Search Toolkit Book for BlastSeqSrcGetSeqArg
Structure used as the second argument to functions satisfying the GetSeqBlkFnPtr signature, associated with index-based implementations of the BlastSeqSrc interface. More...
#include <algo/blast/core/blast_seqsrc.h>
Collaboration diagram for BlastSeqSrcGetSeqArg:
Public Attributes | |
| Int4 | oid |
| Oid in BLAST database, index in an array of sequences, etc [in]. More... | |
| EBlastEncoding | encoding |
| Encoding of sequence, i.e. More... | |
| Boolean | reset_ranges |
| This option allows the BLAST engine to communicate with the BlastSeqSrc that the offset ranges for a given OID should be reset and the entire sequence data should be fetched. More... | |
| Boolean | check_oid_exclusion |
| Check whether an OID is excluded due to overlapping filtering. More... | |
| BLAST_SequenceBlk * | seq |
| Sequence to return, if NULL, it should allocated by GetSeqBlkFnPtr (using BlastSeqBlkNew or BlastSetUp_SeqBlkNew), else its contents are freed (using BlastSequenceBlkClean) and the structure is reused [out]. More... | |
| BlastSeqSrcSetRangesArg * | ranges |
Detailed Description
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.
Definition at line 257 of file blast_seqsrc.h.
Member Data Documentation
◆ check_oid_exclusion
| Boolean BlastSeqSrcGetSeqArg::check_oid_exclusion |
Check whether an OID is excluded due to overlapping filtering.
The disease is rare, and the test for it is somewhat expensive, so it is deferred to the traceback stage. TRUE to enable this test. [in]
Definition at line 279 of file blast_seqsrc.h.
Referenced by BLAST_ComputeTraceback_MT(), Blast_HSPListReevaluateUngapped(), BOOST_AUTO_TEST_CASE(), s_MatchingSequenceInitialize(), and s_SeqDbGetSequence().
◆ encoding
| EBlastEncoding BlastSeqSrcGetSeqArg::encoding |
Encoding of sequence, i.e.
: eBlastEncodingProtein, eBlastEncodingNucleotide, etc [in]
Definition at line 263 of file blast_seqsrc.h.
Referenced by BLAST_ComputeTraceback_MT(), Blast_HSPListReevaluateUngapped(), BLAST_PreliminarySearchEngine(), BOOST_AUTO_TEST_CASE(), NaHashLookupThreadDataNew(), CSeedTop::Run(), s_checkDbSeqSrcFunctions(), s_MatchingSequenceInitialize(), s_MultiSeqGetSequence(), s_QueryFactoryGetSequence(), s_RPSComputeTraceback(), s_ScanSubjectForWordCounts(), s_SeqDbGetSequence(), s_VDBSRC_GetSequence(), and CRandomlyFailMockBlastSeqSrc::x_PopulateBLAST_SequenceBlk().
◆ oid
| Int4 BlastSeqSrcGetSeqArg::oid |
Oid in BLAST database, index in an array of sequences, etc [in].
Definition at line 259 of file blast_seqsrc.h.
Referenced by BLAST_ComputeTraceback_MT(), Blast_HSPListReevaluateUngapped(), BLAST_PreliminarySearchEngine(), BOOST_AUTO_TEST_CASE(), CVdbFastaExtractor::DumpAll(), CRandomlyFailMockBlastSeqSrc::GetSequence(), CSeedTop::Run(), s_checkDbSeqSrcFunctions(), s_MatchingSequenceInitialize(), s_MultiSeqGetSequence(), s_NaHashLookupScanSubjectForWordCounts(), s_QueryFactoryGetSequence(), s_RPSComputeTraceback(), s_ScanSubjectForWordCounts(), s_SeqDbGetSequence(), s_VDBSRC_GetSequence(), and s_VDBSRC_ReleaseSequence().
◆ ranges
| BlastSeqSrcSetRangesArg* BlastSeqSrcGetSeqArg::ranges |
Definition at line 286 of file blast_seqsrc.h.
Referenced by BLAST_ComputeTraceback_MT(), BOOST_AUTO_TEST_CASE(), s_ComputeNumIdentities(), s_MatchingSequenceInitialize(), s_SeqDbGetSequence(), and s_SeqDbReleaseSequence().
◆ reset_ranges
| Boolean BlastSeqSrcGetSeqArg::reset_ranges |
This option allows the BLAST engine to communicate with the BlastSeqSrc that the offset ranges for a given OID should be reset and the entire sequence data should be fetched.
The motivation for this option is to exploit CSeqDB's performance feature that allows to retrieve only pre-selected portions of the sequence data for the traceback stage. BlastSeqSrc implementations that do not have this feature can safely ignore this field. By default, this should be set to FALSE. [in]
Definition at line 273 of file blast_seqsrc.h.
Referenced by BLAST_ComputeTraceback_MT(), BOOST_AUTO_TEST_CASE(), and s_SeqDbGetSequence().
◆ seq
| BLAST_SequenceBlk* BlastSeqSrcGetSeqArg::seq |
Sequence to return, if NULL, it should allocated by GetSeqBlkFnPtr (using BlastSeqBlkNew or BlastSetUp_SeqBlkNew), else its contents are freed (using BlastSequenceBlkClean) and the structure is reused [out].
Definition at line 284 of file blast_seqsrc.h.
Referenced by BLAST_ComputeTraceback_MT(), Blast_HSPListReevaluateUngapped(), BLAST_PreliminarySearchEngine(), BOOST_AUTO_TEST_CASE(), CRandomlyFailMockBlastSeqSrc::ReleaseSequence(), CSeedTop::Run(), s_checkDbSeqSrcFunctions(), s_MatchingSequenceInitialize(), s_MatchingSequenceRelease(), s_MultiSeqGetSequence(), s_MultiSeqReleaseSequence(), s_NaHashLookupScanSubjectForWordCounts(), s_QueryFactoryGetSequence(), s_QueryFactoryReleaseSequence(), s_RPSComputeTraceback(), s_ScanSubjectForWordCounts(), s_SeqDbGetSequence(), s_SeqDbReleaseSequence(), s_SequenceGetProteinRange(), s_SequenceGetTranslatedRange(), s_VDBSRC_GetSequence(), s_VDBSRC_ReleaseSequence(), and CRandomlyFailMockBlastSeqSrc::x_PopulateBLAST_SequenceBlk().
The documentation for this struct was generated from the following file:
- include/algo/blast/core/blast_seqsrc.h
