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NCBI C++ ToolKit: include/algo/blast/core/blast_seqsrc.h File Reference

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

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Declaration of ADT to retrieve sequences for the BLAST engine.

Definition in file blast_seqsrc.h.

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.

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.

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.

Structure used as the argument to function SetRanges.

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

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().

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

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().

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().

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().

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().

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().

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]

Returns

a properly initialized BlastSeqSrc structure or NULL.

Definition at line 90 of file blast_seqsrc.c.

References calloc(), BlastSeqSrcNewInfo::constructor, BlastSeqSrcNewInfo::ctor_argument, BlastSeqSrc::NewFnPtr, NULL, and sfree.

Referenced by MockBlastSeqSrcInit(), MultiSeqBlastSeqSrcInit(), s_QueryFactoryBlastSeqSrcInit(), SeqDbBlastSeqSrcInit(), and SRABlastSeqSrcInit().

Deallocate individual sequence.

Parameters

seq_src the BLAST sequence source [in] getseq_arg contains sequence to deallocate [in|out]

Definition at line 289 of file blast_seqsrc.c.

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

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

How many database sequences to process in one database chunk.

this value is overriden in seqdb implementation, where the number of sequences is determined by the mmaped slice size

Definition at line 385 of file blast_seqsrc.c.

Referenced by BlastSeqSrcIteratorNewEx().

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