Declaration of ADT to retrieve sequences for the BLAST engine. More...

#include <algo/blast/core/ncbi_std.h>
#include <algo/blast/core/blast_def.h>
#include <algo/blast/core/blast_export.h>
#include <algo/blast/core/blast_message.h>
#include <algo/blast/core/blast_encoding.h>

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Classes
struct	BlastSeqSrcSetRangesArg
	Structure used as the argument to function SetRanges. More...

struct	BlastSeqSrcGetSeqArg
	Structure used as the second argument to functions satisfying the GetSeqBlkFnPtr signature, associated with index-based implementations of the BlastSeqSrc interface. More...

Macros
#define	BLAST_SEQSRC_MINGAP 1024
	Minimal gap allowed in range list. More...

#define	BLAST_SEQSRC_OVERHANG 1024
	Extension for each new range added. More...

#define	BLAST_SEQSRC_MINLENGTH 10
	Default minimal sequence length. More...

#define	BLAST_SEQSRC_EXCLUDED -3
	Sequence excluded due to filtering. More...

#define	BLAST_SEQSRC_ERROR -2
	Error while retrieving sequence. More...

#define	BLAST_SEQSRC_EOF -1
	No more sequences available. More...

#define	BLAST_SEQSRC_SUCCESS 0
	Successful sequence retrieval. More...

Typedefs
typedef struct BlastSeqSrc	BlastSeqSrc
	The BlastSeqSrc ADT is an opaque data type that defines an interface which is used by the core BLAST code to retrieve sequences. More...

typedef struct BlastSeqSrcIterator	BlastSeqSrcIterator
	Blast Sequence Source Iterator, designed to be used in conjunction with the BlastSeqSrc to provide MT-safe iteration over the sequences in the BlastSeqSrc. More...

typedef struct BlastSeqSrcNewInfo	BlastSeqSrcNewInfo
	Structure that contains the information needed for BlastSeqSrcNew to fully populate the BlastSeqSrc structure it returns. More...

typedef struct BlastSeqSrcSetRangesArg	BlastSeqSrcSetRangesArg
	Structure used as the argument to function SetRanges. More...

typedef struct BlastSeqSrcGetSeqArg	BlastSeqSrcGetSeqArg
	Structure used as the second argument to functions satisfying the GetSeqBlkFnPtr signature, associated with index-based implementations of the BlastSeqSrc interface. More...

Functions
BlastSeqSrc *	BlastSeqSrcNew (const BlastSeqSrcNewInfo *bssn_info)
	Allocates memory for a BlastSeqSrc structure and then invokes the constructor function defined in its first argument, passing the ctor_argument member of that same structure. More...

BlastSeqSrc *	BlastSeqSrcCopy (const BlastSeqSrc *seq_src)
	Copy function: needed to guarantee thread safety. More...

BlastSeqSrc *	BlastSeqSrcFree (BlastSeqSrc *seq_src)
	Frees the BlastSeqSrc structure by invoking the destructor function set by the user-defined constructor function when the structure is initialized (indirectly, by BlastSeqSrcNew). More...

Int4	BlastSeqSrcGetNumSeqs (const BlastSeqSrc *seq_src)
	Get the number of sequences contained in the sequence source. More...

Int4	BlastSeqSrcGetNumSeqsStats (const BlastSeqSrc *seq_src)
	Get the number of sequences used for calculation of expect values etc. More...

Int4	BlastSeqSrcGetMaxSeqLen (const BlastSeqSrc *seq_src)
	Get the length of the longest sequence in the sequence source. More...

Int4	BlastSeqSrcGetMinSeqLen (const BlastSeqSrc *seq_src)
	Get the length of the longest sequence in the sequence source. More...

Int4	BlastSeqSrcGetAvgSeqLen (const BlastSeqSrc *seq_src)
	Get the average length of all sequences in the sequence source. More...

Int8	BlastSeqSrcGetTotLen (const BlastSeqSrc *seq_src)
	Get the total length of all sequences in the sequence source. More...

Int8	BlastSeqSrcGetTotLenStats (const BlastSeqSrc *seq_src)
	Get the total length of all sequences for calculation of expect value etc. More...

const char *	BlastSeqSrcGetName (const BlastSeqSrc *seq_src)
	Get the Blast Sequence source name (e.g. More...

Boolean	BlastSeqSrcGetIsProt (const BlastSeqSrc *seq_src)
	Find if the Blast Sequence Source contains protein or nucleotide sequences. More...

Boolean	BlastSeqSrcGetSupportsPartialFetching (const BlastSeqSrc *seq_src)
	Find if the Blast Sequence Source supports partial fetching. More...

BlastSeqSrcSetRangesArg *	BlastSeqSrcSetRangesArgNew (Int4 num_ranges)
	new setrangearg More...

Int2	BlastSeqSrcSetRangesArgAddRange (BlastSeqSrcSetRangesArg *arg, Int4 begin, Int4 end, Int4 len)
	add new range More...

BlastSeqSrcSetRangesArg *	BlastSeqSrcSetRangesArgFree (BlastSeqSrcSetRangesArg *arg)
	free setrangearg More...

void	BlastSeqSrcSetRangesArgBuild (BlastSeqSrcSetRangesArg *arg)
	build BlastSeqSrcSetRangesArg from range list More...

void	BlastSeqSrcSetSeqRanges (const BlastSeqSrc seq_src, BlastSeqSrcSetRangesArg setranges_arg)
	Setting the ranges for partial fetching. More...

Int2	BlastSeqSrcGetSequence (const BlastSeqSrc seq_src, BlastSeqSrcGetSeqArg getseq_arg)
	Retrieve an individual sequence. More...

Int4	BlastSeqSrcGetSeqLen (const BlastSeqSrc seq_src, void oid)
	Retrieve sequence length (number of residues/bases) More...

void	BlastSeqSrcReleaseSequence (const BlastSeqSrc seq_src, BlastSeqSrcGetSeqArg getseq_arg)
	Deallocate individual sequence. More...

char *	BlastSeqSrcGetInitError (const BlastSeqSrc *seq_src)
	Function to retrieve NULL terminated string containing the description of an initialization error or NULL. More...

BlastSeqSrcIterator *	BlastSeqSrcIteratorNew (void)
	Allocate and initialize an iterator over a BlastSeqSrc with a default chunk size for MT-safe iteration. More...

BlastSeqSrcIterator *	BlastSeqSrcIteratorNewEx (unsigned int chunk_sz)
	Allocate and initialize an iterator over a BlastSeqSrc. More...

BlastSeqSrcIterator *	BlastSeqSrcIteratorFree (BlastSeqSrcIterator *itr)
	Frees the BlastSeqSrcIterator structure. More...

Int4	BlastSeqSrcIteratorNext (const BlastSeqSrc seq_src, BlastSeqSrcIterator itr)
	Increments the BlastSeqSrcIterator. More...

void	BlastSeqSrcResetChunkIterator (BlastSeqSrc *seq_src)
	Reset the internal "bookmark" of the last chunk for iteration provided by this object. More...

void	BlastSeqSrcSetNumberOfThreads (BlastSeqSrc *seq_src, int nthreads)
	Set the number of threads for MT mode. More...

Variables
const unsigned int	kBlastSeqSrcDefaultChunkSize
	How many database sequences to process in one database chunk. More...

Detailed Description

Declaration of ADT to retrieve sequences for the BLAST engine.

Definition in file blast_seqsrc.h.

Macro Definition Documentation

◆ BLAST_SEQSRC_EOF

#define BLAST_SEQSRC_EOF -1

No more sequences available.

Definition at line 292 of file blast_seqsrc.h.

◆ BLAST_SEQSRC_ERROR

#define BLAST_SEQSRC_ERROR -2

Error while retrieving sequence.

Definition at line 291 of file blast_seqsrc.h.

◆ BLAST_SEQSRC_EXCLUDED

#define BLAST_SEQSRC_EXCLUDED -3

Sequence excluded due to filtering.

Definition at line 290 of file blast_seqsrc.h.

◆ BLAST_SEQSRC_MINGAP

#define BLAST_SEQSRC_MINGAP 1024

Minimal gap allowed in range list.

Definition at line 203 of file blast_seqsrc.h.

◆ BLAST_SEQSRC_MINLENGTH

#define BLAST_SEQSRC_MINLENGTH 10

Default minimal sequence length.

Definition at line 205 of file blast_seqsrc.h.

◆ BLAST_SEQSRC_OVERHANG

#define BLAST_SEQSRC_OVERHANG 1024

Extension for each new range added.

Definition at line 204 of file blast_seqsrc.h.

◆ BLAST_SEQSRC_SUCCESS

#define BLAST_SEQSRC_SUCCESS 0

Successful sequence retrieval.

Definition at line 293 of file blast_seqsrc.h.

Typedef Documentation

◆ BlastSeqSrc

typedef struct BlastSeqSrc BlastSeqSrc

The BlastSeqSrc ADT is an opaque data type that defines an interface which is used by the core BLAST code to retrieve sequences.

The interface currently provides the following services:

Retrieving number of sequences in a set
Retrieving the total length (in bases/residues) of sequences in a set.
Retrieving the length of the longest sequence in a set
Retrieving an individual sequence in a user-specified encoding by ordinal id (index into a set)
Retrieving the length of a given sequence in a set by ordinal id
Allow MT-safe iteration over sequences in a set through the BlastSeqSrcIterator abstraction, as well as resetting of any applicable implementation internal 'bookmarks' which keep track of the iteration progress, as to allow multiple passes over the set of sequences (
See also
BlastSeqSrcResetChunkIterator). Currently available client implementations of the BlastSeqSrc API include:
ReaddbBlastSeqSrcInit (C toolkit)
SeqDbBlastSeqSrcInit (C++ toolkit)
MultiSeqBlastSeqSrcInit (C/C++ toolkit)

For more details, see also Implementing the BlastSeqSrc interface

Definition at line 1 of file blast_seqsrc.h.

◆ BlastSeqSrcGetSeqArg

typedef struct BlastSeqSrcGetSeqArg BlastSeqSrcGetSeqArg

Structure used as the second argument to functions satisfying the GetSeqBlkFnPtr signature, associated with index-based implementations of the BlastSeqSrc interface.

Index-based implementations include BLAST databases or an array/vector of sequences.

◆ BlastSeqSrcIterator

typedef struct BlastSeqSrcIterator BlastSeqSrcIterator

Blast Sequence Source Iterator, designed to be used in conjunction with the BlastSeqSrc to provide MT-safe iteration over the sequences in the BlastSeqSrc.

Definition at line 1 of file blast_seqsrc.h.

◆ BlastSeqSrcNewInfo

typedef struct BlastSeqSrcNewInfo BlastSeqSrcNewInfo

Structure that contains the information needed for BlastSeqSrcNew to fully populate the BlastSeqSrc structure it returns.

Definition at line 1 of file blast_seqsrc.h.

◆ BlastSeqSrcSetRangesArg

typedef struct BlastSeqSrcSetRangesArg BlastSeqSrcSetRangesArg

Structure used as the argument to function SetRanges.

Function Documentation

◆ BlastSeqSrcCopy()

BlastSeqSrc* BlastSeqSrcCopy ( const BlastSeqSrc * seq_src )

Copy function: needed to guarantee thread safety.

Copies the contents of an input BlastSeqSrc, then calls a copier function, provided by the implementation, to achieve multi-thread safety.

Parameters

seq_src BlastSeqSrc to copy [in]

Returns: An MT-safe copy of the structure passed in, NULL in case of memory allocation failure, or, if no copy function was provided by the implementation, a bitwise copy of the input.

Definition at line 138 of file blast_seqsrc.c.

References BlastMemDup(), BlastSeqSrc::CopyFnPtr, and NULL.

Referenced by Blast_RedoAlignmentCore_MT(), BOOST_AUTO_TEST_CASE(), CPrelimSearchThread::CPrelimSearchThread(), NaHashLookupThreadDataNew(), SplitQuery_CreateChunkData(), and SThreadLocalDataArraySetup().

◆ BlastSeqSrcFree()

BlastSeqSrc* BlastSeqSrcFree ( BlastSeqSrc * seq_src )

Frees the BlastSeqSrc structure by invoking the destructor function set by the user-defined constructor function when the structure is initialized (indirectly, by BlastSeqSrcNew).

If the destructor function pointer is not set, a memory leak could occur. Note that it is the implementation's destructor responsibility to free the BlastSeqSrc structure by calling sfree.

Parameters

seq_src BlastSeqSrc to free [in]

Returns: NULL

Definition at line 112 of file blast_seqsrc.c.

References ASSERT, BlastSeqSrc::DeleteFnPtr, BlastSeqSrc::InitErrorStr, NULL, and sfree.

Referenced by Blast_RedoAlignmentCore_MT(), BOOST_AUTO_TEST_CASE(), CBlastPrelimSearch::CBlastPrelimSearch(), CPrelimSearchThread::CPrelimSearchThread(), CSetupFactory::CreateBlastSeqSrc(), NaHashLookupThreadDataFree(), CBlastKmerSearch::Run(), SplitQuery_CreateChunkData(), SThreadLocalDataFree(), CVDBBlastUtil::x_MakeVDBSeqSrc(), CLocalDbAdapter::~CLocalDbAdapter(), CVDBBlastUtil::~CVDBBlastUtil(), and FailingMockSeqSrcTestFixture::~FailingMockSeqSrcTestFixture().

◆ BlastSeqSrcGetAvgSeqLen()

Int4 BlastSeqSrcGetAvgSeqLen ( const BlastSeqSrc * seq_src )

Get the average length of all sequences in the sequence source.

Parameters

seq_src the BLAST sequence source [in]

Definition at line 211 of file blast_seqsrc.c.

References ASSERT, BlastSeqSrc::DataStructure, BlastSeqSrc::GetAvgSeqLen, and NULL.

Referenced by BLAST_PreliminarySearchEngine(), BOOST_AUTO_TEST_CASE(), and s_checkDbSeqSrcFunctions().

◆ BlastSeqSrcGetInitError()

char* BlastSeqSrcGetInitError ( const BlastSeqSrc * seq_src )

Function to retrieve NULL terminated string containing the description of an initialization error or NULL.

This function MUST ALWAYS be called after calling one of the client implementation's Init functions. If the return value is not NULL, invoking any other functionality from the BlastSeqSrc will result in undefined behavior. Caller is responsible for deallocating the return value.

Parameters

seq_src BlastSeqSrc from which to get an error [in]

Returns: error message or NULL

Definition at line 159 of file blast_seqsrc.c.

References BlastSeqSrc::InitErrorStr, NULL, and strdup.

Referenced by BOOST_AUTO_TEST_CASE(), TestUtil::CheckForBlastSeqSrcErrors(), CSetupFactory::CreateBlastSeqSrc(), s_CheckForBlastSeqSrcErrors(), and CVDBBlastUtil::x_MakeVDBSeqSrc().

◆ BlastSeqSrcGetIsProt()

Boolean BlastSeqSrcGetIsProt ( const BlastSeqSrc * seq_src )

Find if the Blast Sequence Source contains protein or nucleotide sequences.

Parameters

seq_src the BLAST sequence source [in]

Definition at line 243 of file blast_seqsrc.c.

References ASSERT, BlastSeqSrc::DataStructure, BlastSeqSrc::GetIsProt, and NULL.

Referenced by BOOST_AUTO_TEST_CASE(), CLocalDbAdapter::IsProtein(), s_checkDbSeqSrcFunctions(), and s_InitSeqInfoSrc().

◆ BlastSeqSrcGetMaxSeqLen()

Int4 BlastSeqSrcGetMaxSeqLen ( const BlastSeqSrc * seq_src )

Get the length of the longest sequence in the sequence source.

Parameters

seq_src the BLAST sequence source [in]

Definition at line 193 of file blast_seqsrc.c.

References ASSERT, BlastSeqSrc::DataStructure, BlastSeqSrc::GetMaxSeqLen, and NULL.

Referenced by BLAST_GapAlignSetUp(), Blast_RedoAlignmentCore_MT(), BOOST_AUTO_TEST_CASE(), and s_checkDbSeqSrcFunctions().

◆ BlastSeqSrcGetMinSeqLen()

Int4 BlastSeqSrcGetMinSeqLen ( const BlastSeqSrc * seq_src )

Get the length of the longest sequence in the sequence source.

Parameters

seq_src the BLAST sequence source [in]

Definition at line 201 of file blast_seqsrc.c.

References ASSERT, BLAST_SEQSRC_MINLENGTH, BlastSeqSrc::DataStructure, BlastSeqSrc::GetMinSeqLen, and NULL.

Referenced by BLAST_GapAlignSetUp().

◆ BlastSeqSrcGetName()

const char* BlastSeqSrcGetName ( const BlastSeqSrc * seq_src )

Get the Blast Sequence source name (e.g.

: BLAST database name). Here the full name (path and file name) should be returned. If an alias file is present the return value should be the full name of the alias file.

Parameters

seq_src the BLAST sequence source [in]

Definition at line 235 of file blast_seqsrc.c.

References ASSERT, BlastSeqSrc::DataStructure, BlastSeqSrc::GetName, and NULL.

Referenced by BlastSetupPreliminarySearchEx(), BOOST_AUTO_TEST_CASE(), CBlastTracebackSearch::CBlastTracebackSearch(), CVDBBlastUtil::FillVDBInfo(), s_checkDbSeqSrcFunctions(), and s_InitSeqInfoSrc().

◆ BlastSeqSrcGetNumSeqs()

Int4 BlastSeqSrcGetNumSeqs ( const BlastSeqSrc * seq_src )

Get the number of sequences contained in the sequence source.

Parameters

seq_src the BLAST sequence source [in]

Definition at line 177 of file blast_seqsrc.c.

References ASSERT, BlastSeqSrc::DataStructure, BlastSeqSrc::GetNumSeqs, and NULL.

Referenced by BLAST_GapAlignSetUp(), BLAST_GetSubjectTotals(), BLAST_PreliminarySearchEngine(), BOOST_AUTO_TEST_CASE(), CBlastFormat::CBlastFormat(), CVDBBlastUtil::CVDBBlastUtil(), CVDBBlastUtil::FillVDBInfo(), CBlastPrelimSearch::Run(), CSeedTop::Run(), s_checkDbSeqSrcFunctions(), s_InitializeSubject(), s_NaHashLookupScanSubjectForWordCounts(), s_RPSPreliminarySearchEngine(), s_ScanSubjectForWordCounts(), CVDBSeqInfoSrc::Size(), and SplitQuery_SetEffectiveSearchSpace().

◆ BlastSeqSrcGetNumSeqsStats()

Int4 BlastSeqSrcGetNumSeqsStats ( const BlastSeqSrc * seq_src )

Get the number of sequences used for calculation of expect values etc.

Parameters

seq_src the BLAST sequence source [in]

Definition at line 185 of file blast_seqsrc.c.

References ASSERT, BlastSeqSrc::DataStructure, BlastSeqSrc::GetNumSeqsStats, and NULL.

Referenced by BLAST_GapAlignSetUp(), BLAST_GetSubjectTotals(), and SplitQuery_SetEffectiveSearchSpace().

◆ BlastSeqSrcGetSeqLen()

Int4 BlastSeqSrcGetSeqLen	(	const BlastSeqSrc *	seq_src,
		void *	oid
	)

Retrieve sequence length (number of residues/bases)

Parameters

seq_src	the BLAST sequence source [in]
oid	ordinal id of the sequence desired (should be Uint4) [in]

Definition at line 281 of file blast_seqsrc.c.

References ASSERT, BlastSeqSrc::DataStructure, and BlastSeqSrc::GetSeqLen.

Referenced by BLAST_GapAlignSetUp(), BLAST_GetSubjectTotals(), BLAST_SetupPartialFetching(), BOOST_AUTO_TEST_CASE(), CVDBSeqInfoSrc::GetLength(), s_checkDbSeqSrcFunctions(), and s_MatchingSequenceInitialize().

◆ BlastSeqSrcGetSequence()

Int2 BlastSeqSrcGetSequence	(	const BlastSeqSrc *	seq_src,
		BlastSeqSrcGetSeqArg *	getseq_arg
	)

Retrieve an individual sequence.

Parameters

seq_src	the BLAST sequence source [in]
getseq_arg	arguments to aid retrieval of sequence data from the BlastSeqSrc [in\|out]

Returns: one of the BLAST_SEQSRC_* defined in blast_seqsrc.h

Definition at line 271 of file blast_seqsrc.c.

References ASSERT, BlastSeqSrc::DataStructure, and BlastSeqSrc::GetSequence.

Referenced by BLAST_ComputeTraceback_MT(), Blast_HSPListReevaluateUngapped(), BLAST_PreliminarySearchEngine(), BOOST_AUTO_TEST_CASE(), CSeedTop::Run(), s_checkDbSeqSrcFunctions(), s_ComputeNumIdentities(), s_MatchingSequenceInitialize(), s_NaHashLookupScanSubjectForWordCounts(), s_RPSComputeTraceback(), and s_ScanSubjectForWordCounts().

◆ BlastSeqSrcGetSupportsPartialFetching()

Boolean BlastSeqSrcGetSupportsPartialFetching ( const BlastSeqSrc * seq_src )

Find if the Blast Sequence Source supports partial fetching.

Parameters

seq_src the BLAST sequence source [in]

Definition at line 251 of file blast_seqsrc.c.

References ASSERT, BlastSeqSrc::DataStructure, FALSE, BlastSeqSrc::GetSupportsPartialFetching, and NULL.

Referenced by BLAST_ComputeTraceback_MT(), Blast_RedoAlignmentCore_MT(), and BLAST_SetupPartialFetching().

◆ BlastSeqSrcGetTotLen()

Int8 BlastSeqSrcGetTotLen ( const BlastSeqSrc * seq_src )

Get the total length of all sequences in the sequence source.

Parameters

seq_src the BLAST sequence source [in]

Definition at line 219 of file blast_seqsrc.c.

References ASSERT, BlastSeqSrc::DataStructure, BlastSeqSrc::GetTotLen, and NULL.

Referenced by BLAST_ComputeTraceback_MT(), BLAST_GapAlignSetUp(), BLAST_GetSubjectTotals(), BLAST_PreliminarySearchEngine(), BOOST_AUTO_TEST_CASE(), CBlastFormat::CBlastFormat(), CVDBBlastUtil::FillVDBInfo(), s_checkDbSeqSrcFunctions(), s_InitializeSubject(), s_RPSPreliminarySearchEngine(), and SplitQuery_SetEffectiveSearchSpace().

◆ BlastSeqSrcGetTotLenStats()

Int8 BlastSeqSrcGetTotLenStats ( const BlastSeqSrc * seq_src )

Get the total length of all sequences for calculation of expect value etc.

Parameters

seq_src the BLAST sequence source [in]

Definition at line 227 of file blast_seqsrc.c.

References ASSERT, BlastSeqSrc::DataStructure, BlastSeqSrc::GetTotLenStats, and NULL.

Referenced by BLAST_GapAlignSetUp(), BLAST_GetSubjectTotals(), and SplitQuery_SetEffectiveSearchSpace().

◆ BlastSeqSrcIteratorFree()

BlastSeqSrcIterator* BlastSeqSrcIteratorFree ( BlastSeqSrcIterator * itr )

Frees the BlastSeqSrcIterator structure.

Parameters

itr	BlastSeqSrcIterator to free [in]

Returns: NULL

Definition at line 412 of file blast_seqsrc.c.

References NULL, BlastSeqSrcIterator::oid_list, and sfree.

Referenced by BLAST_PreliminarySearchEngine(), BOOST_AUTO_TEST_CASE(), NaHashLookupThreadDataFree(), PrintSAMHeader(), CSeedTop::Run(), s_checkDbSeqSrcFunctions(), and s_ScanSubjectForWordCounts().

◆ BlastSeqSrcIteratorNew()

BlastSeqSrcIterator* BlastSeqSrcIteratorNew ( void )

Allocate and initialize an iterator over a BlastSeqSrc with a default chunk size for MT-safe iteration.

Returns: pointer to initialized iterator for BlastSeqSrc

Definition at line 380 of file blast_seqsrc.c.

References BlastSeqSrcIteratorNewEx().

Referenced by BOOST_AUTO_TEST_CASE(), PrintSAMHeader(), and s_checkDbSeqSrcFunctions().

◆ BlastSeqSrcIteratorNewEx()

BlastSeqSrcIterator* BlastSeqSrcIteratorNewEx ( unsigned int chunk_sz )

Allocate and initialize an iterator over a BlastSeqSrc.

Parameters

chunk_sz sets the chunk size of the iterator, if zero use kBlastSeqSrcDefaultChunkSize (above). [in]

Returns: pointer to initialized iterator for BlastSeqSrc

Definition at line 387 of file blast_seqsrc.c.

References calloc(), BlastSeqSrcIterator::chunk_sz, BlastSeqSrcIterator::current_pos, kBlastSeqSrcDefaultChunkSize, malloc(), NULL, BlastSeqSrcIterator::oid_list, sfree, and UINT4_MAX.

Referenced by BLAST_PreliminarySearchEngine(), BlastSeqSrcIteratorNew(), CVdbFastaExtractor::DumpAll(), NaHashLookupThreadDataNew(), CSeedTop::Run(), and s_ScanSubjectForWordCounts().

◆ BlastSeqSrcIteratorNext()

Int4 BlastSeqSrcIteratorNext	(	const BlastSeqSrc *	seq_src,
		BlastSeqSrcIterator *	itr
	)

Increments the BlastSeqSrcIterator.

Parameters

itr	the BlastSeqSrcIterator to increment.
seq_src	the underlying BlastSeqSrc

Returns: one of the BLAST_SEQSRC_* defined in blast_seqsrc.h

Definition at line 425 of file blast_seqsrc.c.

References ASSERT, BlastSeqSrc::DataStructure, and BlastSeqSrc::IterNext.

Referenced by BLAST_PreliminarySearchEngine(), BOOST_AUTO_TEST_CASE(), CVdbFastaExtractor::DumpAll(), PrintSAMHeader(), CSeedTop::Run(), s_checkDbSeqSrcFunctions(), s_NaHashLookupScanSubjectForWordCounts(), and s_ScanSubjectForWordCounts().

◆ BlastSeqSrcNew()

BlastSeqSrc* BlastSeqSrcNew ( const BlastSeqSrcNewInfo * bssn_info )

Allocates memory for a BlastSeqSrc structure and then invokes the constructor function defined in its first argument, passing the ctor_argument member of that same structure.

If the constructor function pointer is not set or there is a memory allocation failure, NULL is returned.

Note: This function need not be called directly by client code as all the implementations of the BlastSeqSrc interface provide a function(s) which call this function (MultiSeqBlastSeqSrcInit, SeqDbBlastSeqSrcInit)

Parameters

bssn_info Structure defining constructor and its argument to be invoked from this function [in]