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NCBI C++ ToolKit: src/app/table2asn/async_token.cpp Source File

;

seh.GetCompleteSeq_entry();

(feat_tree.Empty())

feat_tree.

(

feature::CFeatTree());

feat_tree->AddFeatures(

(scope->GetBioseqHandle(*bioseq)));

map_locus_to_gene.clear();

map_protein_to_mrna.clear();

map_transcript_to_mrna.clear();

feat_tree.ReleaseOrNull();

(

pXref : cds.

()) {

(pXref->IsSetId()) {

pLinkedFeat = FindFeature(pXref->GetId());

pLinkedFeat->IsSetData() &&

pLinkedFeat->GetData().IsGene()) {

(pXref->IsSetData() &&

pXref->GetData().IsGene() &&

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

pGene = FeatFromMap(pXref->GetData().GetGene().GetLocus_tag(), map_locus_to_gene);

pGene = FindGeneByLocusTag(cds);

mappedCds(scope->GetSeq_featHandle(cds));

pGene.Reset(

*

(&mappedGene.GetOriginalFeature()));

(bioseq->IsSetAnnot()) {

(

annot : bioseq->GetAnnot())

(!annot->IsFtable())

;

((**feat_it).IsSetIds())

((**id_it).Equals(

))

((**feat_it).IsSetId() && (**feat_it).GetId().Equals(

))

(!

.empty()) {

it = feat_map.

(

);

(it != feat_map.

()) {

& locus_tag = cds.

(

);

FeatFromMap(locus_tag, map_locus_to_gene);

(

pXref : cds.

()) {

(pXref->IsSetId()) {

pLinkedFeat = FindFeature(pXref->GetId());

pLinkedFeat->IsSetData() &&

pLinkedFeat->GetData().IsRna() &&

pMrna = FindMrnaByQual(cds);

mappedCds(scope->GetSeq_featHandle(cds));

pMrna.Reset(

*

(&mappedMrna.GetOriginalFeature()));

& transcript_id = cds.

(

);

pMrna = FeatFromMap(transcript_id, map_transcript_to_mrna);

& protein_id = cds.

(

);

pMrna = FeatFromMap(protein_id, map_protein_to_mrna);

(!bioseq->IsSetAnnot()) {

(

annot: bioseq->GetAnnot()) {

(!annot->IsFtable()) {

(

feat: annot->GetData().GetFtable()) {

(!feat->CanGetData()) {

&

= feat->GetData();

isgene =

.IsGene();

(feat->IsSetQual()) {

(

qual: feat->GetQual()) {

(!qual->CanGetQual() || !qual->CanGetVal()) {

& name = qual->GetQual();

&

= qual->GetVal();

(name ==

) {

(name ==

) {

(name ==

) {

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

map_locus_to_gene.insert(

User-defined methods of the data storage class.

User-defined methods of the data storage class.

namespace ncbi::objects::

const string & GetNamedQual(const CTempString &qual_name) const

Return a named qualifier.

const_iterator end() const

container_type::value_type value_type

const_iterator find(const key_type &key) const

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

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

CMappedFeat GetBestMrnaForCds(const CMappedFeat &cds_feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)

CMappedFeat GetBestGeneForCds(const CMappedFeat &cds_feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0, CFeatTree::EBestGeneType lookup_type=CFeatTree::eBestGene_TreeOnly)

void Reset(void)

Reset reference object.

bool IsSetQual(void) const

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

bool IsCdregion(void) const

Check if variant Cdregion is selected.

bool IsSetXref(void) const

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

const TData & GetData(void) const

Get the Data member data.

list< CRef< CFeat_id > > TIds

const TXref & GetXref(void) const

Get the Xref member data.

list< CRef< CSeq_feat > > TFtable

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

Magic spell ;-) needed for some weird compilers... very empiric.

const GenericPointer< typename T::ValueType > T2 value

CRef< CSeq_feat > FindGeneByLocusTag(const CSeq_feat &cds) const

CRef< objects::CSeq_feat > ParentGene(const objects::CSeq_feat &cds)

CRef< objects::CSeq_feat > ParentMrna(const objects::CSeq_feat &cds)

CRef< objects::CSeq_feat > FindMrnaByQual(const objects::CSeq_feat &cds) const

CRef< objects::CSeq_feat > FeatFromMap(const string &key, const TFeatMap &) const

CRef< feature::CFeatTree > FeatTree()

CRef< objects::CSeq_feat > FindFeature(const objects::CFeat_id &id)

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