BlastOffsetPair Union Reference

This symbol enables the verbose option in makeblastdb and other BLAST+ search command line applications, as well as the option to submit searches to the test server in NCBI for remote BLAST searches #define _BLAST_DEBUG 1. More...

#include <algo/blast/core/blast_def.h>

Public Attributes
struct {
Uint4   q_off
	Query offset. More...
Uint4   s_off
	Subject offset. More...
}	qs_offsets
	Query/subject offset pair. More...
struct {
Uint4   s_start
	Start offset of pattern in subject. More...
Uint4   s_end
	End offset of pattern in subject. More...
}	phi_offsets
	Pattern offsets in subject (PHI BLAST only) More...

Detailed Description

This symbol enables the verbose option in makeblastdb and other BLAST+ search command line applications, as well as the option to submit searches to the test server in NCBI for remote BLAST searches #define _BLAST_DEBUG 1.

Structure holding a pair of offsets. Used for storing offsets for the initial seeds. In most programs the offsets are query offset and subject offset of an initial word match. For PHI BLAST, the offsets are start and end of the pattern occurrence in subject, with no query information, because all pattern occurrences in subjects are aligned to all pattern occurrences in query.

Definition at line 141 of file blast_def.h.

Member Data Documentation

struct { ... } BlastOffsetPair::phi_offsets

Pattern offsets in subject (PHI BLAST only)

Referenced by PHIGetGappedScore(), CSeedTop::Run(), and s_PHISaveInitialHit().

q_off

Uint4 BlastOffsetPair::q_off

Query offset.

Definition at line 143 of file blast_def.h.

Referenced by BLAST_GetGappedScore(), BLAST_GetUngappedHSPList(), BLAST_SaveInitialHit(), BlastNaExtendJumper(), BOOST_AUTO_TEST_CASE(), compare_offsets(), JumperNaWordFinder(), MB_IndexedWordFinder(), s_AddToRPSBucket(), s_AdjustInitialHSPOffsets(), s_BlastCompressedAaScanSubject(), s_BlastDynProgNtGappedAlignment(), s_BlastLookupRetrieve(), s_BlastMBLookupRetrieve(), s_BlastMBLookupRetrieve2(), s_BlastNaExtend(), s_BlastNaExtendAligned(), s_BlastNaExtendDirect(), s_BlastProtGappedAlignment(), s_BlastRPSWordFinder_OneHit(), s_BlastRPSWordFinder_TwoHit(), s_BlastSmallNaExtend(), s_BlastSmallNaExtendAlignedOneByte(), s_CompareOffsetPairsByDiagQuery(), s_GetUngappedHSPContext(), s_TranslateHSPsToDNAPCoord(), TestFixture::ScanCheckHitsCore(), TestFixture::ScanOffsetTestCore(), NuclWordFinderTextFixture::setupSequenceOffsets(), and ShortRead_IndexedWordFinder().

struct { ... } BlastOffsetPair::qs_offsets

Query/subject offset pair.

Referenced by BLAST_GetGappedScore(), BLAST_GetUngappedHSPList(), BLAST_SaveInitialHit(), BlastNaExtendJumper(), BOOST_AUTO_TEST_CASE(), compare_offsets(), JumperNaWordFinder(), MB_IndexedWordFinder(), s_AddToRPSBucket(), s_AdjustInitialHSPOffsets(), s_BlastCompressedAaScanSubject(), s_BlastDynProgNtGappedAlignment(), s_BlastLookupRetrieve(), s_BlastMBLookupRetrieve(), s_BlastMBLookupRetrieve2(), s_BlastNaExtend(), s_BlastNaExtendAligned(), s_BlastNaExtendDirect(), s_BlastProtGappedAlignment(), s_BlastRPSWordFinder_OneHit(), s_BlastRPSWordFinder_TwoHit(), s_BlastSmallNaExtend(), s_BlastSmallNaExtendAlignedOneByte(), s_CompareOffsetPairsByDiagQuery(), s_GetUngappedHSPContext(), s_TranslateHSPsToDNAPCoord(), TestFixture::ScanCheckHitsCore(), TestFixture::ScanOffsetTestCore(), NuclWordFinderTextFixture::setupSequenceOffsets(), ShortRead_IndexedWordFinder(), and TestFixture::SkipMaskedRangesCore().

s_end

Uint4 BlastOffsetPair::s_end

End offset of pattern in subject.

Definition at line 148 of file blast_def.h.

Referenced by BOOST_AUTO_TEST_CASE(), PHIGetGappedScore(), CSeedTop::Run(), and s_PHISaveInitialHit().

s_off

Uint4 BlastOffsetPair::s_off

Subject offset.

Definition at line 144 of file blast_def.h.

Referenced by BLAST_GetGappedScore(), BLAST_GetUngappedHSPList(), BLAST_SaveInitialHit(), BlastNaExtendJumper(), BOOST_AUTO_TEST_CASE(), compare_offsets(), JumperNaWordFinder(), MB_IndexedWordFinder(), s_AddToRPSBucket(), s_BlastCompressedAaScanSubject(), s_BlastDynProgNtGappedAlignment(), s_BlastLookupRetrieve(), s_BlastMBLookupRetrieve(), s_BlastMBLookupRetrieve2(), s_BlastNaExtend(), s_BlastNaExtendAligned(), s_BlastNaExtendDirect(), s_BlastProtGappedAlignment(), s_BlastRPSWordFinder_OneHit(), s_BlastRPSWordFinder_TwoHit(), s_BlastSmallNaExtend(), s_BlastSmallNaExtendAlignedOneByte(), s_CompareOffsetPairsByDiagQuery(), s_TranslateHSPsToDNAPCoord(), TestFixture::ScanCheckHitsCore(), TestFixture::ScanOffsetTestCore(), NuclWordFinderTextFixture::setupSequenceOffsets(), ShortRead_IndexedWordFinder(), and TestFixture::SkipMaskedRangesCore().

s_start

Uint4 BlastOffsetPair::s_start

Start offset of pattern in subject.

Definition at line 147 of file blast_def.h.

Referenced by BOOST_AUTO_TEST_CASE(), PHIGetGappedScore(), CSeedTop::Run(), and s_PHISaveInitialHit().

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The documentation for this union was generated from the following file:

• include/algo/blast/core/blast_def.h