NCBI C++ ToolKit
Public Attributes | List of all members
BlastHSP Struct Reference

Search Toolkit Book for BlastHSP

Structure holding all information about an HSP. More...

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

+ Collaboration diagram for BlastHSP:

Public Attributes

Int4 score
 This HSP's raw score. More...
 
Int4 num_ident
 Number of identical base pairs in this HSP. More...
 
double bit_score
 Bit score, calculated from score. More...
 
double evalue
 This HSP's e-value. More...
 
BlastSeg query
 Query sequence info. More...
 
BlastSeg subject
 Subject sequence info. More...
 
Int4 context
 Context number of query. More...
 
GapEditScriptgap_info
 ALL gapped alignment is here. More...
 
Int4 num
 How many HSP's are linked together for sum statistics evaluation? If unset (0), this HSP is not part of a linked set, i.e. More...
 
Int2 comp_adjustment_method
 which mode of composition adjustment was used; relevant only for blastp and tblastn More...
 
SPHIHspInfopat_info
 In PHI BLAST, information about this pattern match. More...
 
Int4 num_positives
 
BlastHSPMappingInfomap_info
 

Detailed Description

Structure holding all information about an HSP.

Definition at line 126 of file blast_hits.h.

Member Data Documentation

◆ bit_score

double BlastHSP::bit_score

◆ comp_adjustment_method

Int2 BlastHSP::comp_adjustment_method

which mode of composition adjustment was used; relevant only for blastp and tblastn

Definition at line 139 of file blast_hits.h.

Referenced by Blast_HSPClone(), s_BlastHSPCopy(), s_BuildScoreList(), s_CalculateScoreVectorSize(), and s_HSPListFromDistinctAlignments().

◆ context

Int4 BlastHSP::context

◆ evalue

double BlastHSP::evalue

◆ gap_info

GapEditScript* BlastHSP::gap_info

◆ map_info

BlastHSPMappingInfo* BlastHSP::map_info

◆ num

Int4 BlastHSP::num

How many HSP's are linked together for sum statistics evaluation? If unset (0), this HSP is not part of a linked set, i.e.

value 0 is treated the same way as 1.

Definition at line 135 of file blast_hits.h.

Referenced by Blast_HSPClone(), BLAST_LinkHsps(), BOOST_AUTO_TEST_CASE(), s_BlastHSPCopy(), s_BuildScoreList(), s_CalculateScoreVectorSize(), s_CombineLinkedHSPSets(), s_LinkedHSPSetArraySetUp(), s_MergeLinkedHSPSets(), s_SumHSPEvalue(), and LinkHspTestFixture::testUnevenGapLinkHsps().

◆ num_ident

Int4 BlastHSP::num_ident

◆ num_positives

Int4 BlastHSP::num_positives

◆ pat_info

SPHIHspInfo* BlastHSP::pat_info

◆ query

BlastSeg BlastHSP::query

Query sequence info.

Definition at line 131 of file blast_hits.h.

Referenced by BLAST_GetGappedScore(), Blast_HSPCalcLengthAndGaps(), Blast_HSPClone(), Blast_HSPGetAdjustedOffsets(), Blast_HSPGetQueryCoverage(), Blast_HSPInit(), Blast_HSPListPurgeHSPsWithCommonEndpoints(), Blast_HSPListsMerge(), Blast_HSPListSubjectBestHit(), Blast_HSPReevaluateWithAmbiguitiesGapped(), Blast_HSPReevaluateWithAmbiguitiesUngapped(), Blast_HSPUpdateWithTraceback(), Blast_TracebackFromHSPList(), BlastGetOffsetsForGappedAlignment(), BlastGetStartForGappedAlignmentNucl(), BlastHSPStreamMerge(), BlastIntervalTreeAddHSP(), BlastIntervalTreeContainsHSP(), BlastIntervalTreeMasksHSP(), BlastIntervalTreeNumRedundant(), BlastNaExtendJumper(), BOOST_AUTO_TEST_CASE(), checkReevaluateResultsGapped(), checkReevaluateResultsUngappedNucl(), checkReevaluateResultsUngappedTransl(), DoAnchoredSearch(), FindPartialyCoveredQueries(), JumperFindSpliceSignals(), MakeSplicedSeg(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), s_AdjustSubjectForSraSearch(), s_AdjustSubjectForTranslatedSraSearch(), s_Blast_HSPGetNumIdentitiesAndPositives(), s_Blast_HSPGetOOFNumIdentitiesAndPositives(), s_BlastEvenGapLinkHSPs(), s_BlastHSPBestHitRun(), s_BlastHSPBestHitRun_RPS(), s_BlastHSPCopy(), s_BlastHSPCullingRun(), s_BlastHSPListRPSUpdate(), s_BlastMergeTwoHSPs(), s_BlastUnevenGapLinkHSPs(), s_CollectSeqAlignData(), s_CompareHSPsByContextSubjectOffset(), s_ComputeAlignmentScore(), s_ComputeBtopAndIdentity(), s_ComputeChainScore(), s_CutOffGapEditScript(), s_ExtendAlignment(), s_FindAdapters(), s_FindBestPairs(), s_FindBestPath(), s_FindFragmentStart(), s_FindPolyATails(), s_FindRearrangedPairs(), s_FindSpliceJunctions(), s_FindSpliceJunctionsForGap(), s_FindSpliceJunctionsForOverlaps(), s_FwdCompareHSPs(), s_FwdCompareHSPsTransl(), s_FwdCompareLinkedHSPSets(), s_GetHSPList(), s_GetOverlapCost(), s_GetTraceback(), s_HitlistReapContained(), s_HSPChainListInsertOne(), s_HSPChainListInsertOne_OLD(), s_HSPEndDiag(), s_HSPIsContained(), s_HSPOffsetBinarySearch(), s_HSPOffsetEndBinarySearch(), s_HSPQueryRangeIsContained(), s_HSPQueryRangeIsMasklevelContained(), s_HSPsHaveCommonEndpoint(), s_HSPStartDiag(), s_ImportFromHitlist(), s_IntervalTreeHasHSPEndpoint(), s_IntronToGap(), s_LinkedHSPSetArrayIndexQueryEnds(), s_LinkedHSPSetsAdmissible(), s_MergeHSPs(), s_MergeLinkedHSPSets(), s_OOFBlastHSP2SeqAlign(), s_PHITracebackFromHSPList(), s_QueryEndCompareHSPs(), s_QueryOffsetCompareHSPs(), s_RedoOneAlignment(), s_RemoveOverlaps(), s_ResultHspToDistinctAlign(), s_RevCompareHSPs(), s_RevCompareHSPsTbn(), s_RevCompareHSPsTbx(), s_RevCompareHSPsTransl(), s_SaveSubjectOverhangs(), s_SetAdapter(), s_SetPolyATail(), s_SetupHSPForGappedReevaluateTest(), s_SetupHSPForUngappedReevaluateNucl(), s_SetupHSPListBlastn(), s_SetupHSPListForUngappedReevaluateTransl(), s_SetupHSPListTransl(), s_TestChains(), s_TestCutoffs(), s_TestHSPRanges(), s_TrimChainEndToSubjPos(), s_TrimChainStartToSubjPos(), s_TrimHSP(), s_TrimOverlap(), s_UpdateReevaluatedHSP(), ScoreCompareHSPs(), setupHSPList(), LinkHspTestFixture::setupHSPListForMiddleInsertTest(), LinkHspTestFixture::setupHSPListNucl(), LinkHspTestFixture::setupHSPListTransl(), CTracebackSearchTestFixture::x_GetSampleHspStream(), CTracebackSearchTestFixture::x_GetSelfHitHspStream(), x_NonTranslatedHSPToStdSeg(), x_UngappedHSPToDenseDiag(), and x_UngappedHSPToStdSeg().

◆ score

Int4 BlastHSP::score

This HSP's raw score.

Definition at line 127 of file blast_hits.h.

Referenced by BLAST_GetGappedScore(), Blast_HitListUpdate(), Blast_HSPClone(), Blast_HSPInit(), Blast_HSPListAdjustOddBlastnScores(), Blast_HSPListGetBitScores(), Blast_HSPListGetEvalues(), Blast_HSPListPHIGetBitScores(), Blast_HSPListReapByRawScore(), Blast_HSPUpdateWithTraceback(), BlastHSPStreamMerge(), BlastIntervalTreeMasksHSP(), BOOST_AUTO_TEST_CASE(), checkReevaluateResultsGapped(), checkReevaluateResultsUngappedNucl(), checkReevaluateResultsUngappedTransl(), DoAnchoredScan(), h_score_compare_hsps(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), s_AddNextHSP(), s_BlastHitListInsertHSPListInHeap(), s_BlastHSP2SeqAlign(), s_BlastHSPBestHitRun(), s_BlastHSPBestHitRun_RPS(), s_BlastHSPCopy(), s_BlastHSPCullingFinal(), s_BlastHSPMapperSplicedPairedRun(), s_BlastMergeTwoHSPs(), s_BuildScoreList(), s_CalculateScoreVectorSize(), s_CompareHSPsByContextScore(), s_CompareHSPsByContextSubjectOffset(), s_ComputeChainScore(), s_DominateTest(), s_EvalueCompareHSPLists(), s_ExtendAlignment(), s_FindBestPath(), s_FindSpliceJunctions(), s_FindSpliceJunctionsForOverlaps(), s_GetHSPList(), s_HitlistEvaluateAndPurge(), s_HitlistReapContained(), s_HSPIsContained(), s_HSPListNormalizeScores(), s_HSPListRescaleScores(), s_HSPPHIGetEvalue(), s_HSPQueryRangeIsContained(), s_HSPQueryRangeIsMasklevelContained(), s_HSPsHaveCommonEndpoint(), s_LinkedHSPSetArraySetUp(), s_MergeHSPs(), s_QueryEndCompareHSPs(), s_QueryOffsetCompareHSPs(), s_ResultHspToDistinctAlign(), s_SetAdapter(), s_SetupHSPForGappedReevaluateTest(), s_SetupHSPForUngappedReevaluateNucl(), s_SetupHSPListBlastn(), s_SetupHSPListForUngappedReevaluateTransl(), s_SetupHSPListTransl(), s_SortHspWrapRawScore(), s_TrimChainEndToSubjPos(), s_TrimChainStartToSubjPos(), s_TrimHSP(), s_UpdateReevaluatedHSP(), ScoreCompareHSPs(), setupHSPList(), LinkHspTestFixture::setupHSPListForMiddleInsertTest(), LinkHspTestFixture::setupHSPListNucl(), LinkHspTestFixture::setupHSPListTransl(), LinkHspTestFixture::testUnevenGapLinkHsps(), CTracebackSearchTestFixture::x_GetSampleHspStream(), CTracebackSearchTestFixture::x_GetSelfHitHspStream(), x_score_compare_hsps(), and CPhiblastTestFixture::x_SetupHSPList().

◆ subject

BlastSeg BlastHSP::subject

Subject sequence info.

Definition at line 132 of file blast_hits.h.

Referenced by BLAST_GetGappedScore(), Blast_HSPAdjustSubjectOffset(), Blast_HSPCalcLengthAndGaps(), Blast_HSPClone(), Blast_HSPGetAdjustedOffsets(), Blast_HSPGetPartialSubjectTranslation(), Blast_HSPGetTargetTranslation(), Blast_HSPInit(), Blast_HSPListAdjustOffsets(), Blast_HSPListPurgeHSPsWithCommonEndpoints(), Blast_HSPListsMerge(), Blast_HSPReevaluateWithAmbiguitiesGapped(), Blast_HSPReevaluateWithAmbiguitiesUngapped(), Blast_HSPUpdateWithTraceback(), BLAST_SetupPartialFetching(), Blast_TracebackFromHSPList(), BlastGetOffsetsForGappedAlignment(), BlastGetStartForGappedAlignmentNucl(), BlastHitList2SeqAlign_OMF(), BlastHSPStreamMerge(), BlastIntervalTreeAddHSP(), BlastIntervalTreeContainsHSP(), BlastIntervalTreeMasksHSP(), BlastIntervalTreeNumRedundant(), BlastNaExtendJumper(), BOOST_AUTO_TEST_CASE(), checkReevaluateResultsGapped(), checkReevaluateResultsUngappedNucl(), checkReevaluateResultsUngappedTransl(), DoAnchoredSearch(), JumperFindSpliceSignals(), MakeSplicedSeg(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), s_AdjustNegativeSubjFrameInBlastn(), s_AdjustSubjectForSraSearch(), s_AdjustSubjectForTranslatedSraSearch(), s_Blast_HSPGetNumIdentitiesAndPositives(), s_Blast_HSPGetOOFNumIdentitiesAndPositives(), s_BLAST_OneSubjectResults2CSeqAlign(), s_BlastEvenGapLinkHSPs(), s_BlastHSPCopy(), s_BlastHSPListRPSUpdate(), s_BlastHSPMapperSplicedPairedRun(), s_BlastMergeTwoHSPs(), s_CollectSeqAlignData(), s_CompareHSPsByContextSubjectOffset(), s_ComputeBtopAndIdentity(), s_ComputeChainScore(), s_CutOffGapEditScript(), s_DominateTest(), s_ExtendAlignment(), s_FindBestPairs(), s_FindBestPath(), s_FindFragmentStart(), s_FindSpliceJunctions(), s_FindSpliceJunctionsForGap(), s_FindSpliceJunctionsForOverlaps(), s_FwdCompareHSPs(), s_FwdCompareHSPsTransl(), s_FwdCompareLinkedHSPSets(), s_GetHSPList(), s_GetTraceback(), s_HitlistReapContained(), s_HSPChainListInsertOne(), s_HSPChainListInsertOne_OLD(), s_HSPEndDiag(), s_HSPIsContained(), s_HSPsHaveCommonEndpoint(), s_HSPStartDiag(), s_IntronToGap(), s_LinkedHSPSetsAdmissible(), s_MergeHSPs(), s_MidpointTreeContainsHSP(), s_MidpointTreeHasHSPEndpoint(), s_OOFBlastHSP2SeqAlign(), s_PHITracebackFromHSPList(), s_QueryEndCompareHSPs(), s_QueryOffsetCompareHSPs(), s_RedoOneAlignment(), s_ResultHspToDistinctAlign(), s_RevCompareHSPs(), s_RevCompareHSPsTbn(), s_RevCompareHSPsTbx(), s_RevCompareHSPsTransl(), s_SaveSubjectOverhangs(), s_SetupHSPForGappedReevaluateTest(), s_SetupHSPForUngappedReevaluateNucl(), s_SetupHSPListBlastn(), s_SetupHSPListForUngappedReevaluateTransl(), s_SetupHSPListTransl(), s_TestChains(), s_TestCutoffs(), s_TestHSPRanges(), s_TrimChainEndToSubjPos(), s_TrimChainStartToSubjPos(), s_TrimHSP(), s_TrimOverlap(), s_UpdateReevaluatedHSP(), ScoreCompareHSPs(), setupHSPList(), LinkHspTestFixture::setupHSPListForMiddleInsertTest(), LinkHspTestFixture::setupHSPListNucl(), LinkHspTestFixture::setupHSPListTransl(), CTracebackSearchTestFixture::x_GetSampleHspStream(), CTracebackSearchTestFixture::x_GetSelfHitHspStream(), x_NonTranslatedHSPToStdSeg(), x_UngappedHSPToDenseDiag(), and x_UngappedHSPToStdSeg().


The documentation for this struct was generated from the following file:
Modified on Tue Jun 18 13:33:14 2024 by modify_doxy.py rev. 669887