NCBI C++ ToolKit
Classes | Typedefs | Functions | Variables
asn1.cpp File Reference
#include <ncbi_pch.hpp>
#include <algo/gnomon/asn1.hpp>
#include <algo/sequence/gene_model.hpp>
#include <objects/general/general__.hpp>
#include <objects/seqset/Bioseq_set.hpp>
#include <objects/seqfeat/seqfeat__.hpp>
#include <objects/seqloc/seqloc__.hpp>
#include <objects/seq/seq__.hpp>
#include <objects/seqalign/seqalign__.hpp>
#include "gnomon_seq.hpp"
#include <algo/gnomon/id_handler.hpp>
#include <objects/seq/seqport_util.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/seq_vector.hpp>
#include <objmgr/seq_annot_ci.hpp>
#include <objmgr/feat_ci.hpp>
#include <objmgr/align_ci.hpp>
+ Include dependency graph for asn1.cpp:

Go to the source code of this file.

Go to the SVN repository for this file.

Classes

struct  SModelData
 
class  CAnnotationASN1::CImplementationData
 

Typedefs

typedef map< string, stringTAttributes
 

Functions

 USING_SCOPE (ncbi::objects)
 
void CollectAttributes (const CAlignModel &a, TAttributes &attributes)
 
void ParseAttributes (TAttributes &attributes, CAlignModel &a)
 
Int8 GetModelId (const CSeq_align &seq_align)
 
void NameAnnot (CSeq_annot &annot, const string &name)
 
void ExpandSupport (const CSupportInfoSet &src, CSupportInfoSet &dst, IEvidence &evidence)
 
int CollectUserField (const CUser_field &field, const string &name, vector< string > &values)
 
string ModelMethod (const CGeneModel &model)
 
CRef< CSpliced_exonspliced_exon (const CModelExon &e, EStrand strand)
 
CRef< CProduct_posNucPosToProtPos (int nultripos)
 
CRef< CSeq_alignAlignModelToSeqalign (const CAlignModel &model, CSeq_id &mrnaid, CSeq_id &contigid, bool is_align, bool is_protalign, bool stop_found)
 
CRef< CUser_objectGetModelEvidenceUserObject (const CSeq_feat_Handle &feat)
 
void RestoreModelMethod (const CSeq_feat_Handle &feat, CAlignModel &model)
 
void RestoreModelAttributes (const CSeq_feat_Handle &feat_handle, CAlignModel &model)
 
void RestoreModelReadingFrame (const CSeq_feat_Handle &feat, CAlignModel &model)
 
CAlignModelRestoreModel (const CSeq_feat_Handle &internal_feat, const CSeq_feat_Handle &cds_feat, const CSeq_align &align)
 
CAlignModelRestoreModelFromPublicMrnaFeature (const CSeq_feat_Handle &feat)
 
CAlignModelRestoreModelFromInternalGnomonFeature (const CSeq_feat_Handle &feat)
 
bool IsGnomonConstructed (const CSeq_align &seq_align)
 
void ExtractSupportModels (Int8 model_id, TAlignModelList &evidence_models, list< CRef< CSeq_align > > &evidence_alignments, CSeq_entry_Handle seq_entry_handle, map< string, CRef< CSeq_annot > > &seq_annot_map, set< Int8 > &processed_ids)
 

Variables

const string kGnomonConstructed = "Is [re]constructed alignment"
 

Typedef Documentation

◆ TAttributes

Definition at line 60 of file asn1.cpp.

Function Documentation

◆ AlignModelToSeqalign()

CRef<CSeq_align> AlignModelToSeqalign ( const CAlignModel model,
CSeq_id mrnaid,
CSeq_id contigid,
bool  is_align,
bool  is_protalign,
bool  stop_found 
)

Definition at line 752 of file asn1.cpp.

References _ASSERT, CUser_object::AddField(), CInDelInfo::eGenomeCorrect, CInDelInfo::eGenomeNotCorrect, eMinus, eNa_strand_minus, eNa_strand_plus, ePlus, CGeneModel::ePolyA, CSpliced_seg_Base::eProduct_type_protein, CSpliced_seg_Base::eProduct_type_transcript, CGeneModel::eReversed, CSeq_align_Base::eType_partial, CGeneModel::Exons(), CGeneModel::FrameShifts(), CModelExon::GetFrom(), CRange_Base::GetFrom(), CGeneModel::GetInDels(), COpenRange< Position >::GetLength(), CModelExon::GetTo(), CRange_Base::GetTo(), i, CGeneModel::ID(), int, CInDelInfo::IsInsertion(), CInDelInfo::IsMismatch(), CSpliced_exon_Base::IsSetParts(), CInDelInfo::Len(), len, CModelExon::Limits(), CInDelInfo::Loc(), CInDelInfo::SSource::m_range, CModelExon::m_source, NON_CONST_ITERATE, COpenRange< Position >::NotEmpty(), NucPosToProtPos(), CGeneModel::Orientation(), CAlignModel::PolyALen(), CSpliced_seg_Base::SetExons(), CSeq_align_Base::SetExt(), CSpliced_seg_Base::SetGenomic_id(), CSpliced_seg_Base::SetGenomic_strand(), CIdHandler::SetId(), CSeq_align_Base::SetId(), CSpliced_exon_Base::SetParts(), CSpliced_seg_Base::SetPoly_a(), CSpliced_seg_Base::SetProduct_id(), CSpliced_seg_Base::SetProduct_length(), CSpliced_seg_Base::SetProduct_strand(), CSpliced_seg_Base::SetProduct_type(), CSeq_align_Base::SetSegs(), CObject_id_Base::SetStr(), CUser_object_Base::SetType(), CSeq_align_Base::SetType(), spliced_exon(), CGeneModel::Status(), CGeneModel::Strand(), string, swap(), CAlignModel::TargetLen(), CGeneModel::TranscriptExon(), CGeneModel::TranscriptLimits(), and types.

Referenced by CAlignModel::MakeSeqAlign(), and CAnnotationASN1::CImplementationData::model2spliced_seq_align().

◆ CollectAttributes()

void CollectAttributes ( const CAlignModel a,
TAttributes attributes 
)

◆ CollectUserField()

int CollectUserField ( const CUser_field field,
const string name,
vector< string > &  values 
)

◆ ExpandSupport()

void ExpandSupport ( const CSupportInfoSet src,
CSupportInfoSet dst,
IEvidence evidence 
)

◆ ExtractSupportModels()

void ExtractSupportModels ( Int8  model_id,
TAlignModelList evidence_models,
list< CRef< CSeq_align > > &  evidence_alignments,
CSeq_entry_Handle  seq_entry_handle,
map< string, CRef< CSeq_annot > > &  seq_annot_map,
set< Int8 > &  processed_ids 
)

◆ GetModelEvidenceUserObject()

CRef<CUser_object> GetModelEvidenceUserObject ( const CSeq_feat_Handle feat)

◆ GetModelId()

Int8 GetModelId ( const CSeq_align seq_align)

Definition at line 65 of file gnomon_objmgr.cpp.

References CSeq_align_Base::CanGetId(), and CSeq_align_Base::GetId().

◆ IsGnomonConstructed()

bool IsGnomonConstructed ( const CSeq_align seq_align)

◆ ModelMethod()

string ModelMethod ( const CGeneModel model)

◆ NameAnnot()

void NameAnnot ( CSeq_annot annot,
const string name 
)

◆ NucPosToProtPos()

CRef<CProduct_pos> NucPosToProtPos ( int  nultripos)

◆ ParseAttributes()

void ParseAttributes ( TAttributes attributes,
CAlignModel a 
)

Referenced by RestoreModelAttributes().

◆ RestoreModel()

CAlignModel* RestoreModel ( const CSeq_feat_Handle internal_feat,
const CSeq_feat_Handle cds_feat,
const CSeq_align align 
)

◆ RestoreModelAttributes()

void RestoreModelAttributes ( const CSeq_feat_Handle feat_handle,
CAlignModel model 
)

◆ RestoreModelFromInternalGnomonFeature()

CAlignModel* RestoreModelFromInternalGnomonFeature ( const CSeq_feat_Handle feat)

◆ RestoreModelFromPublicMrnaFeature()

CAlignModel* RestoreModelFromPublicMrnaFeature ( const CSeq_feat_Handle feat)

◆ RestoreModelMethod()

void RestoreModelMethod ( const CSeq_feat_Handle feat,
CAlignModel model 
)

◆ RestoreModelReadingFrame()

void RestoreModelReadingFrame ( const CSeq_feat_Handle feat,
CAlignModel model 
)

◆ spliced_exon()

CRef<CSpliced_exon> spliced_exon ( const CModelExon e,
EStrand  strand 
)

◆ USING_SCOPE()

USING_SCOPE ( ncbi::objects  )

Variable Documentation

◆ kGnomonConstructed

const string kGnomonConstructed = "Is [re]constructed alignment"
Modified on Thu Jul 18 16:02:05 2024 by modify_doxy.py rev. 669887