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USING_SCOPE (objects) template<class L , class R > bool s_TooFar (const L &left, const R &right, double score) template<class Left , class Right > bool s_EvaluateNewScore (const Left &left, const Right &right, double &rscore, bool &openrgn, bool rightanchor=false) template<class L , class R > bool s_ForwardStep (const L &left, R &right, int leftprot, int rightprot) template<class L > bool s_ForwardStep (const L &left, CIntron &right) template<class L > bool s_ForwardStep (const L &left, CIntergenic &right, bool rightanchor) template<class L , class R > void s_MakeStep (vector< L > &lvec, vector< R > &rvec, int leftprot, int rightprot) template<class L > void s_MakeStep (vector< L > &lvec, vector< CIntron > &rvec) template<class L > void s_MakeStep (const CSeqScores &seqscr, vector< L > &lvec, vector< CIntergenic > &rvec, bool rightanchor=false) void s_MakeStep (const CSeqScores &seqscr, const CExonParameters &exon_params, EStrand strand, int point, vector< CIntergenic > &lvec, vector< CSingleExon > &rvec) template<class R > void s_MakeStep (const CSeqScores &seqscr, const CExonParameters &exon_params, EStrand strand, int point, vector< CIntergenic > &lvec, vector< R > rvec[][3]) template<class R > void s_MakeStep (const CSeqScores &seqscr, const CExonParameters &exon_params, EStrand strand, int point, vector< CIntron > lvec[][3], vector< R > &rvec) void s_MakeStep (const CSeqScores &seqscr, const CExonParameters &exon_params, EStrand strand, int point, vector< CIntron > lvec[][3], vector< CInternalExon > rvec[][3]) template<class L1 , class L2 > void s_MakeStep (const CSeqScores &seqscr, const CIntronParameters &intron_params, EStrand strand, int point, vector< L1 > lvec1[][3], vector< L2 > lvec2[][3], vector< CIntron > rvec[][3], int shift) double AddProbabilities (double scr1, double scr2) template<class T > void Out (T t, int w, CNcbiOstream &to=cout) void Out (double t, int w, CNcbiOstream &to=cout, int prec=1) void AddSupport (const TGeneModelList &align_list, TSignedSeqRange inside_range, CGeneModel &gene, TSignedSeqRange reading_frame) ◆ AddProbabilities() double AddProbabilities ( double scr1, double scr2 ) ◆ AddSupport()Definition at line 486 of file parse.cpp.
References _ASSERT, CGeneModel::AddSupport(), CGeneModel::Continuous(), CGeneModel::eFullSupCDS, COpenRange< Position >::Empty(), CGeneModel::eNested, CGeneModel::ePolyA, CGeneModel::eWall, CGeneModel::Exons(), CGeneModel::Extend(), CGeneModel::FrameShifts(), i, CGeneModel::ID(), Include(), CGeneModel::InsertTrustedmRNA(), CGeneModel::InsertTrustedProt(), CGeneModel::isCompatible(), ITERATE, CGeneModel::Limits(), CGeneModel::MaxCdsLimits(), NULL, CGeneModel::ReadingFrame(), CGeneModel::ReplaceSupport(), CGeneModel::SetStrand(), set< Key, Compare >::size(), CGeneModel::Status(), CGeneModel::Strand(), CGeneModel::Support(), CGeneModel::TrustedmRNA(), CGeneModel::TrustedProt(), and CGeneModel::Type().
Referenced by CParse::GetGenes().
◆ Out() [1/2] ◆ Out() [2/2]Definition at line 467 of file parse.cpp.
References t.
Referenced by CFlatItemFormatter::End(), CQueryFilter::FilterAlignments(), CMergeTreeThread::Main(), CMergeTree::Print(), CParse::PrintInfo(), CMergeyApp::Run(), CIdMapperTestApp::Run(), CFlatItemFormatter::Start(), CQuerySet::ToBestSeqAlignSet(), CAlignResultsSet::ToBestSeqAlignSet(), CQuerySet::ToSeqAlignSet(), CAlignResultsSet::ToSeqAlignSet(), CProjectFileWriter::WriteFile(), CMergeTree::x_Dot(), CMergeTree::x_Dot_Edges(), CMergeTree::x_Dot_Nodes(), CInstancedAligner::x_GetCleanupInstances(), CIdMapperTestApp::x_HandleAlignments(), CIdMapperTestApp::x_HandleEntries(), CIdMapperTestApp::x_HandleFeatures(), CInversionMergeAligner::x_HandleSingleStrandMerging(), CInversionMergeAligner::x_MergeSeqAlignSet(), CMergeAligner::x_MergeSeqAlignSet(), CMergeTree::x_Print(), CNgAlignApp::x_PrintNoHitList(), CInstancedAligner::x_RunCleanup(), CProjectFileWriter::x_WriteFile(), CProjectFileWriter::x_WriteGtf(), and CProjectFileWriter::x_WriteObject().
◆ s_EvaluateNewScore()template<class Left , class Right >
◆ s_ForwardStep() [1/3] ◆ s_ForwardStep() [2/3] ◆ s_ForwardStep() [3/3]template<class L , class R >
◆ s_MakeStep() [1/8] ◆ s_MakeStep() [2/8] ◆ s_MakeStep() [3/8] ◆ s_MakeStep() [4/8] ◆ s_MakeStep() [5/8]template<class L1 , class L2 >
◆ s_MakeStep() [6/8] ◆ s_MakeStep() [7/8]template<class L >
void s_MakeStep ( vector< L > & lvec, vector< CIntron > & rvec ) inline ◆ s_MakeStep() [8/8]template<class L , class R >
void s_MakeStep ( vector< L > & lvec, vector< R > & rvec, int leftprot, int rightprot ) inline ◆ s_TooFar()template<class L , class R >
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