Search Toolkit Book for BlastQueryInfo
The query related information. More...
#include <algo/blast/core/blast_query_info.h>
Collaboration diagram for BlastQueryInfo:
Public Attributes | |
| Int4 | first_context |
| Index of the first element of the context array. More... | |
| Int4 | last_context |
| Index of the last element of the context array. More... | |
| int | num_queries |
| Number of query sequences. More... | |
| BlastContextInfo * | contexts |
| Information per context. More... | |
| Uint4 | max_length |
| Length of the longest among the concatenated queries. More... | |
| Uint4 | min_length |
| Length of the shortest among the concatenated queries. More... | |
| struct SPHIQueryInfo * | pattern_info |
| Counts of PHI BLAST pattern occurrences, used in PHI BLAST only. More... | |
Detailed Description
The query related information.
Definition at line 80 of file blast_query_info.h.
Member Data Documentation
◆ contexts
| BlastContextInfo* BlastQueryInfo::contexts |
Information per context.
Definition at line 84 of file blast_query_info.h.
Referenced by BLAST_CalcEffLengths(), BLAST_ComplementMaskLocations(), BLAST_CreateMixedFrameDNATranslation(), BLAST_GetGappedScore(), Blast_GetOneQueryStructs(), BLAST_GetUngappedHSPList(), Blast_HSPListGetEvalues(), Blast_HSPListReapByQueryCoverage(), Blast_HSPListReevaluateUngapped(), Blast_HSPListSubjectBestHit(), Blast_Message2TSearchMessages(), Blast_ScoreBlkKbpGappedCalc(), Blast_ScoreBlkKbpUngappedCalc(), Blast_SetPHIPatternInfo(), BLAST_SmithWatermanGetGappedScore(), Blast_TracebackFromHSPList(), BlastHitSavingParametersUpdate(), BlastInitialWordParametersNew(), BlastInitialWordParametersUpdate(), BlastIntervalTreeAddHSP(), BlastIntervalTreeMasksHSP(), BlastMaskLocDNAToProtein(), BlastNaExtendJumper(), BlastQueryInfoDup(), BlastQueryInfoFree(), BlastQueryInfoGetEffSearchSpace(), BlastQueryInfoGetQueryLength(), BlastQueryInfoNew(), BlastQueryInfoSetEffSearchSpace(), BlastSetUp_MaskQuery(), BlastSetup_Validate(), BOOST_AUTO_TEST_CASE(), CalculateLinkHSPCutoffs(), CBlastAncillaryData::CBlastAncillaryData(), TestUtil::CreateProtQueryInfo(), CBlastQueryInfo::DebugDump(), DoAnchoredSearch(), FindPartialyCoveredQueries(), CEffectiveSearchSpaceCalculator::GetEffSearchSpaceForContext(), ILocalQueryData::IsValidQuery(), MakeSomeInvalidKBP(), MakeSomeValidKBP(), PhiBlastGetEffectiveNumberOfPatterns(), PHIGetGappedScore(), printBlastHitSavingParameters(), printBlastInitialWordParamters(), PrintSAM(), QueryInfo_GetSeqBufLen(), CDeltaBlast::Run(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), s_BlastAaWordFinder_TwoHit(), s_BlastEvenGapLinkHSPs(), s_BlastFindSmallestLambda(), s_BlastFindValidKarlinBlk(), s_BlastHSPBestHitRun(), s_BlastHSPCullingRun(), s_BlastHSPMapperSplicedPairedRun(), s_BlastSmallNaExtend(), s_BlastSmallNaExtendAlignedOneByte(), s_CalculateMaxLength(), s_ChainingAlignment(), s_ComputeNumIdentities(), s_CreateHSP(), s_CreateHSPForWordHit(), s_CreateSeqAlign(), s_FillScoreBlkWithBadKbp(), s_FillSearchSpace(), s_Finalize(), s_FindAdapters(), s_FindPolyATails(), s_FindRearrangedPairs(), s_FindSpliceJunctions(), s_GetAlignParams(), s_GetEstimatedPhiExpect(), s_GetFilteringLocationsForOneContext(), s_GetInitialWordParameters(), s_GetQueryInfo(), s_GetQueryStrandOffset(), s_GetTranslatedQueryDNALength(), s_HitlistEvaluateAndPurge(), s_HSPQueryRangeIsMasklevelContained(), s_ImportFromHitlist(), s_InvalidateQueryContexts(), s_IsPlusStrand(), s_JumperScoreBlkFill(), s_QueryInfo_SetContext(), s_RestrictSeqLocs_Multiframe(), s_RPSComputeTraceback(), s_SetUpLocalBlastSequenceBlk(), s_SetupQueryInfoForReevaluateTest(), s_SumHSPEvalue(), s_TranslateHSPsToDNAPCoord(), s_TrimChainEndToSubjPos(), s_TrimChainStartToSubjPos(), s_TypeOfWord(), LinkHspTestFixture::setupCutoffScores(), SetupQueries_OMF(), TestFixture::SetUpQuery(), SetupQueryInfo_OMF(), 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().
◆ first_context
| Int4 BlastQueryInfo::first_context |
Index of the first element of the context array.
Definition at line 81 of file blast_query_info.h.
Referenced by BLAST_CalcEffLengths(), BLAST_ComplementMaskLocations(), BLAST_GetGappedScore(), Blast_ScoreBlkKbpGappedCalc(), Blast_ScoreBlkKbpUngappedCalc(), BLAST_SmithWatermanGetGappedScore(), Blast_TracebackFromHSPList(), BlastHitSavingParametersUpdate(), BlastInitialWordParametersNew(), BlastInitialWordParametersUpdate(), BlastQueryInfoNew(), BlastSetUp_GetFilteringLocations(), BlastSetUp_MaskQuery(), BlastSetup_Validate(), BOOST_AUTO_TEST_CASE(), CContextTranslator::CContextTranslator(), CBlastQueryInfo::DebugDump(), ILocalQueryData::IsValidQuery(), printBlastHitSavingParameters(), printBlastInitialWordParamters(), s_AdjustFirstContext(), s_BlastFindSmallestLambda(), s_BlastFindValidKarlinBlk(), s_CalculateMaxLength(), s_ChainingAlignment(), s_FillSearchSpace(), s_GetAlignParams(), s_InvalidateQueryContexts(), s_JumperScoreBlkFill(), s_RPSComputeTraceback(), CSequenceDataTester::x_TestSingleProtein_Local(), and CSplitQueryTestFixture::x_ValidateQueryInfoForChunk().
◆ last_context
| Int4 BlastQueryInfo::last_context |
Index of the last element of the context array.
Definition at line 82 of file blast_query_info.h.
Referenced by BLAST_CreateMixedFrameDNATranslation(), BLAST_GetGappedScore(), Blast_GetOneQueryStructs(), Blast_RedoAlignmentCore_MT(), Blast_TracebackFromHSPList(), BlastHitSavingParametersNew(), BlastHitSavingParametersUpdate(), BlastInitialWordParametersNew(), BlastMaskLocDNAToProtein(), BlastMaskLocProteinToDNA(), BlastQueryInfoDup(), BlastQueryInfoNew(), BlastSetUp_GetFilteringLocations(), BlastSetUp_MaskQuery(), BlastSetup_ScoreBlkInit(), BOOST_AUTO_TEST_CASE(), CalculateLinkHSPCutoffs(), CBlastQueryInfo::DebugDump(), JumperNaWordFinder(), MapperWordHitsNew(), QueryInfo_GetSeqBufLen(), s_BlastHSPCullingNew(), s_BlastHSPCullingPipeNew(), s_ChainingAlignment(), s_GetAlignParams(), s_GetQueryInfo(), s_JumperScoreBlkFill(), s_QueryInfo_SetContext(), s_RPSComputeTraceback(), s_SetupQueryInfoForReevaluateTest(), LinkHspTestFixture::setupScoreBlk(), SplitQuery_SetEffectiveSearchSpace(), and CSplitQueryTestFixture::x_ValidateQueryInfoForChunk().
◆ max_length
| Uint4 BlastQueryInfo::max_length |
Length of the longest among the concatenated queries.
Definition at line 85 of file blast_query_info.h.
Referenced by Blast_RedoAlignmentCore_MT(), BOOST_AUTO_TEST_CASE(), TestUtil::CreateProtQueryInfo(), CBlastQueryInfo::DebugDump(), JumperNaWordFinder(), s_BlastSearchEngineOneContext(), s_CalculateMaxLength(), s_GetAlignParams(), s_RPSComputeTraceback(), SetupQueryInfo_OMF(), CPssmEngine::x_InitializeQueryInfo(), and CSplitQueryTestFixture::x_ValidateQueryInfoForChunk().
◆ min_length
| Uint4 BlastQueryInfo::min_length |
Length of the shortest among the concatenated queries.
Definition at line 87 of file blast_query_info.h.
Referenced by BOOST_AUTO_TEST_CASE(), and SetupQueryInfo_OMF().
◆ num_queries
| int BlastQueryInfo::num_queries |
Number of query sequences.
Definition at line 83 of file blast_query_info.h.
Referenced by BLAST_ComputeTraceback_MT(), BLAST_GetGappedScore(), Blast_GetOneQueryStructs(), Blast_Message2TSearchMessages(), Blast_RedoAlignmentCore_MT(), Blast_TracebackFromHSPList(), BlastHitSavingParametersNew(), BlastMaskLocDNAToProtein(), BlastMaskLocProteinToDNA(), BlastQueryInfoNew(), BlastSetUp_GetFilteringLocations(), BOOST_AUTO_TEST_CASE(), CBlastPrelimSearch::ComputeBlastHSPResults(), CBlastQueryInfo::DebugDump(), DoAnchoredSearch(), FindPartialyCoveredQueries(), MapperWordHitsNew(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), s_BlastEvenGapLinkHSPs(), s_BlastSetUpAuxStructures(), s_Finalize(), s_FindAdapters(), s_FindPolyATails(), s_FindRearrangedPairs(), s_RPSComputeTraceback(), s_RPSPreliminarySearchEngine(), SetupQueries_OMF(), SThreadLocalDataArraySetup(), CSequenceDataTester::x_TestSingleSequence_Local(), and CSplitQueryTestFixture::x_ValidateQueryInfoForChunk().
◆ pattern_info
| struct SPHIQueryInfo* BlastQueryInfo::pattern_info |
Counts of PHI BLAST pattern occurrences, used in PHI BLAST only.
Definition at line 89 of file blast_query_info.h.
Referenced by Blast_SetPHIPatternInfo(), BlastBuildSearchResultSet(), BlastQueryInfoDup(), BlastQueryInfoFree(), LocalBlastResults2SeqAlign(), PhiBlastGetEffectiveNumberOfPatterns(), PHIGetGappedScore(), PHIGetPatternOccurrences(), s_GetEstimatedPhiExpect(), s_PhiBlastCutoffScore(), s_PHITracebackFromHSPList(), and CSplitQueryTestFixture::x_ValidateQueryInfoForChunk().
The documentation for this struct was generated from the following file:
- include/algo/blast/core/blast_query_info.h
