Search Toolkit Book for BlastContextInfo

The context related information. More...

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

Public Attributes
Int4	query_offset
	Offset of this query, strand or frame in the concatenated super-query. More...

Int4	query_length
	Length of this query, strand or frame. More...

Int8	eff_searchsp
	Effective search space for this context. More...

Int4	length_adjustment
	Length adjustment for boundary conditions. More...

Int4	query_index
	Index of query (same for all frames) More...

Int1	frame
	Frame number (-1, -2, -3, 0, 1, 2, or 3) More...

Boolean	is_valid
	Determine if this context is valid or not. More...

Int4	segment_flags
	Flags describing segments for paired reads. More...

Detailed Description

The context related information.

Definition at line 60 of file blast_query_info.h.

Member Data Documentation

◆ eff_searchsp

Int8 BlastContextInfo::eff_searchsp

Effective search space for this context.

Definition at line 64 of file blast_query_info.h.

Referenced by BLAST_CalcEffLengths(), Blast_HSPListGetEvalues(), BlastHitSavingParametersUpdate(), BlastQueryInfoGetEffSearchSpace(), BlastQueryInfoSetEffSearchSpace(), BOOST_AUTO_TEST_CASE(), CBlastQueryInfo::DebugDump(), CEffectiveSearchSpaceCalculator::GetEffSearchSpaceForContext(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), s_AdjustEvaluesForComposition(), s_BlastEvenGapLinkHSPs(), s_FillSearchSpace(), s_GetEstimatedPhiExpect(), s_GetQueryInfo(), s_SetupQueryInfoForReevaluateTest(), s_SumHSPEvalue(), and CSplitQueryTestFixture::x_ValidateQueryInfoForChunk().

◆ frame

Int1 BlastContextInfo::frame

◆ is_valid

Boolean BlastContextInfo::is_valid

Determine if this context is valid or not.

This field should be set only by the setup code and read by subsequent stages of the BLAST search

Definition at line 68 of file blast_query_info.h.

Referenced by BLAST_CalcEffLengths(), BLAST_ComplementMaskLocations(), Blast_ScoreBlkKbpGappedCalc(), Blast_ScoreBlkKbpUngappedCalc(), BLAST_SmithWatermanGetGappedScore(), BlastHitSavingParametersUpdate(), BlastInitialWordParametersNew(), BlastInitialWordParametersUpdate(), BlastQueryInfoNew(), BlastSetUp_MaskQuery(), BlastSetup_Validate(), BOOST_AUTO_TEST_CASE(), CBlastQueryInfo::DebugDump(), ILocalQueryData::IsValidQuery(), MakeSomeInvalidKBP(), MakeSomeValidKBP(), printBlastHitSavingParameters(), printBlastInitialWordParamters(), s_BlastFindSmallestLambda(), s_BlastFindValidKarlinBlk(), s_FillScoreBlkWithBadKbp(), s_GetAlignParams(), s_GetFilteringLocationsForOneContext(), s_InvalidateQueryContexts(), s_JumperScoreBlkFill(), s_QueryInfo_SetContext(), s_SetupQueryInfoForReevaluateTest(), TestFixture::SetUpQuery(), NuclWordFinderTextFixture::setupSequences(), and CSplitQueryTestFixture::x_ValidateQueryInfoForChunk().

◆ length_adjustment

Int4 BlastContextInfo::length_adjustment

Length adjustment for boundary conditions.

Definition at line 65 of file blast_query_info.h.

Referenced by BLAST_CalcEffLengths(), Blast_SetPHIPatternInfo(), BOOST_AUTO_TEST_CASE(), CBlastQueryInfo::DebugDump(), PhiBlastGetEffectiveNumberOfPatterns(), s_AdjustEvaluesForComposition(), s_BlastEvenGapLinkHSPs(), and s_SumHSPEvalue().

◆ query_index

Int4 BlastContextInfo::query_index

Index of query (same for all frames)

Definition at line 66 of file blast_query_info.h.

Referenced by Blast_Message2TSearchMessages(), BlastQueryInfoNew(), CBlastQueryInfo::DebugDump(), ILocalQueryData::IsValidQuery(), s_InvalidateQueryContexts(), s_RestrictSeqLocs_Multiframe(), and CSplitQueryTestFixture::x_ValidateQueryInfoForChunk().

◆ query_length

Int4 BlastContextInfo::query_length

Length of this query, strand or frame.

Definition at line 63 of file blast_query_info.h.

Referenced by BLAST_CalcEffLengths(), BLAST_ComplementMaskLocations(), BLAST_CreateMixedFrameDNATranslation(), BLAST_GetGappedScore(), Blast_GetOneQueryStructs(), Blast_HSPListGetEvalues(), Blast_HSPListReapByQueryCoverage(), Blast_HSPListSubjectBestHit(), Blast_ScoreBlkKbpUngappedCalc(), BLAST_SmithWatermanGetGappedScore(), Blast_TracebackFromHSPList(), BlastHitSavingParametersUpdate(), BlastInitialWordParametersNew(), BlastInitialWordParametersUpdate(), BlastIntervalTreeAddHSP(), BlastIntervalTreeMasksHSP(), BlastMaskLocDNAToProtein(), BlastNaExtendJumper(), BlastQueryInfoGetQueryLength(), BlastSetUp_MaskQuery(), BOOST_AUTO_TEST_CASE(), CalculateLinkHSPCutoffs(), TestUtil::CreateProtQueryInfo(), CBlastQueryInfo::DebugDump(), DoAnchoredSearch(), FindPartialyCoveredQueries(), JumperGoodAlign(), QueryInfo_GetSeqBufLen(), CDeltaBlast::Run(), s_AdjustEvaluesForComposition(), s_BlastEvenGapLinkHSPs(), s_BlastHSPCullingRun(), s_BlastHSPMapperSplicedPairedRun(), s_BlastSmallNaExtend(), s_BlastSmallNaExtendAlignedOneByte(), s_CalculateMaxLength(), s_ChainingAlignment(), s_FillSearchSpace(), s_Finalize(), s_FindAdapters(), s_FindPolyATails(), s_FindSpliceJunctions(), s_GetFilteringLocationsForOneContext(), s_GetInitialWordParameters(), s_GetQueryInfo(), s_GetTranslatedQueryDNALength(), s_QueryInfo_SetContext(), s_SetUpLocalBlastSequenceBlk(), s_SetupQueryInfoForReevaluateTest(), s_SumHSPEvalue(), s_TypeOfWord(), LinkHspTestFixture::setupCutoffScores(), SetupQueries_OMF(), TestFixture::SetUpQuery(), NuclWordFinderTextFixture::setupSequences(), ShortRead_IndexedWordFinder(), CMagicBlast::x_BuildResultSet(), CQuerySplitter::x_ComputeContextOffsets_NonTranslatedQueries(), CQuerySplitter::x_ComputeContextOffsets_TranslatedQueries(), CPssmEngine::x_InitializeQueryInfo(), CSplitQueryTestFixture::x_TestCContextTranslator(), CSequenceDataTester::x_TestLocalStrand(), CSequenceDataTester::x_TestSingleProtein_Local(), and CSplitQueryTestFixture::x_ValidateQueryInfoForChunk().

◆ query_offset

Int4 BlastContextInfo::query_offset

Offset of this query, strand or frame in the concatenated super-query.

Definition at line 61 of file blast_query_info.h.

Referenced by BLAST_ComplementMaskLocations(), BLAST_CreateMixedFrameDNATranslation(), BLAST_GetGappedScore(), Blast_GetOneQueryStructs(), BLAST_GetUngappedHSPList(), Blast_HSPListReevaluateUngapped(), Blast_ScoreBlkKbpUngappedCalc(), BLAST_SmithWatermanGetGappedScore(), Blast_TracebackFromHSPList(), BlastHitSavingParametersUpdate(), BlastInitialWordParametersNew(), BlastNaExtendJumper(), BlastSetUp_MaskQuery(), BOOST_AUTO_TEST_CASE(), CalculateLinkHSPCutoffs(), CBlastQueryInfo::DebugDump(), DoAnchoredSearch(), QueryInfo_GetSeqBufLen(), CDeltaBlast::Run(), s_BlastAaWordFinder_TwoHit(), s_BlastSmallNaExtend(), s_BlastSmallNaExtendAlignedOneByte(), s_ChainingAlignment(), s_ComputeNumIdentities(), s_FindAdapters(), s_FindPolyATails(), s_FindSpliceJunctions(), s_GetFilteringLocationsForOneContext(), s_GetQueryInfo(), s_GetQueryStrandOffset(), s_QueryInfo_SetContext(), s_RPSComputeTraceback(), s_SetUpLocalBlastSequenceBlk(), s_TranslateHSPsToDNAPCoord(), s_TrimChainEndToSubjPos(), s_TrimChainStartToSubjPos(), s_TypeOfWord(), SetupQueries_OMF(), TestFixture::SetUpQuery(), NuclWordFinderTextFixture::setupSequences(), ShortRead_IndexedWordFinder(), CQuerySplitter::x_ComputeContextOffsets_NonTranslatedQueries(), CQuerySplitter::x_ComputeContextOffsets_TranslatedQueries(), CPssmEngine::x_InitializeQueryInfo(), CSplitQueryTestFixture::x_TestCContextTranslator(), CSequenceDataTester::x_TestLocalStrand(), CSequenceDataTester::x_TestSingleProtein_Local(), and CSplitQueryTestFixture::x_ValidateQueryInfoForChunk().

◆ segment_flags

Int4 BlastContextInfo::segment_flags

Flags describing segments for paired reads.

Definition at line 72 of file blast_query_info.h.

Referenced by BlastQueryInfoNew(), PrintSAM(), s_BlastHSPMapperSplicedPairedRun(), s_CreateSeqAlign(), s_FindRearrangedPairs(), SetupQueryInfo_OMF(), and CMagicBlast::x_BuildResultSet().

The documentation for this struct was generated from the following file:

include/algo/blast/core/blast_query_info.h

Public Attributes