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NCBI C++ ToolKit: src/objtools/cleanup/gene_qual_normalization.cpp Source File

(!gene.GetData().IsGene() ||

gene.GetData().GetGene().IsSetLocus() ||

!gene.GetData().GetGene().IsSetLocus_tag() ||

(

it : cds.GetXref()) {

(it->IsSetData() && it->GetData().IsGene()) {

(it->GetData().GetGene().IsSetLocus()) {

locus = it->GetData().GetGene().GetLocus();

(it->GetData().GetGene().IsSetLocus_tag()) {

locus_tag = it->GetData().GetGene().GetLocus_tag();

gene.GetData().GetGene().IsSetLocus_tag() &&

!

(locus_tag, gene.GetData().GetGene().GetLocus_tag())) {

(

it : cds.

()) {

(it->IsSetData() && it->GetData().IsGene()) {

(it->GetData().GetGene().IsSetLocus()) {

locus = it->GetData().GetGene().GetLocus();

(it->GetData().GetGene().IsSetLocus_tag()) {

locus_tag = it->GetData().GetGene().GetLocus_tag();

gene.

().SetGene().SetLocus(locus);

gene_xref->SetData().SetGene().ResetLocus();

vector<CCleanup::TFeatGenePair> rval;

pair<CSeq_feat_Handle, bool> TFeatOkPair;

TGeneCDSMap gene_cds;

tr->SetIgnoreMissingGeneXref();

(

->GetData().IsCdregion()) {

TGeneCDSMap::iterator smit = gene_cds.find(gene);

(smit == gene_cds.end()) {

gene_cds[gene] = {

->GetSeq_feat_Handle(), ok_to_map };

gene_cds[gene].second =

;

(

copy_pair : gene_cds) {

(copy_pair.second.second) {

rval.push_back({ copy_pair.second.first, copy_pair.first });

any_change =

;

(

copy_pair : cds_gene_pairs) {

new_cds->

(*(copy_pair.first.GetOriginalSeq_feat()));

new_gene->

(*(copy_pair.second.GetOriginalSeq_feat()));

gene_edit.

(*new_gene);

any_change =

;

User-defined methods of the data storage class.

const string & GetLineage(void) const

bool IsSetLineage(void) const

static vector< TFeatGenePair > GetNormalizableGeneQualPairs(CBioseq_Handle bsh)

static bool NormalizeGeneQuals(CSeq_feat &cds, CSeq_feat &gene)

CSeq_feat_EditHandle –.

namespace ncbi::objects::

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

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

bool IsMappablePair(const CSeq_feat &cds, const CSeq_feat &gene)

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

void Replace(const CSeq_feat &new_feat) const

Replace the feature with new Seq-feat object.

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

#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 IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

static bool Equal(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2, ECase use_case=eCase)

Test for equality of a substring with another string.

bool IsSetLocus_tag(void) const

systematic gene name (e.g., MI0001, ORF0069) Check if a value has been assigned to Locus_tag data mem...

bool IsSetLocus(void) const

Official gene symbol Check if a value has been assigned to Locus data member.

const TLocus_tag & GetLocus_tag(void) const

Get the Locus_tag member data.

TXref & SetXref(void)

Assign a value to Xref data member.

bool IsSetXref(void) const

cite other relevant features Check if a value has been assigned to Xref data member.

bool IsGene(void) const

Check if variant Gene is selected.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

const TGene & GetGene(void) const

Get the variant data.

const TSource & GetSource(void) const

Get the variant data.

bool IsSource(void) const

Check if variant Source is selected.

@ e_Source

source of materials, includes Org-ref

@ eMol_na

just a nucleic acid

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