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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/gene__validator_8cpp_source.html below:

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

53 using namespace

sequence;

96 const CGene_ref

& gene = m_Feat.GetData().GetGene();

98

m_Imp.IncrementGeneCount();

108 "There is a gene feature where all fields are empty"

);

112 "Comment has same value as gene locus"

);

118 for

(

auto

it : locus_tag) {

119 if

(

isspace

((

unsigned char

)(it)) != 0 ) {

122 "' should be a single word without any spaces"

);

130 "Gene locus and locus_tag '"

+ gene.

GetLocus

() +

"' match"

);

132 if

(m_Feat.IsSetComment() &&

NStr::EqualCase

(m_Feat.GetComment(), locus_tag)) {

134 "Comment has same value as gene locus_tag"

);

136 if

(m_Feat.IsSetQual()) {

137 for

(

auto

it : m_Feat.GetQual()) {

138 if

(it->IsSetQual() &&

NStr::EqualNocase

(it->GetQual(),

"old_locus_tag"

) && it->IsSetVal()) {

141 "old_locus_tag has same value as gene locus_tag"

);

143 "Gene locus_tag and old_locus_tag '"

+ locus_tag +

"' match"

);

145 if

(

NStr::Find

(it->GetVal(),

","

) != string::npos) {

147 "old_locus_tag has comma, multiple old_locus_tags should be split into separate qualifiers"

);

152

}

else if

(m_Imp.DoesAnyGeneHaveLocusTag() &&

155 "Missing gene locus tag"

);

159

m_Imp.ValidateDbxref(gene.

GetDb

(), m_Feat);

162 if

(m_Imp.IsRefSeq() && gene.

IsSetSyn

()) {

163 for

(

auto

it : gene.

GetSyn

()) {

164 if

(sc_BadGeneSyn.find (it.c_str()) != sc_BadGeneSyn.end()) {

166 "Uninformative gene synonym '"

+ it +

"'"

);

171 "gene synonym has same value as gene locus"

);

178

&& !m_Imp.IsGpipe()) {

180 "gene description has same value as gene locus"

);

185 "gene synonym without gene locus or description"

);

189

ValidateCharactersInField (gene.

GetLocus

(),

"Gene locus"

);

195 "gene locus "

+ gene.

GetLocus

() +

" has SGML"

);

199 "gene locus_tag "

+ gene.

GetLocus_tag

() +

" has SGML"

);

202 string

desc = gene.

GetDesc

();

205 "gene description "

+ gene.

GetDesc

() +

" has SGML"

);

209 for

(

auto

it : gene.

GetSyn

()) {

212 "gene synonym "

+ it +

" has SGML"

);

218

x_ValidateMultiIntervalGene();

227

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

NStr::IsBlank

(m_Feat.GetData().GetGene().GetLocus_tag()))) {

237 if

( !operon || !operon->

IsSetQual

() ) {

243 if

(

label

.empty() ) {

247 for

(

auto

qual_iter : operon->

GetQual

()) {

253 "Operon is same as gene - "

+ qual.

GetVal

());

265

loc->

SetInt

().SetFrom(from);

266

loc->

SetInt

().SetTo(to);

268

loc->

SetInt

().SetFrom(to);

269

loc->

SetInt

().SetTo(from);

284

mobile_elements.clear();

300 const

CSeq_loc& loc = m_Feat.GetLocation();

301

CSeq_loc_CI

(loc);

309

gap_start =

.GetRange().GetFrom() + 1;

311

gap_start =

.GetRange().GetTo() + 1;

317

gap_end =

.GetRange().GetTo();

319

gap_end =

.GetRange().GetFrom();

335

CSeq_loc_CI

(loc);

340 if

(

.GetRange().GetFrom() != 0) {

353 if

.GetRange().GetFrom() != 0) {

369 const

CSeq_loc& loc = m_Feat.GetLocation();

370

CSeq_loc_CI

(loc);

375 if

(m_Feat.IsSetExcept() && m_Feat.IsSetExcept_text()

376

NStr::FindNoCase

(m_Feat.GetExcept_text(),

"trans-splicing"

) != string::npos) {

381 if

(x_AllIntervalGapsAreMobileElements()) {

392

}

else if

(m_Imp.IsSmallGenomeSet()) {

394 "Multiple interval gene feature in small genome set - " 395 "set trans-splicing exception if appropriate"

);

398 "Gene feature on non-segmented sequence should not " 399 "have multiple intervals"

);

401

}

catch

(

const

exception& e ) {

402 if

(

NStr::Find

(e.what(),

"Error: Cannot resolve"

) == string::npos) {

404 string

(

"Exception while validating multi-interval genes. EXCEPTION: "

) +

420 for

( CSeq_loc_CI

(loc);

; ++

) {

429 if

(loc.GetId()->IsOther()) {

440 if

((*it)->IsOther()) {

456 bool

completeness =

false

;

459 if

(diter->GetMolinfo().IsSetTech() && diter->GetMolinfo().GetTech() ==

CMolInfo::eTech_wgs

) {

463

completeness =

true

;

470 if

(diter->GetSource().IsSetDivision()

static CRef< CScope > m_Scope

@ eErr_GENERIC_SgmlPresentInText

@ eErr_SEQ_FEAT_InvalidOperonMatchesGene

@ eErr_SEQ_FEAT_ExceptionRequiresLocusTag

@ eErr_SEQ_FEAT_MissingGeneLocusTag

@ eErr_SEQ_FEAT_LocusTagHasSpace

@ eErr_SEQ_FEAT_MultiIntervalGene

@ eErr_INTERNAL_Exception

@ eErr_SEQ_FEAT_OldLocusTagBadFormat

@ eErr_SEQ_FEAT_RedundantFields

@ eErr_SEQ_FEAT_LocusTagProblem

@ eErr_SEQ_FEAT_GeneRefHasNoData

@ eErr_SEQ_FEAT_LocusTagGeneLocusMatch

@ eErr_SEQ_FEAT_UndesiredGeneSynonym

@Gb_qual.hpp User-defined methods of the data storage class.

bool x_AllIntervalGapsAreMobileElements()

void x_ValidateMultiIntervalGene()

void x_ValidateExceptText(const string &text) override

@ eSubtype_mobile_element

virtual void x_ValidateExceptText(const string &text)

Cache various information for one validation run.

CBioseq_Handle GetBioseqHandleFromLocation(CScope *scope, const CSeq_loc &loc, const CTSE_Handle &tse)

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

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

static const char si[8][64]

Public API for finding the gene(s) on a given feature using the same criteria as the flatfile generat...

static bool s_LocIntervalsSpanOrigin(const CSeq_loc &loc, CBioseq_Handle bsh)

static const char *const sc_BadGeneSynText[]

static bool s_IsLocDirSub(const CSeq_loc &loc, const CTSE_Handle &tse, CCacheImpl &cache, CScope *scope)

DEFINE_STATIC_ARRAY_MAP(TBadGeneSynSet, sc_BadGeneSyn, sc_BadGeneSynText)

CStaticArraySet< const char *, PCase_CStr > TBadGeneSynSet

bool s_HasMobileElementForInterval(TSeqPos from, TSeqPos to, CBioseq_Handle bsh)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

@ eDiag_Info

Informational message.

@ eDiag_Error

Error message.

@ eDiag_Warning

Warning message.

string GetLabel(const CSeq_id &id)

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

Override Assign() to incorporate cache invalidation.

@ fFGL_Content

Include its content if there is any.

bool IsOneBioseq(const CSeq_loc &loc, CScope *scope)

Returns true if all embedded CSeq_ids represent the same CBioseq, else false.

@ eOverlap_Contained

2nd contained within 1st extremes

CConstRef< CSeq_feat > GetOverlappingOperon(const CSeq_loc &loc, CScope &scope)

vector< TFeatScore > TFeatScores

void GetOverlappingFeatures(const CSeq_loc &loc, CSeqFeatData::E_Choice feat_type, CSeqFeatData::ESubtype feat_subtype, EOverlapType overlap_type, TFeatScores &feats, CScope &scope, const TBestFeatOpts opts=0, CGetOverlappingFeaturesPlugin *plugin=NULL)

Find all features overlapping the location.

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

TSeqPos GetBioseqLength(void) const

CConstRef< CSeq_id > GetSeqId(void) const

Get id which can be used to access this bioseq handle Throws an exception if none is available.

CScope & GetScope(void) const

Get scope this handle belongs to.

#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 int CompareNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive compare of a substring with another string.

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 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 EqualCase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-sensitive equality of a substring with another string.

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

Compare of a substring with another string.

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

Case-insensitive equality of a substring with another 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.

static const char label[]

bool IsSetSyn(void) const

synonyms for locus Check if a value has been assigned to Syn data member.

const TSyn & GetSyn(void) const

Get the Syn member data.

const TDesc & GetDesc(void) const

Get the Desc member data.

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.

bool IsSetDesc(void) const

descriptive name Check if a value has been assigned to Desc data member.

bool IsSetDb(void) const

ids in other dbases Check if a value has been assigned to Db data member.

bool IsSetAllele(void) const

Official allele designation Check if a value has been assigned to Allele data member.

const TDb & GetDb(void) const

Get the Db member data.

bool IsSetMaploc(void) const

descriptive map location Check if a value has been assigned to Maploc data member.

const TLocus_tag & GetLocus_tag(void) const

Get the Locus_tag member data.

const TLocus & GetLocus(void) const

Get the Locus member data.

const TAllele & GetAllele(void) const

Get the Allele member data.

const TMaploc & GetMaploc(void) const

Get the Maploc member data.

const TVal & GetVal(void) const

Get the Val 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.

bool CanGetVal(void) const

Check if it is safe to call GetVal method.

const TQual & GetQual(void) const

Get the Qual member data.

bool CanGetQual(void) const

Check if it is safe to call GetQual method.

ENa_strand

strand of nucleic acid

@ eCompleteness_complete

complete biological entity

@ eTech_wgs

whole genome shotgun sequencing

@ e_Genbank

GenBank specific info.

@ e_Molinfo

info on the molecule and techniques

@ e_Source

source of materials, includes Org-ref

static void text(MDB_val *v)

#define FOR_EACH_SEQID_ON_BIOSEQ(Itr, Var)

FOR_EACH_SEQID_ON_BIOSEQ EDIT_EACH_SEQID_ON_BIOSEQ.

#define FOR_EACH_KEYWORD_ON_GENBANKBLOCK(Itr, Var)

FOR_EACH_KEYWORD_ON_GENBANKBLOCK EDIT_EACH_KEYWORD_ON_GENBANKBLOCK.

bool ContainsSgml(const string &str)

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