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NCBI C++ ToolKit: include/algo/blast/core/blast_program.h File Reference

Definitions for various programs supported by core BLAST. More...

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enum   EBlastProgramType {
  eBlastTypeBlastp = ( (0x1<<0) | (0x1<<1) ) , eBlastTypeBlastn = ( (0x1<<2) | (0x1<<3) ) , eBlastTypeBlastx , eBlastTypeTblastn ,
  eBlastTypeTblastx , eBlastTypePsiBlast = ( (0x1<<6) | eBlastTypeBlastp) , eBlastTypePsiTblastn = ( (0x1<<6) | eBlastTypeTblastn) , eBlastTypeRpsBlast = ( (0x1<<7) | eBlastTypeBlastp) ,
  eBlastTypeRpsTblastn = ( (0x1<<7) | eBlastTypeBlastx) , eBlastTypePhiBlastp = ( (0x1<<8) | eBlastTypeBlastp) , eBlastTypePhiBlastn = ( (0x1<<8) | eBlastTypeBlastn) , eBlastTypeMapping = (eBlastTypeBlastn | (0x1<<9) ) ,
  eBlastTypeUndefined = 0x0
}   Defines the engine's notion of the different applications of the BLAST algorithm. More...
 

Definitions for various programs supported by core BLAST.

Definition in file blast_program.h.

◆ MAPPING_MASK #define MAPPING_MASK   (0x1<<9)

This bit is on for fast mapping of short reads.

Definition at line 66 of file blast_program.h.

◆ NUCLEOTIDE_QUERY_MASK #define NUCLEOTIDE_QUERY_MASK   (0x1<<2)

This bit is on if the query is nucleotide.

Definition at line 52 of file blast_program.h.

◆ NUCLEOTIDE_SUBJECT_MASK #define NUCLEOTIDE_SUBJECT_MASK   (0x1<<3)

This bit is on if the subject is nucleotide.

Definition at line 54 of file blast_program.h.

◆ PATTERN_QUERY_MASK #define PATTERN_QUERY_MASK   (0x1<<8)

This bit is on if the query includes a pattern (PHI-BLAST)

Definition at line 64 of file blast_program.h.

◆ PROTEIN_QUERY_MASK #define PROTEIN_QUERY_MASK   (0x1<<0)

This bit is on if the query is protein.

Definition at line 48 of file blast_program.h.

◆ PROTEIN_SUBJECT_MASK #define PROTEIN_SUBJECT_MASK   (0x1<<1)

This bit is on if the subject is protein.

Definition at line 50 of file blast_program.h.

◆ PSSM_QUERY_MASK #define PSSM_QUERY_MASK   (0x1<<6)

This bit is on if the query is a PSSM (PSI-BLAST)

Definition at line 60 of file blast_program.h.

◆ PSSM_SUBJECT_MASK #define PSSM_SUBJECT_MASK   (0x1<<7)

This bit is on if the subject is a PSSM (RPS-BLAST)

Definition at line 62 of file blast_program.h.

◆ TRANSLATED_QUERY_MASK #define TRANSLATED_QUERY_MASK   (0x1<<4)

This bit is on if the query is translated.

Definition at line 56 of file blast_program.h.

◆ TRANSLATED_SUBJECT_MASK #define TRANSLATED_SUBJECT_MASK   (0x1<<5)

This bit is on if the subject is translated.

Definition at line 58 of file blast_program.h.

◆ EBlastProgramType

Defines the engine's notion of the different applications of the BLAST algorithm.

Enumerator eBlastTypeBlastp  eBlastTypeBlastn  eBlastTypeBlastx  eBlastTypeTblastn  eBlastTypeTblastx  eBlastTypePsiBlast  eBlastTypePsiTblastn  eBlastTypeRpsBlast  eBlastTypeRpsTblastn  eBlastTypePhiBlastp  eBlastTypePhiBlastn  eBlastTypeMapping  eBlastTypeUndefined 

Definition at line 72 of file blast_program.h.

◆ Blast_ProgramIsMapping()

Definition at line 76 of file blast_program.c.

References MAPPING_MASK, and SAFE_CAST_INT_TO_BOOLEAN.

Referenced by BLAST_CalcEffLengths(), BLAST_PreliminarySearchEngine(), BlastChooseNaLookupTable(), BlastQueryInfoNew(), BlastScoringOptionsValidate(), BlastSetup_ScoreBlkInit(), CSetupFactory::CreateHspWriter(), s_BlastSearchEngineOneContext(), s_FillContigMBTable(), and SetupQueryInfo_OMF().

◆ Blast_ProgramIsNucleotide()

Definition at line 82 of file blast_program.c.

References Blast_QueryIsNucleotide(), Blast_QueryIsTranslated(), Blast_SubjectIsNucleotide(), and Blast_SubjectIsTranslated().

Referenced by BLAST_FillExtensionOptions(), BLAST_FillScoringOptions(), BLAST_PreliminarySearchEngine(), BlastExtensionOptionsNew(), BlastInitialWordOptionsNew(), BlastInitialWordParametersNew(), BlastScoringOptionsNew(), BlastScoringOptionsValidate(), LogBlastOptions(), LookupTableOptionsValidate(), s_BlastSearchEngineCore(), s_BlastSearchEngineOneContext(), and CBlastOptionsLocal::SetSubjectBestHit().

◆ Blast_ProgramIsPhiBlast()

Returns true if program is PHI-BLAST (i.e.

: involves a pattern)

Parameters

Definition at line 70 of file blast_program.c.

References PATTERN_QUERY_MASK, and SAFE_CAST_INT_TO_BOOLEAN.

Referenced by BLAST_CalcEffLengths(), BLAST_ComputeTraceback_MT(), Blast_HSPListPurgeHSPsWithCommonEndpoints(), Blast_HSPListSubjectBestHit(), Blast_RunFullSearch(), Blast_SetPHIPatternInfo(), BlastBuildSearchResultSet(), BlastHitSavingParametersUpdate(), BlastInitialWordOptionsValidate(), BlastInitialWordParametersNew(), BlastSetup_ScoreBlkInit(), BOOST_AUTO_TEST_CASE(), BuildBlastAncillaryData(), CBlastTracebackSearch::CBlastTracebackSearch(), CSetupFactory::CreateLookupTable(), LocalBlastResults2SeqAlign(), LookupTableOptionsValidate(), CBlastTracebackSearch::Run(), CBlastTracebackSearch::RunSimple(), s_AddMask(), s_BlastSearchEngineCore(), s_PHITracebackFromHSPList(), SplitQuery_ShouldSplit(), and CBlastTracebackSearch::x_Init().

◆ Blast_ProgramIsPsiBlast() ◆ Blast_ProgramIsRpsBlast()

Returns true if program is RPS-BLAST (i.e.

: involves a PSSM as subject)

Parameters

Definition at line 73 of file blast_program.c.

References PSSM_SUBJECT_MASK, and SAFE_CAST_INT_TO_BOOLEAN.

Referenced by BLAST_ComputeTraceback_MT(), BLAST_FillLookupTableOptions(), BLAST_GetGappedScore(), Blast_HSPListGetEvalues(), BLAST_PreliminarySearchEngine(), BLAST_SmithWatermanGetGappedScore(), Blast_TracebackFromHSPList(), BlastExtensionParametersNew(), BlastScoringOptionsValidate(), BlastSetupPreliminarySearchEx(), BOOST_AUTO_TEST_CASE(), CSetupFactory::CreateScoreBlock(), LookupTableOptionsValidate(), s_BlastHSPBestHitNew(), s_BlastHSPCollectorNew(), s_BlastHSPCollectorRun_RPS(), s_BlastHSPListRPSUpdate(), s_BlastSearchEngineCore(), s_HSPListPostTracebackUpdate(), s_RPSPreliminarySearchEngine(), CBlastTracebackSearch::x_Init(), and CBlastAppArgs::x_IssueWarningsForIgnoredOptions().

◆ Blast_ProgramIsValid()

Returns true if program is not undefined.

Parameters

Definition at line 87 of file blast_program.c.

References eBlastTypeBlastn, eBlastTypeBlastp, eBlastTypeBlastx, eBlastTypeMapping, eBlastTypePhiBlastn, eBlastTypePhiBlastp, eBlastTypePsiBlast, eBlastTypePsiTblastn, eBlastTypeRpsBlast, eBlastTypeRpsTblastn, eBlastTypeTblastn, eBlastTypeTblastx, FALSE, and TRUE.

Referenced by BLAST_GetNumberOfContexts().

◆ Blast_QueryIsNucleotide()

Returns true if the query is nucleotide.

Parameters

Definition at line 43 of file blast_program.c.

References NUCLEOTIDE_QUERY_MASK, and SAFE_CAST_INT_TO_BOOLEAN.

Referenced by BLAST_FrameToContext(), BLAST_GetNumberOfContexts(), Blast_ProgramIsNucleotide(), BOOST_AUTO_TEST_CASE(), CPhiBlastArgs::ExtractAlgorithmOptions(), FrameNumber2NetworkFrame(), s_AddMask(), s_BlastEvenGapLinkHSPs(), s_BlastSetup_GetStrand(), s_CreateBlastMask(), CBlastOptions::SetFilterString(), CBlastQuerySourceOM::x_CalculateMasks(), CQuerySplitter::x_ComputeQueryContextsForChunks(), and CBlastOptionsBuilder::x_ProcessOneOption().

◆ Blast_QueryIsPattern() ◆ Blast_QueryIsProtein()

Returns true if the query is protein.

Parameters

Definition at line 40 of file blast_program.c.

References PROTEIN_QUERY_MASK, and SAFE_CAST_INT_TO_BOOLEAN.

Referenced by BLAST_ContextToFrame(), Blast_GetQueryIndexFromContext(), BlastHSPStreamNew(), CheckMTByQueries_QuerySize(), CObjMgrFree_LocalQueryData::CObjMgrFree_LocalQueryData(), CQueryOptionsArgs::ExtractAlgorithmOptions(), PackedSeqLocToMaskedQueryRegions(), CBlastFormatterApp::PrintFormattedOutput(), CBlastFormatterVdbApp::PrintFormattedOutput(), CBlastDemoApplication::Run(), s_BlastSetup_GetStrand(), s_ImportQueries(), CBlastOptions::SetFilterString(), CBlastExtendTestFixture::setupStructures(), CQuerySplitter::x_ComputeContextOffsets_NonTranslatedQueries(), CQuerySplitter::x_ComputeContextOffsets_TranslatedQueries(), CQuerySplitter::x_ComputeQueryContextsForChunks(), CSequenceDataTester::x_IsProtein(), and CBlastAppArgs::x_IssueWarningsForIgnoredOptions().

◆ Blast_QueryIsPssm() ◆ Blast_QueryIsTranslated()

Returns true if the query is translated.

Parameters

Definition at line 60 of file blast_program.c.

References SAFE_CAST_INT_TO_BOOLEAN, and TRANSLATED_QUERY_MASK.

Referenced by BLAST_FrameToContext(), BLAST_GetNumberOfContexts(), Blast_GetQueryIndexFromContext(), BLAST_GetSuggestedThreshold(), Blast_HSPGetAdjustedOffsets(), BLAST_MainSetUp(), Blast_ProgramIsNucleotide(), Blast_ScoreBlkKbpUngappedCalc(), BlastHitSavingOptionsNew(), BlastHitSavingParametersNew(), BLASTHspListToSeqAlign(), BlastQueryInfoGetQueryLength(), BOOST_AUTO_TEST_CASE(), CBlastQueryFilteredFrames::CBlastQueryFilteredFrames(), CRemoteBlast::ConvertToRemoteMasks(), FrameNumber2NetworkFrame(), CCmdLineBlastXML2ReportData::GetQueryGeneticCode(), NetworkFrame2FrameNumber(), s_AddMask(), s_AdjustFirstContext(), s_BlastEvenGapLinkHSPs(), s_CreateBlastMask(), CBlastOptions::SetFilterString(), SetupQueries_OMF(), SetupQueryInfo_OMF(), SplitQuery_CalculateNumChunks(), SplitQuery_GetChunkSize(), SplitQuery_GetOverlapChunkSize(), CBlastQuerySourceOM::x_AutoDetectGeneticCodes(), CBlastQuerySourceOM::x_CalculateMasks(), CQuerySplitter::x_ComputeChunkRanges(), CQuerySplitter::x_ComputeContextOffsets_NonTranslatedQueries(), CQuerySplitter::x_ComputeContextOffsets_TranslatedQueries(), CQuerySplitter::x_ComputeContextOffsetsForChunks(), and CQuerySplitter::x_ComputeQueryContextsForChunks().

◆ Blast_SubjectIsNucleotide() ◆ Blast_SubjectIsProtein() ◆ Blast_SubjectIsPssm() ◆ Blast_SubjectIsTranslated()

Returns true if the subject is translated.

Parameters

Definition at line 63 of file blast_program.c.

References SAFE_CAST_INT_TO_BOOLEAN, and TRANSLATED_SUBJECT_MASK.

Referenced by BLAST_CalcEffLengths(), BLAST_ComputeTraceback_MT(), BLAST_FillExtensionOptions(), BLAST_FrameToContext(), BLAST_GapAlignSetUp(), BLAST_GetGappedScore(), BLAST_GetSuggestedThreshold(), Blast_HSPGetAdjustedOffsets(), Blast_HSPListReevaluateUngapped(), BLAST_LinkHsps(), BLAST_PreliminarySearchEngine(), Blast_ProgramIsNucleotide(), BLAST_SetupPartialFetching(), Blast_TracebackFromHSPList(), Blast_TracebackGetEncoding(), BlastExtensionOptionsNew(), BlastHitSavingOptionsNew(), BlastHitSavingParametersNew(), BOOST_AUTO_TEST_CASE(), CalculateLinkHSPCutoffs(), CMultiSeqInfo::CMultiSeqInfo(), CQueryFactoryInfo::CQueryFactoryInfo(), CCmdLineBlastXML2ReportData::GetDbGeneticCode(), s_BlastEvenGapLinkHSPs(), s_BlastSearchEngineCore(), s_BlastSearchEngineOneContext(), s_MatchingSequenceInitialize(), s_SumHSPEvalue(), CBlastOptionsLocal::SetProgram(), SetupSubjects_OMF(), and CBlastQuerySourceOM::x_AutoDetectGeneticCodes().

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