NCBI C++ ToolKit
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BlastQueryInfo Struct Reference

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...
 
BlastContextInfocontexts
 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 SPHIQueryInfopattern_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(), BSearchContextInfo(), 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_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

◆ last_context

Int4 BlastQueryInfo::last_context

◆ max_length

Uint4 BlastQueryInfo::max_length

◆ 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(), BSearchContextInfo(), and SetupQueryInfo_OMF().

◆ num_queries

int BlastQueryInfo::num_queries

◆ pattern_info

struct SPHIQueryInfo* BlastQueryInfo::pattern_info

The documentation for this struct was generated from the following file:
Modified on Mon May 27 04:36:34 2024 by modify_doxy.py rev. 669887