One sequence segment within an HSP. More...

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

Public Attributes
Int2	frame
	Translation frame. More...

Int4	offset
	Start of hsp. More...

Int4	end
	End of hsp. More...

Int4	gapped_start
	Where the gapped extension started. More...

Detailed Description

One sequence segment within an HSP.

Definition at line 96 of file blast_hits.h.

Member Data Documentation

◆ end

Int4 BlastSeg::end

End of hsp.

Definition at line 99 of file blast_hits.h.

Referenced by BLAST_GetGappedScore(), Blast_HSPAdjustSubjectOffset(), Blast_HSPCalcLengthAndGaps(), Blast_HSPGetAdjustedOffsets(), Blast_HSPGetPartialSubjectTranslation(), Blast_HSPGetQueryCoverage(), Blast_HSPGetTargetTranslation(), Blast_HSPInit(), Blast_HSPListAdjustOffsets(), Blast_HSPListPurgeHSPsWithCommonEndpoints(), Blast_HSPListsMerge(), Blast_HSPListSubjectBestHit(), Blast_HSPReevaluateWithAmbiguitiesUngapped(), Blast_HSPUpdateWithTraceback(), BLAST_SetupPartialFetching(), BlastGetOffsetsForGappedAlignment(), BlastGetStartForGappedAlignmentNucl(), BlastHitList2SeqAlign_OMF(), 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_OneSubjectResults2CSeqAlign(), s_BlastEvenGapLinkHSPs(), s_BlastHSPBestHitRun(), s_BlastHSPBestHitRun_RPS(), s_BlastHSPCopy(), s_BlastMergeTwoHSPs(), s_BlastSegGetTranslatedOffsets(), s_BlastUnevenGapLinkHSPs(), s_CompareHSPsByContextSubjectOffset(), s_ComputeAlignmentScore(), s_ComputeBtopAndIdentity(), s_CutOffGapEditScript(), s_ExtendAlignment(), s_FindAdapters(), s_FindBestPairs(), s_FindBestPath(), s_FindFragmentStart(), s_FindPolyATails(), s_FindSpliceJunctions(), s_FindSpliceJunctionsForGap(), s_FindSpliceJunctionsForOverlaps(), s_GetHSPList(), s_HitlistReapContained(), s_HSPEndDiag(), s_HSPIsContained(), s_HSPOffsetEndBinarySearch(), s_HSPQueryRangeIsContained(), s_HSPQueryRangeIsMasklevelContained(), s_HSPsHaveCommonEndpoint(), s_ImportFromHitlist(), s_IntervalTreeHasHSPEndpoint(), s_IntronToGap(), s_LinkedHSPSetArrayIndexQueryEnds(), s_LinkedHSPSetsAdmissible(), s_MergeHSPs(), s_MidpointTreeContainsHSP(), s_MidpointTreeHasHSPEndpoint(), s_QueryEndCompareHSPs(), s_QueryOffsetCompareHSPs(), s_ResultHspToDistinctAlign(), s_RevCompareHSPsTbn(), s_RevCompareHSPsTbx(), 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().

◆ frame

Int2 BlastSeg::frame

Translation frame.

Definition at line 97 of file blast_hits.h.

Referenced by BLAST_GetGappedScore(), Blast_HSPGetAdjustedOffsets(), Blast_HSPGetPartialSubjectTranslation(), Blast_HSPGetTargetTranslation(), Blast_HSPInit(), Blast_HSPListsMerge(), Blast_HSPListSubjectBestHit(), BLAST_SetupPartialFetching(), Blast_TracebackFromHSPList(), BlastHSPStreamMerge(), BOOST_AUTO_TEST_CASE(), MakeSplicedSeg(), s_AdjustNegativeSubjFrameInBlastn(), s_AdjustSubjectForTranslatedSraSearch(), s_BlastHSPCopy(), s_BlastMergeTwoHSPs(), s_BlastSegGetTranslatedOffsets(), s_CollectSeqAlignData(), s_FindAdapters(), s_FindBestPairs(), s_FindFragmentStart(), s_FindPolyATails(), s_FindRearrangedPairs(), s_GetHSPList(), s_GetTraceback(), s_HitlistReapContained(), s_HSPChainListInsertOne(), s_HSPChainListInsertOne_OLD(), s_HSPIsContained(), s_HSPsHaveCommonEndpoint(), s_LinkedHSPSetsAdmissible(), s_OOFBlastHSP2SeqAlign(), s_ResultHspToDistinctAlign(), s_RevCompareHSPsTbn(), s_RevCompareHSPsTbx(), s_SetAdapter(), s_SetPolyATail(), s_SetupHSPListBlastn(), s_SetupHSPListForUngappedReevaluateTransl(), s_SetupHSPListTransl(), LinkHspTestFixture::setupHSPListForMiddleInsertTest(), LinkHspTestFixture::setupHSPListNucl(), LinkHspTestFixture::setupHSPListTransl(), x_NonTranslatedHSPToStdSeg(), x_UngappedHSPToDenseDiag(), and x_UngappedHSPToStdSeg().

◆ gapped_start

Int4 BlastSeg::gapped_start

Where the gapped extension started.

Definition at line 100 of file blast_hits.h.

Referenced by Blast_HSPAdjustSubjectOffset(), Blast_HSPGetPartialSubjectTranslation(), Blast_HSPInit(), Blast_HSPListAdjustOffsets(), Blast_TracebackFromHSPList(), BlastGetStartForGappedAlignmentNucl(), BlastHSPStreamMerge(), BOOST_AUTO_TEST_CASE(), s_AdjustSubjectForSraSearch(), s_AdjustSubjectForTranslatedSraSearch(), s_BlastHSPCopy(), s_BlastMergeTwoHSPs(), s_GetHSPList(), s_PHITracebackFromHSPList(), s_RedoOneAlignment(), CTracebackSearchTestFixture::x_GetSampleHspStream(), and CTracebackSearchTestFixture::x_GetSelfHitHspStream().

◆ offset

Int4 BlastSeg::offset

Start of hsp.

Definition at line 98 of file blast_hits.h.

Referenced by BLAST_GetGappedScore(), Blast_HSPAdjustSubjectOffset(), Blast_HSPCalcLengthAndGaps(), Blast_HSPGetAdjustedOffsets(), Blast_HSPGetPartialSubjectTranslation(), Blast_HSPGetQueryCoverage(), Blast_HSPGetTargetTranslation(), Blast_HSPInit(), Blast_HSPListAdjustOffsets(), Blast_HSPListPurgeHSPsWithCommonEndpoints(), Blast_HSPListsMerge(), Blast_HSPListSubjectBestHit(), 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(), FindPartialyCoveredQueries(), JumperFindSpliceSignals(), MakeSplicedSeg(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), s_AdjustSubjectForSraSearch(), s_AdjustSubjectForTranslatedSraSearch(), s_Blast_HSPGetNumIdentitiesAndPositives(), s_Blast_HSPGetOOFNumIdentitiesAndPositives(), s_BLAST_OneSubjectResults2CSeqAlign(), s_BlastEvenGapLinkHSPs(), s_BlastHSPBestHitRun(), s_BlastHSPBestHitRun_RPS(), s_BlastHSPCopy(), s_BlastHSPMapperSplicedPairedRun(), s_BlastMergeTwoHSPs(), s_BlastSegGetTranslatedOffsets(), s_BlastUnevenGapLinkHSPs(), s_CollectSeqAlignData(), s_CompareHSPsByContextSubjectOffset(), s_ComputeAlignmentScore(), s_ComputeBtopAndIdentity(), s_ComputeChainScore(), s_CutOffGapEditScript(), s_DominateTest(), s_ExtendAlignment(), s_FindAdapters(), s_FindBestPath(), s_FindFragmentStart(), s_FindPolyATails(), s_FindSpliceJunctions(), s_FindSpliceJunctionsForGap(), s_FindSpliceJunctionsForOverlaps(), s_FwdCompareHSPs(), s_FwdCompareHSPsTransl(), s_FwdCompareLinkedHSPSets(), s_GetHSPList(), s_GetOverlapCost(), s_HitlistReapContained(), s_HSPChainListInsertOne(), s_HSPChainListInsertOne_OLD(), s_HSPIsContained(), s_HSPOffsetBinarySearch(), s_HSPQueryRangeIsContained(), s_HSPQueryRangeIsMasklevelContained(), s_HSPsHaveCommonEndpoint(), s_HSPStartDiag(), s_ImportFromHitlist(), s_IntervalTreeHasHSPEndpoint(), s_IntronToGap(), s_LinkedHSPSetsAdmissible(), s_MergeHSPs(), s_MergeLinkedHSPSets(), s_MidpointTreeContainsHSP(), s_MidpointTreeHasHSPEndpoint(), s_OOFBlastHSP2SeqAlign(), s_QueryEndCompareHSPs(), s_QueryOffsetCompareHSPs(), s_RemoveOverlaps(), s_ResultHspToDistinctAlign(), s_RevCompareHSPs(), s_RevCompareHSPsTbn(), s_RevCompareHSPsTbx(), s_RevCompareHSPsTransl(), s_SaveSubjectOverhangs(), s_SetAdapter(), 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: