#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>
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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.
