#include <ncbi_pch.hpp>
#include <corelib/ncbiapp.hpp>
#include <corelib/ncbienv.hpp>
#include <corelib/ncbiargs.hpp>
#include <algo/gnomon/annot.hpp>
#include "gnomon_engine.hpp"
#include <algo/gnomon/gnomon_model.hpp>
#include <algo/gnomon/gnomon.hpp>
#include <algo/gnomon/id_handler.hpp>
#include <objects/seqloc/Seq_loc.hpp>
Include dependency graph for annot.cpp:
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Functions USING_SCOPE (objects) bool s_AlignScoreOrder (const CGeneModel &ap, const CGeneModel &bp) TSignedSeqRange WalledCdsLimits (const CGeneModel &a) TSignedSeqRange GetWallLimits (const CGeneModel &m, bool external=false) pair< TSignedSeqRange, bool > GetGeneWallLimits (const list< TGeneModelList::iterator > &models, bool external=false) bool s_AlignSeqOrder (const CGeneModel &ap, const CGeneModel &bp) void FindPartials (TGeneModelList &models, TGeneModelList &aligns, EStrand strand) Function Documentation ◆ FindPartials() void FindPartials ( TGeneModelList & models, TGeneModelList & aligns, EStrand strand )Definition at line 366 of file annot.cpp.
References CGeneModel::AddExon(), CGeneModel::eNested, CGeneModel::eWall, GetWallLimits(), limits, and CGeneModel::SetGeneID().
Referenced by CGnomonAnnotator::Predict().
◆ GetGeneWallLimits() pair<TSignedSeqRange, bool> GetGeneWallLimits ( const list< TGeneModelList::iterator > & models, bool external =false )
Definition at line 335 of file annot.cpp.
References GetWallLimits().
Referenced by CGnomonAnnotator::Predict().
◆ GetWallLimits() TSignedSeqRange GetWallLimits ( const CGeneModel & m, bool external =false )
Definition at line 323 of file annot.cpp.
References CGeneModel::Limits(), CGeneModel::MaxCdsLimits(), COpenRange< Position >::NotEmpty(), CGeneModel::OpenCds(), CGeneModel::ReadingFrame(), and CGeneModel::RealCdsLimits().
Referenced by FindPartials(), GetGeneWallLimits(), CGnomonAnnotator::Predict(), and s_AlignSeqOrder().
◆ s_AlignScoreOrder() bool s_AlignScoreOrder ( const CGeneModel & ap, const CGeneModel & bp )Definition at line 63 of file annot.cpp.
References CGeneModel::Score().
Referenced by CGnomonAnnotator::Predict().
◆ s_AlignSeqOrder() bool s_AlignSeqOrder ( const CGeneModel & ap, const CGeneModel & bp )Definition at line 355 of file annot.cpp.
References a, b, and GetWallLimits().
Referenced by CGnomonAnnotator::Predict().
◆ USING_SCOPE() USING_SCOPE ( objects ) ◆ WalledCdsLimits() TSignedSeqRange WalledCdsLimits ( const CGeneModel & a )Definition at line 318 of file annot.cpp.
References a, and CGeneModel::eWall.
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