::xCheckLen().

operator=()

CBioseq& CBioseq::operator= ( const CBioseq &  value )

private

PackAsDeltaSeq()

void CBioseq::PackAsDeltaSeq

(

bool

gaps_ok = false

)

Convert a raw nucleotide sequence with occasional ambiguities or gaps into a tighter (but somewhat more complex) delta-seq representation.

Definition at line 365 of file Bioseq.cpp.

References CDelta_ext::AddAndSplit(), CODING_CASE, data, CSeq_data_Base::e_Ncbi2na, CSeq_inst_Base::eRepr_delta, ERR_POST_X, CDelta_ext_Base::Get(), CSeq_inst_Base::GetLength(), CSeq_inst_Base::GetSeq_data(), CSeq_inst::IsAa(), CSeq_inst_Base::IsSetExt(), CSeq_inst_Base::IsSetSeq_data(), CSeq_inst_Base::ResetExt(), CSeq_inst_Base::ResetSeq_data(), CSeq_data_Base::SelectionName(), CSeq_inst_Base::SetExt(), CBioseq_Base::SetInst(), CSeq_inst_Base::SetRepr(), and Warning().

SetParentEntry()

void CBioseq::SetParentEntry ( CSeq_entry *  entry )

inlineprivate

Definition at line 168 of file Bioseq.hpp.

References m_ParentEntry.

Referenced by CSeq_entry::Parentize(), and CSeq_entry::ParentizeOneLevel().

UserOp_Assign()

void CBioseq::UserOp_Assign ( const CSerialUserOp &  source )

protectedvirtual

Will be called after copying the datatool-generated members.

Implements CSerialUserOp.

Definition at line 88 of file Bioseq.cpp.

UserOp_Equals()

bool CBioseq::UserOp_Equals ( const CSerialUserOp &  object ) const

protectedvirtual

Will be called after comparing the datatool-generated members.

Implements CSerialUserOp.

Definition at line 92 of file Bioseq.cpp.

x_SeqLoc_To_DeltaExt()

void CBioseq::x_SeqLoc_To_DeltaExt ( const CSeq_loc &  loc, CDelta_ext &  ext  )

staticprivate

Definition at line 100 of file Bioseq.cpp.

References CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CPacked_seqint_Base::Get(), CSeq_loc_mix_Base::Get(), CPacked_seqpnt_Base::GetId(), CSeq_loc_Base::GetMix(), CSeq_loc_Base::GetPacked_int(), CSeq_loc_Base::GetPacked_pnt(), CPacked_seqpnt_Base::GetPoints(), CPacked_seqpnt_Base::GetStrand(), CPacked_seqpnt_Base::IsSetStrand(), ITERATE, pi, CDelta_ext_Base::Set(), CDelta_seq_Base::SetLoc(), CSeq_loc::SetPnt(), and CSeq_loc_Base::Which().

Referenced by CBioseq().

Friends And Related Function Documentation

CSeq_entry

friend class CSeq_entry

friend

Definition at line 153 of file Bioseq.hpp.

Member Data Documentation

m_ParentEntry

CSeq_entry* CBioseq::m_ParentEntry

private

Definition at line 147 of file Bioseq.hpp.

Referenced by GetParentEntry(), and SetParentEntry().

sm_ConstructedId

int CBioseq::sm_ConstructedId = 0

staticprivate

Definition at line 151 of file Bioseq.hpp.

Referenced by CBioseq().

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The documentation for this class was generated from the following files:

• include/objects/seq/Bioseq.hpp
• src/objects/seq/Bioseq.cpp
• src/objects/seqset/Bioseq_set.cpp
• src/objects/seqset/Seq_entry.cpp