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... | |
| GapEditScript * | gap_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... | |
| SPHIHspInfo * | pat_info |
| In PHI BLAST, information about this pattern match. More... | |
| Int4 | num_positives |
| BlastHSPMappingInfo * | map_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 |
Bit score, calculated from score.
Definition at line 129 of file blast_hits.h.
Referenced by Blast_HSPClone(), Blast_HSPListGetBitScores(), Blast_HSPListPHIGetBitScores(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), s_BlastHSPCopy(), s_BuildScoreList(), s_CalculateScoreVectorSize(), and s_HSPListNormalizeScores().
◆ 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 |
Context number of query.
Definition at line 133 of file blast_hits.h.
Referenced by BLAST_GetGappedScore(), Blast_HSPClone(), Blast_HSPInit(), Blast_HSPListGetBitScores(), Blast_HSPListGetEvalues(), Blast_HSPListReapByQueryCoverage(), Blast_HSPListReevaluateUngapped(), Blast_HSPListsMerge(), Blast_HSPListSubjectBestHit(), Blast_HSPReevaluateWithAmbiguitiesGapped(), Blast_HSPReevaluateWithAmbiguitiesUngapped(), Blast_TracebackFromHSPList(), BlastHSPStreamMerge(), BlastIntervalTreeAddHSP(), BlastIntervalTreeContainsHSP(), BlastIntervalTreeMasksHSP(), BlastIntervalTreeNumRedundant(), BOOST_AUTO_TEST_CASE(), DoAnchoredSearch(), FindPartialyCoveredQueries(), s_BlastEvenGapLinkHSPs(), s_BlastHSPBestHitRun(), s_BlastHSPBestHitRun_RPS(), s_BlastHSPCollectorRun(), s_BlastHSPCollectorRun_RPS(), s_BlastHSPCopy(), s_BlastHSPListRPSUpdate(), s_BlastHSPMapperSplicedPairedRun(), s_CompareHSPsByContextScore(), s_CompareHSPsByContextSubjectOffset(), s_ComputeNumIdentities(), s_FindSpliceJunctions(), s_FwdCompareHSPs(), s_FwdCompareHSPsTransl(), s_GetHSPList(), s_GetTraceback(), s_HSPQueryRangeIsMasklevelContained(), s_ImportFromHitlist(), s_LinkedHSPSetArraySetUp(), s_QueryEndCompareHSPs(), s_QueryOffsetCompareHSPs(), s_ResultHspToDistinctAlign(), s_RevCompareHSPs(), s_RevCompareHSPsTbn(), s_RevCompareHSPsTbx(), s_RevCompareHSPsTransl(), s_ScoreCompareHSPWithContext(), s_SumHSPEvalue(), s_TestChains(), setupHSPList(), and LinkHspTestFixture::setupHSPListNucl().
◆ evalue
| double BlastHSP::evalue |
This HSP's e-value.
Definition at line 130 of file blast_hits.h.
Referenced by Blast_HSPClone(), Blast_HSPListGetEvalues(), Blast_HSPListReapByEvalue(), Blast_HSPResultsApplyMasklevel(), BLAST_LinkHsps(), BlastNaExtendJumper(), BOOST_AUTO_TEST_CASE(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), s_AdjustEvaluesForComposition(), s_Blast_HSPListReapByPrelimEvalue(), s_BlastCheckBestEvalue(), s_BlastEvenGapLinkHSPs(), s_BlastGetBestEvalue(), s_BlastHSPBestHitRun(), s_BlastHSPBestHitRun_RPS(), s_BlastHSPCopy(), s_BlastHSPCullingFinal(), s_BlastHSPCullingPipeRun(), s_BlastUnevenGapLinkHSPs(), s_BuildScoreList(), s_CalculateScoreVectorSize(), s_CombineLinkedHSPSets(), s_CreateHSP(), s_CreateHSPForWordHit(), s_EvalueCompareHSPs(), s_HSPPHIGetEvalue(), CRedoAlignmentTestFixture::setUpHSPList(), ShortRead_IndexedWordFinder(), and CPhiblastTestFixture::x_SetupHSPList().
◆ gap_info
| GapEditScript* BlastHSP::gap_info |
ALL gapped alignment is here.
Definition at line 134 of file blast_hits.h.
Referenced by Blast_HSPCalcLengthAndGaps(), Blast_HSPClone(), Blast_HSPFree(), Blast_HSPGetAdjustedOffsets(), Blast_HSPInit(), Blast_HSPReevaluateWithAmbiguitiesGapped(), Blast_HSPUpdateWithTraceback(), BOOST_AUTO_TEST_CASE(), checkReevaluateResultsGapped(), MakeSplicedSeg(), s_Blast_HSPGetNumIdentitiesAndPositives(), s_Blast_HSPGetOOFNumIdentitiesAndPositives(), s_BlastHSP2SeqAlign(), s_BlastHSPCopy(), s_BlastHSPRPSUpdate(), s_BlastMergeTwoHSPs(), s_CorrectUASequence(), s_CutOffGapEditScript(), s_ExtendAlignment(), s_FindSpliceJunctionsForGap(), s_FindSpliceJunctionsForOverlaps(), s_MergeHSPs(), s_OOFBlastHSP2SeqAlign(), s_SetupHSPForGappedReevaluateTest(), s_TestChains(), s_TestHSPRanges(), s_TrimHSP(), and s_UpdateReevaluatedHSP().
◆ map_info
| BlastHSPMappingInfo* BlastHSP::map_info |
Definition at line 146 of file blast_hits.h.
Referenced by Blast_HSPClone(), Blast_HSPFree(), BlastNaExtendJumper(), JumperFindSpliceSignals(), MakeSplicedSeg(), s_ComputeAlignmentScore(), s_ComputeBtopAndIdentity(), s_ComputeChainScore(), s_CreateHSP(), s_CreateHSPForWordHit(), s_ExtendAlignment(), s_FindSpliceJunctions(), s_FindSpliceJunctionsForGap(), s_FindSpliceJunctionsForOverlaps(), s_GetOverlapCost(), s_IntronToGap(), s_MergeHSPs(), s_SaveSubjectOverhangs(), s_SetAdapter(), s_SetPolyATail(), s_TestHSPRanges(), s_TrimChainEndToSubjPos(), s_TrimChainStartToSubjPos(), s_TrimHSP(), and ShortRead_IndexedWordFinder().
◆ 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 |
Number of identical base pairs in this HSP.
Definition at line 128 of file blast_hits.h.
Referenced by Blast_HSPClone(), Blast_HSPGetNumIdentities(), Blast_HSPGetNumIdentitiesAndPositives(), BLASTHspListToSeqAlign(), BlastNaExtendJumper(), BOOST_AUTO_TEST_CASE(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), s_BlastHSPCopy(), s_BuildScoreList(), s_CalculateScoreVectorSize(), s_ComputeAlignmentScore(), s_CreateHSP(), s_CreateHSPForWordHit(), s_FindSpliceJunctionsForOverlaps(), s_FixNumIdent(), s_HSPListFromDistinctAlignments(), s_HSPTest(), s_TestCutoffs(), CRedoAlignmentTestFixture::setUpHSPList(), and ShortRead_IndexedWordFinder().
◆ num_positives
| Int4 BlastHSP::num_positives |
Definition at line 144 of file blast_hits.h.
Referenced by Blast_HSPClone(), Blast_HSPGetNumIdentitiesAndPositives(), s_BuildScoreList(), and s_CalculateScoreVectorSize().
◆ pat_info
| SPHIHspInfo* BlastHSP::pat_info |
In PHI BLAST, information about this pattern match.
Definition at line 142 of file blast_hits.h.
Referenced by Blast_HSPClone(), Blast_HSPFree(), PHIBlast_HSPResultsSplit(), PHIGetGappedScore(), s_BlastHSPCopy(), s_PHITracebackFromHSPList(), CPhiblastTestFixture::x_CheckSplitResults(), and CPhiblastTestFixture::x_SetupHSPList().
◆ 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_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:
- include/algo/blast/core/blast_hits.h
