NCBI C++ ToolKit
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BlastContextInfo Struct Reference

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...
 

Detailed Description

The context related information.

Definition at line 46 of file blast_query_info.h.

Member Data Documentation

Int8 BlastContextInfo::eff_searchsp
Int1 BlastContextInfo::frame
Boolean BlastContextInfo::is_valid
Int4 BlastContextInfo::length_adjustment
Int4 BlastContextInfo::query_index
Int4 BlastContextInfo::query_length

Length of this query, strand or frame.

Definition at line 49 of file blast_query_info.h.

Referenced by BLAST_CalcEffLengths(), BLAST_ComplementMaskLocations(), BLAST_CreateMixedFrameDNATranslation(), BLAST_GetGappedScore(), Blast_GetOneQueryStructs(), Blast_HSPListGetEvalues(), Blast_HSPListReapByQueryCoverage(), Blast_ScoreBlkKbpUngappedCalc(), BLAST_SmithWatermanGetGappedScore(), Blast_TracebackFromHSPList(), BlastHitSavingParametersUpdate(), BlastInitialWordParametersNew(), BlastInitialWordParametersUpdate(), BlastIntervalTreeAddHSP(), BlastIntervalTreeMasksHSP(), BlastMaskLocDNAToProtein(), BlastQueryInfoGetQueryLength(), BlastSetUp_MaskQuery(), BOOST_AUTO_TEST_CASE(), CalculateLinkHSPCutoffs(), ContextOffsetsToOffsetArray(), TestUtil::CreateProtQueryInfo(), CBlastQueryInfo::DebugDump(), OffsetArrayToContextOffsets(), QueryInfo_GetSeqBufLen(), CDeltaBlast::Run(), s_AdjustEvaluesForComposition(), s_BlastEvenGapLinkHSPs(), s_BlastHSPCullingRun(), s_BlastSmallNaExtend(), s_BlastSmallNaExtendAlignedOneByte(), s_CalculateMaxLength(), s_FillSearchSpace(), s_GetFilteringLocationsForOneContext(), s_GetInitialWordParameters(), s_GetQueryInfo(), s_GetTranslatedQueryDNALength(), s_SetUpLocalBlastSequenceBlk(), s_SetupQueryInfoForReevaluateTest(), s_SumHSPEvalue(), s_TypeOfWord(), LinkHspTestFixture::setupCutoffScores(), SetupQueries_OMF(), TestFixture::SetUpQuery(), NuclWordFinderTextFixture::setupSequences(), 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().

Int4 BlastContextInfo::query_offset

The documentation for this struct was generated from the following file:
Modified on Wed Jul 01 12:46:33 2015 by modify_doxy.py rev. 426318