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CAnnotationASN1::CImplementationData Class Reference

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Public Member Functions

 CImplementationData (const string &contig_name, const CResidueVec &seq, IEvidence &evdnc, int genetic_code, int sh)
 
void ResetASN1 ()
 
void AddModel (const CAlignModel &model)
 

Public Attributes

CRef< CSeq_entrymain_seq_entry
 

Private Types

typedef map< Int8, CRef< CSeq_feat > > TGeneMap
 

Private Member Functions

void CreateModelProducts (SModelData &model)
 
CRef< CSeq_featcreate_internal_feature (const SModelData &md)
 
CRef< CSeq_featcreate_cdregion_feature (SModelData &md)
 
CRef< CSeq_alignmodel2spliced_seq_align (SModelData &md)
 
CRef< CSeq_loccreate_packed_int_seqloc (const CGeneModel &model, TSignedSeqRange limits_on_mrna=TSignedSeqRange::GetWhole())
 
CRef< CUser_objectcreate_ModelEvidence_user_object (const CGeneModel &model)
 
void AddInternalFeature (const SModelData &md)
 
void DumpEvidence (const SModelData &md)
 

Private Attributes

string contig_name
 
CRef< CSeq_idcontig_sid
 
CEResidueVec contig_seq
 
int gencode
 
int shift
 
CBioseq_set::TSeq_setnucprots
 
CSeq_annotgnomon_models_annot
 
CSeq_annot::C_Data::TFtablefeature_table
 
CSeq_annot::C_Data::TFtableinternal_feature_table
 
set< Int8models_in_internal_feature_table
 
TGeneMap genes
 
IEvidenceevidence
 
unique_ptr< CFeatureGeneratorfeature_generator
 
CRef< CScopescope
 

Friends

class CAnnotationASN1
 

Detailed Description

Definition at line 103 of file asn1.cpp.

Member Typedef Documentation

◆ TGeneMap

Definition at line 136 of file asn1.cpp.

Constructor & Destructor Documentation

◆ CImplementationData()

CAnnotationASN1::CImplementationData::CImplementationData ( const string contig_name,
const CResidueVec seq,
IEvidence evdnc,
int  genetic_code,
int  sh 
)

Member Function Documentation

◆ AddInternalFeature()

void CAnnotationASN1::CImplementationData::AddInternalFeature ( const SModelData md)
private

Definition at line 238 of file asn1.cpp.

References md.

◆ AddModel()

void CAnnotationASN1::CImplementationData::AddModel ( const CAlignModel model)

◆ create_cdregion_feature()

CRef< CSeq_feat > CAnnotationASN1::CImplementationData::create_cdregion_feature ( SModelData md)
private

◆ create_internal_feature()

CRef< CSeq_feat > CAnnotationASN1::CImplementationData::create_internal_feature ( const SModelData md)
private

◆ create_ModelEvidence_user_object()

CRef< CUser_object > CAnnotationASN1::CImplementationData::create_ModelEvidence_user_object ( const CGeneModel model)
private

◆ create_packed_int_seqloc()

CRef< CSeq_loc > CAnnotationASN1::CImplementationData::create_packed_int_seqloc ( const CGeneModel model,
TSignedSeqRange  limits_on_mrna = TSignedSeqRange::GetWhole() 
)
private

◆ CreateModelProducts()

void CAnnotationASN1::CImplementationData::CreateModelProducts ( SModelData model)
private

◆ DumpEvidence()

void CAnnotationASN1::CImplementationData::DumpEvidence ( const SModelData md)
private

◆ model2spliced_seq_align()

CRef< CSeq_align > CAnnotationASN1::CImplementationData::model2spliced_seq_align ( SModelData md)
private

◆ ResetASN1()

void CAnnotationASN1::CImplementationData::ResetASN1 ( )

Friends And Related Function Documentation

◆ CAnnotationASN1

friend class CAnnotationASN1
friend

Definition at line 143 of file asn1.cpp.

Member Data Documentation

◆ contig_name

string CAnnotationASN1::CImplementationData::contig_name
private

Definition at line 123 of file asn1.cpp.

◆ contig_seq

CEResidueVec CAnnotationASN1::CImplementationData::contig_seq
private

Definition at line 125 of file asn1.cpp.

Referenced by CImplementationData().

◆ contig_sid

CRef<CSeq_id> CAnnotationASN1::CImplementationData::contig_sid
private

Definition at line 124 of file asn1.cpp.

Referenced by ResetASN1().

◆ evidence

IEvidence& CAnnotationASN1::CImplementationData::evidence
private

Definition at line 138 of file asn1.cpp.

◆ feature_generator

unique_ptr<CFeatureGenerator> CAnnotationASN1::CImplementationData::feature_generator
private

Definition at line 140 of file asn1.cpp.

Referenced by CImplementationData(), and CreateModelProducts().

◆ feature_table

CSeq_annot::C_Data::TFtable* CAnnotationASN1::CImplementationData::feature_table
private

Definition at line 132 of file asn1.cpp.

Referenced by ResetASN1().

◆ gencode

int CAnnotationASN1::CImplementationData::gencode
private

Definition at line 127 of file asn1.cpp.

◆ genes

TGeneMap CAnnotationASN1::CImplementationData::genes
private

Definition at line 137 of file asn1.cpp.

◆ gnomon_models_annot

CSeq_annot* CAnnotationASN1::CImplementationData::gnomon_models_annot
private

Definition at line 131 of file asn1.cpp.

Referenced by ResetASN1().

◆ internal_feature_table

CSeq_annot::C_Data::TFtable* CAnnotationASN1::CImplementationData::internal_feature_table
private

Definition at line 133 of file asn1.cpp.

Referenced by ResetASN1().

◆ main_seq_entry

CRef<CSeq_entry> CAnnotationASN1::CImplementationData::main_seq_entry

Definition at line 109 of file asn1.cpp.

Referenced by ResetASN1().

◆ models_in_internal_feature_table

set<Int8> CAnnotationASN1::CImplementationData::models_in_internal_feature_table
private

Definition at line 134 of file asn1.cpp.

◆ nucprots

CBioseq_set::TSeq_set* CAnnotationASN1::CImplementationData::nucprots
private

Definition at line 130 of file asn1.cpp.

Referenced by CreateModelProducts(), and ResetASN1().

◆ scope

CRef<CScope> CAnnotationASN1::CImplementationData::scope
private

Definition at line 141 of file asn1.cpp.

Referenced by CImplementationData().

◆ shift

int CAnnotationASN1::CImplementationData::shift
private

Definition at line 128 of file asn1.cpp.


The documentation for this class was generated from the following file:
Modified on Fri Mar 01 10:06:38 2024 by modify_doxy.py rev. 669887