Search Toolkit Book for BlastHSPList
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 |
The allocated size of the hsp_array.
Definition at line 159 of file blast_hits.h.
Referenced by Blast_HSPListAppend(), Blast_HSPListNew(), Blast_HSPListSaveHSP(), Blast_HSPListsMerge(), Blast_TracebackFromHSPList(), BOOST_AUTO_TEST_CASE(), s_BlastHSPCullingFinal(), s_BlastHSPListsCombineByScore(), s_GetHSPList(), CTracebackSearchTestFixture::x_GetSampleHspStream(), and CTracebackSearchTestFixture::x_GetSelfHitHspStream().
◆ best_evalue
| double BlastHSPList::best_evalue |
Smallest e-value for HSPs in this list.
Filled after e-values are calculated. Necessary because HSPs are sorted by score, but highest scoring HSP may not have the lowest e-value if sum statistics is used.
Definition at line 162 of file blast_hits.h.
Referenced by Blast_HitListUpdate(), Blast_HSPListGetEvalues(), Blast_HSPListPHIGetEvalues(), Blast_HSPListReapByQueryCoverage(), Blast_HSPResultsApplyMasklevel(), BLAST_LinkHsps(), Blast_RedoAlignmentCore_MT(), BlastHSPCBSStreamClose(), BOOST_AUTO_TEST_CASE(), s_AdjustEvaluesForComposition(), s_BlastCheckBestEvalue(), s_BlastHitListInsertHSPListInHeap(), s_BlastHSPCullingFinal(), s_BlastHSPCullingPipeRun(), s_EvalueCompareHSPLists(), s_HitlistEvaluateAndPurge(), and CPhiblastTestFixture::x_CheckIncreasingBestEvalues().
◆ do_not_reallocate
| Boolean BlastHSPList::do_not_reallocate |
Is reallocation of the hsp_array allowed?
Definition at line 161 of file blast_hits.h.
Referenced by Blast_HSPListAppend(), Blast_HSPListSaveHSP(), Blast_HSPListsMerge(), BOOST_AUTO_TEST_CASE(), s_GetHSPList(), CTracebackSearchTestFixture::x_GetSampleHspStream(), and CTracebackSearchTestFixture::x_GetSelfHitHspStream().
◆ 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 |
The maximal number of HSPs allowed to be saved.
Definition at line 160 of file blast_hits.h.
Referenced by Blast_HitListMerge(), Blast_HSPListNew(), Blast_HSPListSaveHSP(), BOOST_AUTO_TEST_CASE(), s_GetHSPList(), CTracebackSearchTestFixture::x_GetSampleHspStream(), and CTracebackSearchTestFixture::x_GetSelfHitHspStream().
◆ 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 |
The ordinal id of the subject sequence this HSP list is for.
Definition at line 154 of file blast_hits.h.
Referenced by BLAST_ComputeTraceback_MT(), Blast_HitListMerge(), Blast_RedoAlignmentCore_MT(), BLAST_SetupPartialFetching(), BlastHitList2SeqAlign_OMF(), BlastHSPStreamBatchRead(), BlastHSPStreamMerge(), BLASTPrelminSearchHitListToStdSeg(), BOOST_AUTO_TEST_CASE(), DoAnchoredSearch(), PHIBlast_HSPResultsSplit(), s_BLAST_OneSubjectResults2CSeqAlign(), s_BlastHSPBestHitRun(), s_BlastHSPCollectorRun(), s_BlastHSPCollectorRun_RPS(), s_BlastHSPCullingFinal(), s_BlastHSPCullingRun(), s_BlastHSPMapperSplicedPairedRun(), s_BlastHSPStreamCountNumOids(), s_BlastSearchEngineOneContext(), s_ComputeNumIdentities(), s_EvalueCompareHSPLists(), s_ExportToHitlist(), s_GetHSPList(), s_HSPListFromDistinctAlignments(), s_ImportFromHitlist(), s_RPSComputeTraceback(), s_SortHSPListByOid(), s_TrimResultsByTotalHSPLimitEx(), setupHSPList(), testHSPStream(), CPhiblastTestFixture::x_CheckSplitResults(), CTracebackSearchTestFixture::x_GetSampleHspStream(), CTracebackSearchTestFixture::x_GetSelfHitHspStream(), and CPhiblastTestFixture::x_SetupHSPList().
◆ query_index
| Int4 BlastHSPList::query_index |
Index of the query which this HSPList corresponds to.
Set to 0 if not applicable
Definition at line 155 of file blast_hits.h.
Referenced by Blast_HSPResultsInsertHSPList(), Blast_RedoAlignmentCore_MT(), Blast_TracebackFromHSPList(), BlastHSPStreamClose(), BlastHSPStreamMerge(), BlastHSPStreamRead(), s_BlastHSPBestHitRun_RPS(), s_BlastHSPCollectorRun_RPS(), s_BlastHSPCullingFinal(), s_ExportToHitlist(), s_RPSComputeTraceback(), s_RPSPreliminarySearchEngine(), and s_TrimResultsByTotalHSPLimitEx().
The documentation for this struct was generated from the following file:
- include/algo/blast/core/blast_hits.h
