NCBI C++ ToolKit
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#include <ncbi_pch.hpp>
#include <algo/gnomon/gnomon_model.hpp>
#include <algo/gnomon/gnomon_exception.hpp>
#include <objects/general/Object_id.hpp>
#include "hmm.hpp"
#include "parse.hpp"
#include "hmm_inlines.hpp"
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Classes | |
struct | SRState |
Functions | |
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) |
double AddProbabilities | ( | double | scr1, |
double | scr2 | ||
) |
Definition at line 325 of file parse.cpp.
References BadScore(), and log.
Referenced by CParse::CParse().
void AddSupport | ( | const TGeneModelList & | align_list, |
TSignedSeqRange | inside_range, | ||
CGeneModel & | gene, | ||
TSignedSeqRange | reading_frame | ||
) |
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().
void Out | ( | double | t, |
int | w, | ||
CNcbiOstream & | to = cout , |
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int | prec = 1 |
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) |
void Out | ( | T | t, |
int | w, | ||
CNcbiOstream & | to = cout |
||
) |
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().
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inline |
Definition at line 69 of file parse.cpp.
References BadScore(), and len.
Referenced by s_ForwardStep().
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Definition at line 176 of file parse.cpp.
References BadScore(), s_EvaluateNewScore(), s_TooFar(), CHMM_State::Score(), CHMM_State::UpdateLeftState(), and CHMM_State::UpdateScore().
Definition at line 155 of file parse.cpp.
References BadScore(), s_EvaluateNewScore(), s_TooFar(), CHMM_State::Score(), CHMM_State::UpdateLeftState(), and CHMM_State::UpdateScore().
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Definition at line 121 of file parse.cpp.
References BadScore(), and s_EvaluateNewScore().
Referenced by s_MakeStep().
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Definition at line 254 of file parse.cpp.
References BadScore(), and s_MakeStep().
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Definition at line 262 of file parse.cpp.
References BadScore(), and s_MakeStep().
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Definition at line 289 of file parse.cpp.
References BadScore(), and s_MakeStep().
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Definition at line 276 of file parse.cpp.
References BadScore(), and s_MakeStep().
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Definition at line 309 of file parse.cpp.
References BadScore(), and s_MakeStep().
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Definition at line 234 of file parse.cpp.
References i, kTooFarLen, CSeqScores::LeftAlignmentBoundary(), max(), s_ForwardStep(), and CHMM_State::Stop().
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Definition at line 211 of file parse.cpp.
References i, kTooFarLen, max(), s_ForwardStep(), and CHMM_State::Stop().
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Definition at line 198 of file parse.cpp.
References i, and s_ForwardStep().
Referenced by CParse::CParse(), and s_MakeStep().
Definition at line 47 of file parse.cpp.
References BadScore(), kTooFarLen, and len.
Referenced by s_ForwardStep().
USING_SCOPE | ( | objects | ) |