CGeneCache Class Reference

Search Toolkit Book for CGeneCache

#include <objtools/validator/gene_cache.hpp>

Collaboration diagram for CGeneCache:

Public Member Functions
	CGeneCache ()
	~CGeneCache ()
CConstRef< CSeq_feat >	GetGeneFromCache (const CSeq_feat *feat, CScope &scope)
CConstRef< CSeq_feat >	GetmRNAFromCache (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

typedef map<const CSeq_feat*, CConstRef<CSeq_feat> > CGeneCache::TFeatGeneMap

private

Definition at line 93 of file gene_cache.hpp.

TSeqTreeMap

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

private

Definition at line 96 of file gene_cache.hpp.

Constructor & Destructor Documentation

CGeneCache()

CGeneCache::CGeneCache ( )

inline

Definition at line 81 of file gene_cache.hpp.

~CGeneCache()

CGeneCache::~CGeneCache ( )

inline

Definition at line 82 of file gene_cache.hpp.

Member Function Documentation

Clear()

void CGeneCache::Clear ( void  )

inline

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
	)

Definition at line 79 of file gene_cache.cpp.

References CScope::GetBioseqHandle().

Referenced by CCdregionValidator::x_HasGoodParent(), CValidError_bioseq::x_MatchesOverlappingFeaturePartial(), CCdregionValidator::x_ValidateFarProducts(), and CSingleFeatValidator::x_ValidateGeneId().

GetGeneFromCache()

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

Definition at line 106 of file gene_cache.cpp.

References GetGeneForFeature(), CMappedFeat::GetSeq_feat(), and CScope::GetSeq_featHandle().

Referenced by CCdregionValidator::CCdregionValidator(), CMRNAValidator::CMRNAValidator(), CValidError_imp::GetCachedGene(), CValidError_feat::IsOverlappingGenePseudo(), CValidError_imp::PostErr(), CRNAValidator::Validate(), CExonValidator::Validate(), CIntronValidator::Validate(), CValidError_bioseq::x_MatchesOverlappingFeaturePartial(), CSingleFeatValidator::x_ValidateGeneXRef(), and CSingleFeatValidator::x_ValidateOldLocusTag().

GetmRNAFromCache()

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

IsPseudo()

bool CGeneCache::IsPseudo ( const CSeq_feat &  feat )

static

Definition at line 156 of file gene_cache.cpp.

References CSeq_feat_Base::GetData(), CSeqFeatData_Base::GetGene(), CSeq_feat_Base::GetPseudo(), CSeqFeatData_Base::IsGene(), CSeq_feat_Base::IsSetPseudo(), x_HasNamedQual(), and x_IsPseudo().

Referenced by CValidError_bioseq::ValidateFeatPartialInContext().

x_HasNamedQual()

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

staticprivate

Definition at line 135 of file gene_cache.cpp.

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

x_IsPseudo()

bool CGeneCache::x_IsPseudo ( const CGene_ref &  gref )

staticprivate

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

private

Definition at line 94 of file gene_cache.hpp.

m_SeqTreeMap

TSeqTreeMap CGeneCache::m_SeqTreeMap

private

Definition at line 97 of file gene_cache.hpp.

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

• include/objtools/validator/gene_cache.hpp
• src/objtools/validator/gene_cache.cpp