NCBI C++ ToolKit
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CGeneCache Class Reference

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#include <objtools/validator/gene_cache.hpp>

+ Collaboration diagram for CGeneCache:

Public Member Functions

 CGeneCache ()
 ~CGeneCache ()
CConstRef< CSeq_featGetGeneFromCache (const CSeq_feat *feat, CScope &scope)
CConstRef< CSeq_featGetmRNAFromCache (const CSeq_feat *feat, CScope &scope)
CRef< feature::CFeatTree > GetFeatTreeFromCache (const CSeq_loc &loc, CScope &scope)
CRef< feature::CFeatTree > GetFeatTreeFromCache (const CSeq_feat &feat, CScope &scope)
CRef< feature::CFeatTree > GetFeatTreeFromCache (CBioseq_Handle bh)
void Clear ()

Static Public Member Functions

static bool IsPseudo (const CSeq_feat &feat)

Private Types

typedef map< const CSeq_feat *, CConstRef< CSeq_feat > > TFeatGeneMap
typedef map< CBioseq_Handle, CRef< feature::CFeatTree > > TSeqTreeMap

Static Private Member Functions

static bool x_IsPseudo (const CGene_ref &gref)
static bool x_HasNamedQual (const CSeq_feat &feat, const string &qual)

Private Attributes

TFeatGeneMap m_FeatGeneMap
TSeqTreeMap m_SeqTreeMap

Detailed Description

Definition at line 78 of file gene_cache.hpp.

Member Typedef Documentation

◆ TFeatGeneMap

Definition at line 93 of file gene_cache.hpp.

◆ TSeqTreeMap

typedef map<CBioseq_Handle, CRef<feature::CFeatTree> > CGeneCache::TSeqTreeMap

Definition at line 96 of file gene_cache.hpp.

Constructor & Destructor Documentation

◆ CGeneCache()

CGeneCache::CGeneCache ( )

Definition at line 81 of file gene_cache.hpp.

◆ ~CGeneCache()

CGeneCache::~CGeneCache ( )

Definition at line 82 of file gene_cache.hpp.

Member Function Documentation

◆ Clear()

void CGeneCache::Clear ( void  )

Definition at line 89 of file gene_cache.hpp.

Referenced by CValidError_imp::SetTSE(), and CValidError_feat::SetTSE().

◆ GetFeatTreeFromCache() [1/3]

CRef< feature::CFeatTree > CGeneCache::GetFeatTreeFromCache ( CBioseq_Handle  bh)

Definition at line 63 of file gene_cache.cpp.

References f().

◆ GetFeatTreeFromCache() [2/3]

CRef< feature::CFeatTree > CGeneCache::GetFeatTreeFromCache ( const CSeq_feat feat,
CScope scope 

Definition at line 100 of file gene_cache.cpp.

References CSeq_feat_Base::GetLocation().

◆ GetFeatTreeFromCache() [3/3]

CRef< feature::CFeatTree > CGeneCache::GetFeatTreeFromCache ( const CSeq_loc loc,
CScope scope 

◆ GetGeneFromCache()

CConstRef< CSeq_feat > CGeneCache::GetGeneFromCache ( const CSeq_feat feat,
CScope scope 

◆ GetmRNAFromCache()

CConstRef<CSeq_feat> CGeneCache::GetmRNAFromCache ( const CSeq_feat feat,
CScope scope 

◆ IsPseudo()

bool CGeneCache::IsPseudo ( const CSeq_feat feat)

◆ x_HasNamedQual()

bool CGeneCache::x_HasNamedQual ( const CSeq_feat feat,
const string qual 

◆ x_IsPseudo()

bool CGeneCache::x_IsPseudo ( const CGene_ref gref)

Definition at line 150 of file gene_cache.cpp.

References CGene_ref_Base::GetPseudo(), and CGene_ref_Base::IsSetPseudo().

Member Data Documentation

◆ m_FeatGeneMap

TFeatGeneMap CGeneCache::m_FeatGeneMap

Definition at line 94 of file gene_cache.hpp.

◆ m_SeqTreeMap

TSeqTreeMap CGeneCache::m_SeqTreeMap

Definition at line 97 of file gene_cache.hpp.

The documentation for this class was generated from the following files:
Modified on Sat May 25 14:19:14 2024 by rev. 669887