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NCBI C++ ToolKit: src/objtools/import/ftable/gtf_annot_assembler.cpp Source File

76 const string

& recType,

77 const

pair<string, string>& featKey,

98 auto

& features = typeIt->second;

99 auto

featIt = features.find(featKey);

100 if

(featIt == features.end()) {

103 return

featIt->second;

111

geneKey.second =

""

;

116 auto

geneParent = geneEntries->second.find(geneKey);

117 if

(geneParent == geneEntries->second.end()) {

120 return

geneParent->second;

132 auto

mrnaParent = mrnaEntries->second.find(mrnaKey);

133 if

(mrnaParent == mrnaEntries->second.end()) {

136 return

mrnaParent->second;

141 const string

type

)

143 static const auto

emptyMap =

TYPEMAP

();

148 return

typeIt->second;

155 if

(record.

Type

() ==

"gene"

) {

169

{

"initial"

"mrna"

170

{

"internal"

"mrna"

171

{

"terminal"

"mrna"

172

{

"start_codon"

"cds"

173

{

"stop_codon"

"cds"

175 auto

recType = record.

Type

();

176 auto

it = typeMap.

find

(recType);

177 if

(it != typeMap.

end

()) {

213

vector<string> ignoredFeatureTypes = {

214 "inter"

"inter_cns"

"intron"

"intron_cns"

216 if

(find(ignoredFeatureTypes.begin(), ignoredFeatureTypes.end(),

217

record.

Type

()) != ignoredFeatureTypes.end()) {

235 auto

handlerIt = handlerMap.find(record.

Type

());

236 if

(handlerIt == handlerMap.end()) {

238 throw

errorUnknownFeatureType;

240

(this->*(handlerIt->second))(record, annot);

262 if

(impliedRecord.

Type

() !=

"mrna"

) {

332 if

(record.

Type

() ==

"gene"

) {

340 min

(recordInt.GetFrom(), featureInt.GetFrom()));

342 max

(recordInt.GetTo(), featureInt.GetTo()));

403 auto

& cdsRef = pCds->

SetData

().SetCdregion();

407 if

(cdsStart == recordLoc.GetFrom()) {

408

cdsRef.SetFrame(record.

Frame

());

413 if

(cdsStop == recordLoc.GetTo()) {

414

cdsRef.SetFrame(record.

Frame

());

427

annot.

SetData

().SetFtable().push_back(pFeature);

448 auto

& geneRef = pFeature->

SetData

().SetGene();

450 if

(!locusTag.empty()) {

451

geneRef.SetLocus_tag(locusTag);

472

pFeature->

SetData

().SetCdregion();

474

pFeature->

SetData

().SetCdregion().SetFrame(record.

Frame

());

487

{

"initial"

"mrna"

488

{

"internal"

"mrna"

489

{

"terminal"

"mrna"

490

{

"start_codon"

"cds"

491

{

"stop_codon"

"cds"

493 string

mappedType(record.

Type

());

494 auto

it = typeMap.

find

(record.

Type

());

495 if

(it != typeMap.

end

()) {

496

mappedType = it->second;

508

record.

Type

() ==

"mrna"

522

pFeature->

SetLocation

().Assign(*pUpdatedLocation);

532

vector<string> ignoredKeys = {

533 "exon_number"

"locus_tag"

541 auto key

= entry.first;

542 if

(find(ignoredKeys.begin(), ignoredKeys.end(),

key

)

543

!= ignoredKeys.end()) {

546 for

(

auto value

: entry.second) {

547 const auto

& existingQuals = pFeature->

GetQual

();

548 bool

isDuplicate =

false

;

549 for

(

auto

qualRef: existingQuals) {

550 if

(qualRef->GetQual() ==

key

&& qualRef->GetVal() ==

value

) {

568 auto

geneEntries =

mpFeatureMap

->GetTypeMapFor(

"gene"

);

569 auto

mrnaEntries =

mpFeatureMap

->GetTypeMapFor(

"mrna"

);

570 auto

cdsEntries =

mpFeatureMap

->GetTypeMapFor(

"cds"

);

572 for

(

auto

mrnaEntry: mrnaEntries) {

574 auto

mrnaKey = mrnaEntry.first;

575 for

(

auto

cdsEntry: cdsEntries) {

576 if

(mrnaKey == cdsEntry.first) {

577

cdsEntry.second->AddSeqFeatXref(mrnaEntry.second->GetId());

578

mrnaEntry.second->AddSeqFeatXref(cdsEntry.second->GetId());

582

mrnaKey.second =

""

;

583 for

(

auto

geneEntry: geneEntries) {

584 if

(mrnaKey == geneEntry.first) {

585

geneEntry.second->AddSeqFeatXref(mrnaEntry.second->GetId());

586

mrnaEntry.second->AddSeqFeatXref(geneEntry.second->GetId());

591 for

(

auto

cdsEntry: cdsEntries) {

592 auto

cdsKey = cdsEntry.first;

594 for

(

auto

geneEntry: geneEntries) {

595 if

(cdsKey == geneEntry.first) {

596

geneEntry.second->AddSeqFeatXref(cdsEntry.second->GetId());

597

cdsEntry.second->AddSeqFeatXref(geneEntry.second->GetId());

@ eExtreme_Positional

numerical value

static string xGetCookedFeatureType(const CGtfImportData &record)

void AddFeature(const CGtfImportData &record, CRef< CSeq_feat > &pFeat)

pair< string, string > FEATKEY

CRef< CSeq_feat > FindGeneParent(const CGtfImportData &record) const

CRef< CSeq_feat > FindMrnaParent(const CGtfImportData &record) const

const TYPEMAP & GetTypeMapFor(const string &type)

map< FEATKEY, CRef< CSeq_feat > > TYPEMAP

static FEATKEY FeatKeyOf(const CGtfImportData &record)

CRef< CSeq_feat > FindFeature(const CGtfImportData &record) const

void AddFeature(const string &recType, const pair< string, string > &featKey, CRef< CSeq_feat > &pFeat)

virtual ~CGtfAnnotAssembler()

void xProcessRecordMrna(const CGtfImportData &, CSeq_annot &)

void xUpdateMrna(const CGtfImportData &, CRef< CSeq_feat > &, CSeq_annot &)

void xAnnotAddFeature(const CGtfImportData &, CRef< CSeq_feat > &, CSeq_annot &)

void xCreateCds(const CGtfImportData &, CRef< CSeq_feat > &, CSeq_annot &)

void xFeatureUpdateLocation(const CGtfImportData &, CRef< CSeq_feat > &)

unique_ptr< CFeatureIdGenerator > mpIdGenerator

void xUpdateCds(const CGtfImportData &, CRef< CSeq_feat > &, CSeq_annot &)

CGtfAnnotAssembler(CImportMessageHandler &)

void xFeatureSetLocation(const CGtfImportData &, CRef< CSeq_feat > &)

unique_ptr< CFeatureMap > mpFeatureMap

void xFeatureSetMrna(const CGtfImportData &, CRef< CSeq_feat > &)

void xProcessRecordGene(const CGtfImportData &, CSeq_annot &)

void xCreateGene(const CGtfImportData &, CRef< CSeq_feat > &, CSeq_annot &)

void xFeatureSetCds(const CGtfImportData &, CRef< CSeq_feat > &)

void xFeatureSetQualifiers(const CGtfImportData &, CRef< CSeq_feat > &)

void ProcessRecord(const CFeatImportData &, CSeq_annot &) override

void xFeatureSetFeatId(const CGtfImportData &, CRef< CSeq_feat > &)

void xCreateMrna(const CGtfImportData &, CRef< CSeq_feat > &, CSeq_annot &)

void xFeatureSetGene(const CGtfImportData &, CRef< CSeq_feat > &)

void xProcessRecordCds(const CGtfImportData &, CSeq_annot &)

void xUpdateGene(const CGtfImportData &, CRef< CSeq_feat > &, CSeq_annot &)

void xAnnotGenerateXrefs(CSeq_annot &)

virtual void FinalizeAnnot(const CAnnotImportData &, CSeq_annot &) override

CCdregion::TFrame Frame() const

string AttributeValueOf(const std::string &) const

const CSeq_loc & Location() const

const std::string & Type() const

void AdjustFeatureType(const std::string &type)

std::string TranscriptId() const

std::string GeneId() const

const ATTRIBUTES & Attributes() const

void AmendMessage(const std::string &amend)

namespace ncbi::objects::

void AddQualifier(const string &qual_name, const string &qual_val)

Add a qualifier to this feature.

static CRef< CSeq_loc > AddLocations(const CSeq_loc &, const CSeq_loc &)

const_iterator end() const

const_iterator find(const key_type &key) const

void Reset(void)

Reset reference object.

void SetLocation(TLocation &value)

Assign a value to Location 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.

void SetId(TId &value)

Assign a value to Id data member.

void SetData(TData &value)

Assign a value to Data data member.

@ eFrame_not_set

not set, code uses one

bool IsInt(void) const

Check if variant Int is selected.

const TInt & GetInt(void) const

Get the variant data.

void SetData(TData &value)

Assign a value to Data data member.

const struct ncbi::grid::netcache::search::fields::KEY key

const GenericPointer< typename T::ValueType > T2 value

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/gtf__annot__assembler_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/import/ftable/gtf_annot_assembler.cpp Source File

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/gtfannotassembler_8cpp_source.html below: