NCBI C++ ToolKit
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BlastHSPList Struct Reference

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The structure to hold all HSPs for a given sequence after the gapped alignment. More...

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

+ Collaboration diagram for BlastHSPList:

Public Attributes

Int4 oid
 The ordinal id of the subject sequence this HSP list is for. More...
 
Int4 query_index
 Index of the query which this HSPList corresponds to. More...
 
BlastHSP ** hsp_array
 Array of pointers to individual HSPs. More...
 
Int4 hspcnt
 Number of HSPs saved. More...
 
Int4 allocated
 The allocated size of the hsp_array. More...
 
Int4 hsp_max
 The maximal number of HSPs allowed to be saved. More...
 
Boolean do_not_reallocate
 Is reallocation of the hsp_array allowed? More...
 
double best_evalue
 Smallest e-value for HSPs in this list. More...
 

Detailed Description

The structure to hold all HSPs for a given sequence after the gapped alignment.

Definition at line 153 of file blast_hits.h.

Member Data Documentation

◆ allocated

Int4 BlastHSPList::allocated

◆ best_evalue

double BlastHSPList::best_evalue

◆ do_not_reallocate

Boolean BlastHSPList::do_not_reallocate

◆ hsp_array

BlastHSP** BlastHSPList::hsp_array

Array of pointers to individual HSPs.

Definition at line 157 of file blast_hits.h.

Referenced by BLAST_GetGappedScore(), Blast_HitListUpdate(), Blast_HSPListAdjustOddBlastnScores(), Blast_HSPListAdjustOffsets(), Blast_HSPListAppend(), Blast_HSPListFree(), Blast_HSPListGetBitScores(), Blast_HSPListGetEvalues(), Blast_HSPListIsSortedByScore(), Blast_HSPListNew(), Blast_HSPListPHIGetBitScores(), Blast_HSPListPHIGetEvalues(), Blast_HSPListPurgeHSPsWithCommonEndpoints(), Blast_HSPListPurgeNullHSPs(), Blast_HSPListReapByEvalue(), Blast_HSPListReapByQueryCoverage(), Blast_HSPListReapByRawScore(), Blast_HSPListReevaluateUngapped(), Blast_HSPListSaveHSP(), Blast_HSPListsMerge(), Blast_HSPListSortByEvalue(), Blast_HSPListSortByScore(), Blast_HSPListSubjectBestHit(), Blast_HSPResultsApplyMasklevel(), BLAST_LinkHsps(), Blast_RedoAlignmentCore_MT(), BLAST_SetupPartialFetching(), Blast_TracebackFromHSPList(), Blast_TrimHSPListByMaxHsps(), BlastHitList2SeqAlign_OMF(), BlastHSPListDup(), BLASTHspListToSeqAlign(), BlastHSPStreamMerge(), BLASTPrelminSearchHitListToStdSeg(), BLASTUngappedHspListToSeqAlign(), BOOST_AUTO_TEST_CASE(), checkReevaluateResultsUngappedTransl(), PHIBlast_HSPResultsSplit(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), s_AdjustEvaluesForComposition(), s_AdjustNegativeSubjFrameInBlastn(), s_AdjustSubjectForSraSearch(), s_AdjustSubjectForTranslatedSraSearch(), s_Blast_HSPListReapByPrelimEvalue(), s_BLAST_OneSubjectResults2CSeqAlign(), s_BlastCheckBestEvalue(), s_BlastEvenGapLinkHSPs(), s_BlastGetBestEvalue(), s_BlastHitListInsertHSPListInHeap(), s_BlastHSPBestHitRun(), s_BlastHSPBestHitRun_RPS(), s_BlastHSPCollectorRun(), s_BlastHSPCollectorRun_RPS(), s_BlastHSPCullingFinal(), s_BlastHSPCullingPipeRun(), s_BlastHSPCullingRun(), s_BlastHSPListInsertHSPInHeap(), s_BlastHSPListRPSUpdate(), s_BlastHSPListsCombineByScore(), s_BlastHSPMapperSplicedPairedRun(), s_BlastUnevenGapLinkHSPs(), s_ComputeNumIdentities(), s_EvalueCompareHSPLists(), s_FixNumIdent(), s_GetHSPList(), s_HitlistEvaluateAndPurge(), s_HSPListNormalizeScores(), s_HSPListRescaleScores(), s_ImportFromHitlist(), s_PHITracebackFromHSPList(), s_TrimResultsByTotalHSPLimit(), s_TrimResultsByTotalHSPLimitEx(), setupHSPList(), LinkHspTestFixture::setupHSPListForMiddleInsertTest(), LinkHspTestFixture::setupHSPListNucl(), LinkHspTestFixture::setupHSPListTransl(), LinkHspTestFixture::testUnevenGapLinkHsps(), CPhiblastTestFixture::x_CheckSplitResults(), CTracebackSearchTestFixture::x_GetSampleHspStream(), and CTracebackSearchTestFixture::x_GetSelfHitHspStream().

◆ hsp_max

Int4 BlastHSPList::hsp_max

◆ hspcnt

Int4 BlastHSPList::hspcnt

Number of HSPs saved.

Definition at line 158 of file blast_hits.h.

Referenced by BLAST_ComputeTraceback_MT(), BLAST_GetGappedScore(), BLAST_GetUngappedHSPList(), Blast_HSPList_IsEmpty(), Blast_HSPListAdjustOddBlastnScores(), Blast_HSPListAdjustOffsets(), Blast_HSPListAppend(), Blast_HSPListFree(), Blast_HSPListGetBitScores(), Blast_HSPListGetEvalues(), Blast_HSPListIsSortedByScore(), Blast_HSPListPHIGetBitScores(), Blast_HSPListPHIGetEvalues(), Blast_HSPListPurgeHSPsWithCommonEndpoints(), Blast_HSPListPurgeNullHSPs(), Blast_HSPListReapByEvalue(), Blast_HSPListReapByQueryCoverage(), Blast_HSPListReapByRawScore(), Blast_HSPListReevaluateUngapped(), Blast_HSPListSaveHSP(), Blast_HSPListsMerge(), Blast_HSPListSortByEvalue(), Blast_HSPListSortByScore(), Blast_HSPListSubjectBestHit(), Blast_HSPResultsApplyMasklevel(), Blast_HSPResultsInsertHSPList(), BLAST_LinkHsps(), BLAST_PreliminarySearchEngine(), Blast_RedoAlignmentCore_MT(), BLAST_SetupPartialFetching(), Blast_TracebackFromHSPList(), Blast_TrimHSPListByMaxHsps(), BlastHitList2SeqAlign_OMF(), BlastHSPListDup(), BLASTHspListToSeqAlign(), BlastHSPStreamMerge(), BLASTPrelminSearchHitListToStdSeg(), BLASTUngappedHspListToSeqAlign(), BOOST_AUTO_TEST_CASE(), PHIBlast_HSPResultsSplit(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), s_AdjustEvaluesForComposition(), s_AdjustNegativeSubjFrameInBlastn(), s_AdjustSubjectForSraSearch(), s_AdjustSubjectForTranslatedSraSearch(), s_Blast_HSPListReapByPrelimEvalue(), s_BLAST_OneSubjectResults2CSeqAlign(), s_BlastCheckBestEvalue(), s_BlastEvenGapLinkHSPs(), s_BlastGetBestEvalue(), s_BlastHitListPurge(), s_BlastHSPBestHitRun(), s_BlastHSPBestHitRun_RPS(), s_BlastHSPCollectorRun(), s_BlastHSPCollectorRun_RPS(), s_BlastHSPCullingFinal(), s_BlastHSPCullingRun(), s_BlastHSPListInsertHSPInHeap(), s_BlastHSPListRPSUpdate(), s_BlastHSPListsCombineByScore(), s_BlastHSPMapperSplicedPairedRun(), s_BlastSearchEngineCore(), s_BlastSearchEngineOneContext(), s_BlastUnevenGapLinkHSPs(), s_CompareHsplistHspcnt(), s_ComputeNumIdentities(), s_EvalueCompareHSPLists(), s_FilterBlastResults(), s_FixNumIdent(), s_GetHSPList(), s_HitlistEvaluateAndPurge(), s_HSPListNormalizeScores(), s_HSPListRescaleScores(), s_ImportFromHitlist(), s_PHITracebackFromHSPList(), s_RPSComputeTraceback(), s_RPSPreliminarySearchEngine(), s_TrimResultsByTotalHSPLimit(), s_TrimResultsByTotalHSPLimitEx(), setupHSPList(), LinkHspTestFixture::setupHSPListForMiddleInsertTest(), LinkHspTestFixture::setupHSPListNucl(), LinkHspTestFixture::setupHSPListTransl(), testHSPStream(), LinkHspTestFixture::testUnevenGapLinkHsps(), CPhiblastTestFixture::x_CheckSplitResults(), CTracebackSearchTestFixture::x_GetSampleHspStream(), and CTracebackSearchTestFixture::x_GetSelfHitHspStream().

◆ oid

Int4 BlastHSPList::oid

◆ query_index

Int4 BlastHSPList::query_index

The documentation for this struct was generated from the following file:
Modified on Wed Feb 28 07:11:34 2024 by modify_doxy.py rev. 669887