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NCBI C++ ToolKit: src/objtools/validator/gene_cache.cpp Source File

sequence;

(smit == m_SeqTreeMap.end()) {

m_SeqTreeMap[bsh] = tr;

GetFeatTreeFromCache(bsh);

GetFeatTreeFromCache(feat.

(), scope);

(it == m_FeatGeneMap.end()) {

m_FeatGeneMap[feat] = gene;

(

it : feat.

()) {

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

static bool IsPseudo(const CSeq_feat &feat)

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

static bool x_IsPseudo(const CGene_ref &gref)

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

namespace ncbi::objects::

container_type::iterator iterator

Include a standard set of the NCBI C++ Toolkit most basic headers.

The NCBI C++ standard methods for dealing with std::string.

CConstRef< CSeq_feat > GetGeneForFeature(const CSeq_feat &feat, CScope &scope)

Finds gene for feature, but obeys SeqFeatXref directives.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CSeq_feat_Handle GetSeq_featHandle(const CSeq_feat &feat, EMissing action=eMissing_Default)

CConstRef< CSeq_feat > GetSeq_feat(void) const

Get current seq-feat.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

bool IsSetPseudo(void) const

pseudogene Check if a value has been assigned to Pseudo data member.

TPseudo GetPseudo(void) const

Get the Pseudo member data.

bool IsSetQual(void) const

qualifiers Check if a value has been assigned to Qual data member.

const TQual & GetQual(void) const

Get the Qual member data.

const TLocation & GetLocation(void) const

Get the Location member data.

bool IsGene(void) const

Check if variant Gene is selected.

const TData & GetData(void) const

Get the Data member data.

TPseudo GetPseudo(void) const

Get the Pseudo member data.

bool IsSetPseudo(void) const

annotated on pseudogene? Check if a value has been assigned to Pseudo data member.

const TGene & GetGene(void) const

Get the variant data.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

bool x_IsPseudo(const CGene_ref &ref)

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

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