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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/gene__names_8cpp_source.html below:

NCBI C++ ToolKit: src/misc/discrepancy/gene_names.cpp Source File

44 static const char

* BadWords[] = {

"putative"

"fragment"

"gene"

"orf"

"like"

};

58 for

(

size_t i

= 0;

< s.size() &&

< 4;

++) {

68 if

(feat.IsSetData() && feat.GetData().IsGene() && feat.GetData().GetGene().CanGetLocus()) {

69 string

locus = feat.GetData().GetGene().GetLocus();

72

m_Objs[word.empty() ?

"[n] gene[s] contain[S] suspect phrase or characters"

"[n] gene[s] contain[S] [(]"

+ word].Add(*

context

.SeqFeatObjRef(feat, &feat));

87

new_feat->

SetData

().SetGene().ResetLocus();

88 context

.ReplaceSeq_feat(*obj, *sf, *new_feat);

103 if

(feat.IsSetData() && feat.GetData().IsGene() && feat.GetData().GetGene().CanGetLocus()) {

104 string

locus = feat.GetData().GetGene().GetLocus();

106

m_Objs[

"[n] bacterial gene[s] [does] not start with lowercase letter"

].Add(*

context

.SeqFeatObjRef(feat, &feat));

121

new_feat->

SetData

().SetGene().ResetLocus();

122 context

.ReplaceSeq_feat(*obj, *sf, *new_feat);

133 if

(feat.IsSetData() && feat.GetData().IsProt() && feat.GetData().GetProt().CanGetName() && feat.GetData().GetProt().CanGetEc() && !feat.GetData().GetProt().GetEc().empty()) {

134 const

list <string>&

names

= feat.GetData().GetProt().GetName();

135 if

names

.empty()) {

139 if

(

str

"hypothetical protein"

str

"unknown protein"

) {

140

m_Objs[

"[n] protein feature[s] [has] an EC number and a protein name of 'unknown protein' or 'hypothetical protein'"

].Add(*

context

.SeqFeatObjRef(feat, &feat)).Fatal();

153

new_feat->

SetData

().SetProt().ResetEc();

154 context

.ReplaceSeq_feat(*obj, *sf, *new_feat);

165 if

(feat.IsSetData() && feat.GetData().IsCdregion() && feat.CanGetProduct()) {

173 if

(

prot

.CanGetName()) {

176

m_Objs[

"[n] hypothetical coding region[s] [has] a gene name"

].Fatal().Add(*

context

.SeqFeatObjRef(feat, gene));

193

new_feat->

SetData

().SetGene().ResetLocus();

194 context

.ReplaceSeq_feat(*obj, *sf, *new_feat,

true

);

203 const string kDuplicateAdjacent

"[n] gene[s] [is] adjacent to another gene with the same locus tag."

;

208 const auto

& genes =

context

.FeatGenes();

209 string

last_locus_tag;

212 if

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

214 const string

& this_locus_tag = gene->GetData().GetGene().GetLocus_tag();

215

m_Objs[

kEmptyStr

][this_locus_tag].Add(*this_disc_obj).Fatal();

216 if

(last_disc_obj && last_locus_tag == this_locus_tag) {

220

last_locus_tag = this_locus_tag;

221

last_disc_obj = this_disc_obj;

232 for

(

auto

& it : m_Objs[

kEmptyStr

].GetMap()) {

233 if

(it.second->GetObjects().size() > 1) {

235 for

(

auto

& obj : it.second->GetObjects()) {

bool IsSetLineage(void) const

namespace ncbi::objects::

#define DISCREPANCY_AUTOFIX(name)

#define DISCREPANCY_CASE(name, type, group, descr)

#define DISCREPANCY_SUMMARIZE(name)

static const struct name_t names[]

static const char * str(char *buf, int n)

static bool HasBadWord(const string &s, string &word)

const string kDuplicateAdjacent

const string kDuplicateLocusTagsTop

static bool Has4Numbers(const string &s)

const string kDuplicateLocusTagsStart

constexpr size_t ArraySize(const Element(&)[Size])

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

Set object to copy of another one.

CBioseq_Handle GetBioseqFromSeqLoc(const CSeq_loc &loc, CScope &scope, CScope::EGetBioseqFlag flag=CScope::eGetBioseq_Loaded)

Retrieve the Bioseq Handle from a location.

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 SIZE_TYPE FindNoCase(const CTempString str, const CTempString pattern, SIZE_TYPE start, SIZE_TYPE end, EOccurrence which=eFirst)

Find the pattern in the specified range of a string using a case insensitive search.

static string & ToLower(string &str)

Convert string to lower case â string& version.

static const char label[]

bool CanGetLocus(void) const

Check if it is safe to call GetLocus method.

bool IsSetLocus(void) const

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

const TLocus & GetLocus(void) const

Get the Locus member data.

bool IsSetData(void) const

the specific data Check if a value has been assigned to Data 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 TProt & GetProt(void) const

Get the variant data.

const TSource & GetSource(void) const

Get the variant data.

void AddComment(CSeq_feat &feat, const string &comment)

static CS_CONTEXT * context

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