CGff3AnnotAssembler Class Reference

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#include "gff3_annot_assembler.hpp"
(Private to src/objtools/import/ftable.)

Inheritance diagram for CGff3AnnotAssembler:

Collaboration diagram for CGff3AnnotAssembler:

Public Member Functions
	CGff3AnnotAssembler (CImportMessageHandler &)
virtual	~CGff3AnnotAssembler ()
void	ProcessRecord (const CFeatImportData &, CSeq_annot &) override
virtual void	FinalizeAnnot (const CAnnotImportData &, CSeq_annot &) override
Public Member Functions inherited from CFeatAnnotAssembler
	CFeatAnnotAssembler (CImportMessageHandler &)
virtual	~CFeatAnnotAssembler ()
virtual void	InitializeAnnot (CSeq_annot &)

Private Member Functions
void	xProcessFeatureDefault (const std::string &, const std::string &, CRef< CSeq_feat >, CSeq_annot &)
void	xProcessFeatureExon (const std::string &, const std::string &, CRef< CSeq_feat >, CSeq_annot &)
void	xProcessFeatureRna (const std::string &, const std::string &, CRef< CSeq_feat >, CSeq_annot &)
void	xProcessFeatureCds (const std::string &, const std::string &, CRef< CSeq_feat >, CSeq_annot &)
void	xAnnotGenerateXrefs (CSeq_annot &)

Static Private Member Functions
static void	xMarkLocationPending (CSeq_feat &)
static bool	xIsLocationPending (const CSeq_feat &)
static void	xUnmarkLocationPending (CSeq_feat &)

Private Attributes
CGff3FeatureMap	mFeatureMap
CGff3PendingFeatureList	mPendingFeatures
map< string, string >	mXrefMap
CFeatureIdGenerator	mIdGenerator

Additional Inherited Members
Protected Attributes inherited from CFeatAnnotAssembler
CImportMessageHandler &	mErrorReporter

Detailed Description

Definition at line 139 of file gff3_annot_assembler.hpp.

Constructor & Destructor Documentation

CGff3AnnotAssembler()

CGff3AnnotAssembler::CGff3AnnotAssembler

(

CImportMessageHandler &

errorReporter

)

Definition at line 56 of file gff3_annot_assembler.cpp.

~CGff3AnnotAssembler()

CGff3AnnotAssembler::~CGff3AnnotAssembler ( )

virtual

Definition at line 64 of file gff3_annot_assembler.cpp.

Member Function Documentation

FinalizeAnnot()

void CGff3AnnotAssembler::FinalizeAnnot ( const CAnnotImportData &  annotData, CSeq_annot &  annot  )

overridevirtual

Reimplemented from CFeatAnnotAssembler.

Definition at line 233 of file gff3_annot_assembler.cpp.

References CSeq_feat::AddSeqFeatXref(), map_checker< Container >::end(), map_checker< Container >::find(), CGff3FeatureMap::FindFeature(), ftable, mFeatureMap, mXrefMap, CSeq_annot_Base::SetData(), and xUnmarkLocationPending().

ProcessRecord()

void CGff3AnnotAssembler::ProcessRecord ( const CFeatImportData &  record_, CSeq_annot &  annot  )

overridevirtual

Implements CFeatAnnotAssembler.

Definition at line 71 of file gff3_annot_assembler.cpp.

References assert, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_exon, CSeqFeatData::eSubtype_misc_RNA, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_ncRNA, CSeqFeatData::eSubtype_rRNA, CSeqFeatData::eSubtype_tmRNA, CSeqFeatData::eSubtype_tRNA, CGff3ImportData::GetData(), CGff3ImportData::Id(), CGff3ImportData::Parent(), xProcessFeatureCds(), xProcessFeatureDefault(), xProcessFeatureExon(), and xProcessFeatureRna().

xAnnotGenerateXrefs()

void CGff3AnnotAssembler::xAnnotGenerateXrefs ( CSeq_annot &  )

private

xIsLocationPending()

bool CGff3AnnotAssembler::xIsLocationPending ( const CSeq_feat &  feat )

staticprivate

Definition at line 275 of file gff3_annot_assembler.cpp.

References CSeq_feat_Base::GetQual(), and CSeq_feat_Base::IsSetQual().

Referenced by xProcessFeatureExon().

xMarkLocationPending()

void CGff3AnnotAssembler::xMarkLocationPending ( CSeq_feat &  feat )

staticprivate

Definition at line 292 of file gff3_annot_assembler.cpp.

References CSeq_feat::AddQualifier().

Referenced by xProcessFeatureRna().

xProcessFeatureCds()

void CGff3AnnotAssembler::xProcessFeatureCds ( const std::string &  recordId, const std::string &  parentId, CRef< CSeq_feat >  pFeature, CSeq_annot &  annot  )

private

Definition at line 122 of file gff3_annot_assembler.cpp.

References CGff3FeatureMap::AddFeature(), FeatUtil::AddLocations(), eExtreme_Positional, eNa_strand_minus, eNa_strand_plus, CGff3FeatureMap::FindFeature(), CSeqFeatData_Base::GetCdregion(), CSeq_feat_Base::GetData(), CFeatureIdGenerator::GetIdFor(), CSeq_feat_Base::GetLocation(), CSeq_loc::GetStart(), mFeatureMap, mIdGenerator, mXrefMap, CSeq_annot_Base::SetData(), and CSeq_feat_Base::SetId().

Referenced by ProcessRecord().

xProcessFeatureDefault()

void CGff3AnnotAssembler::xProcessFeatureDefault ( const std::string &  recordId, const std::string &  parentId, CRef< CSeq_feat >  pFeature, CSeq_annot &  annot  )

private

Definition at line 102 of file gff3_annot_assembler.cpp.

References CGff3FeatureMap::AddFeature(), CSeq_feat_Base::GetData(), CFeatureIdGenerator::GetIdFor(), CSeqFeatData::GetSubtype(), mFeatureMap, mIdGenerator, CSeq_annot_Base::SetData(), CSeq_feat_Base::SetId(), CSeqFeatData::SubtypeValueToName(), and NStr::ToLower().

Referenced by ProcessRecord().

xProcessFeatureExon()

void CGff3AnnotAssembler::xProcessFeatureExon ( const std::string &  recordId, const std::string &  parentId, CRef< CSeq_feat >  pFeature, CSeq_annot &  annot  )

private

Definition at line 207 of file gff3_annot_assembler.cpp.

References CGff3PendingFeatureList::AddFeature(), FeatUtil::AddLocations(), CGff3FeatureMap::FindFeature(), CSeq_feat_Base::GetLocation(), mFeatureMap, mPendingFeatures, CSeq_feat_Base::SetLocation(), xIsLocationPending(), and xUnmarkLocationPending().

Referenced by ProcessRecord().

xProcessFeatureRna()

void CGff3AnnotAssembler::xProcessFeatureRna ( const std::string &  recordId, const std::string &  parentId, CRef< CSeq_feat >  pFeature, CSeq_annot &  annot  )

private

Definition at line 174 of file gff3_annot_assembler.cpp.

References CGff3FeatureMap::AddFeature(), FeatUtil::AddLocations(), CGff3PendingFeatureList::FindPendingFeatures(), CFeatureIdGenerator::GetIdFor(), CSeq_feat_Base::GetLocation(), CGff3PendingFeatureList::MarkFeaturesDone(), mFeatureMap, mIdGenerator, mPendingFeatures, mXrefMap, CSeq_annot_Base::SetData(), CSeq_feat_Base::SetId(), CSeq_feat_Base::SetLocation(), and xMarkLocationPending().

Referenced by ProcessRecord().

xUnmarkLocationPending()

void CGff3AnnotAssembler::xUnmarkLocationPending ( CSeq_feat &  feat )

staticprivate

Definition at line 301 of file gff3_annot_assembler.cpp.

References CSeq_feat::RemoveQualifier().

Referenced by FinalizeAnnot(), and xProcessFeatureExon().

Member Data Documentation

mFeatureMap

CGff3FeatureMap CGff3AnnotAssembler::mFeatureMap

private

Definition at line 198 of file gff3_annot_assembler.hpp.

Referenced by FinalizeAnnot(), xProcessFeatureCds(), xProcessFeatureDefault(), xProcessFeatureExon(), and xProcessFeatureRna().

mIdGenerator

CFeatureIdGenerator CGff3AnnotAssembler::mIdGenerator

private

Definition at line 201 of file gff3_annot_assembler.hpp.

Referenced by xProcessFeatureCds(), xProcessFeatureDefault(), and xProcessFeatureRna().

mPendingFeatures

CGff3PendingFeatureList CGff3AnnotAssembler::mPendingFeatures

private

Definition at line 199 of file gff3_annot_assembler.hpp.

Referenced by xProcessFeatureExon(), and xProcessFeatureRna().

mXrefMap

map<string,string> CGff3AnnotAssembler::mXrefMap

private

Definition at line 200 of file gff3_annot_assembler.hpp.

Referenced by FinalizeAnnot(), xProcessFeatureCds(), and xProcessFeatureRna().

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The documentation for this class was generated from the following files:

• src/objtools/import/ftable/gff3_annot_assembler.hpp
• src/objtools/import/ftable/gff3_annot_assembler.cpp