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NCBI C++ ToolKit: src/objtools/readers/gtf_reader.cpp Source File

& strGtfType,

& strRawAttributes )

(

u=0; u <

.size(); ++u ) {

(strGtfType ==

) {

(strGtfType ==

) {

(

.empty() &&

.empty() ) {

& strAnnotName,

& strAnnotTitle,

( uFlags, strAnnotName, strAnnotTitle, resolver, pRL)

(

& lineData: readerData) {

(recType ==

|| recType ==

|| recType ==

);

(recType ==

|| recType ==

|| recType ==

);

(recType ==

) {

}

(recType ==

|| recType ==

) {

& xAttributes = x.

();

& yAttributes = y.

();

xit = xAttributes.

();

yit = yAttributes.begin();

(xit != xAttributes.end() && yit != yAttributes.end()) {

(xit->first < yit->first) {

}

(yit->first < xit->first) {

(xVals.

()) {

.AddValue(xit->first,

);

set_intersection(begin(xVals), end(xVals),

begin(yVals), end(yVals),

inserter(commonVals, commonVals.

()));

(!commonVals.

()) {

(

&

: commonVals) {

featId =

->GetFeatureIdFor(gff,

);

(line.

() || line[0] ==

);

& qualName,

(!values.

()) {

& parentType,

(parentType ==

) {

& quals = feature.

();

(

it = quals.begin(); it != quals.end();

) {

& qualKey = (*it)->GetQual();

qualKey ==

||

qualKey ==

||

qualKey ==

||

qualKey ==

) {

& qualVal = (*it)->GetVal();

(prevAttributes.

(qualKey, qualVal) && (!

.HasValue(qualKey, qualVal))) {

it = quals.erase(it);

& recType,

& parentType,

(parentType ==

) {

& parentType,

parentFeatId =

->GetFeatureIdFor(record, parentType);

->AddRecordForId(parentFeatId, record);

->AddRecordForId(parentFeatId, record);

& childTypeToAttribs = parentIt->second;

(

childIt = childTypeToAttribs.find(recType);

childIt != childTypeToAttribs.end()) {

& childAttributes = childIt->second;

childAttributes = accumulatedAttributes;

childTypeToAttribs.emplace(recType, attribs);

& prefix,

seqNum(1);

strFeatureId = prefix;

(strFeatureId.empty()) {

strFeatureId =

;

strFeatureId +=

;

feature.

().SetLocal().SetStr(strFeatureId);

featId =

->GetFeatureIdFor(record,

);

(record.

() ==

) ?

,

,

(ignoredAttrs.contains(name)) {

featId =

->GetFeatureIdFor(gff,

);

(!transcriptId.empty()) {

(

geneId = gff.

(); !geneId.empty()) {

(it->second != geneId) {

=

+ geneId +

+ transcriptId +

+ it->second +

;

(rec_type ==

||

(rec_type)) {

(

biotype = attrs.

(

);

attrs.

(

);

featId =

->GetFeatureIdFor(record,

);

pFeature->SetData().SetRna().SetType(rna_type);

pFeature->SetData().SetRna().SetExt().SetName(product);

(rec_type ==

) {

& featId)

featIt->second;

geneSynonym =

.ValueOf(

);

(!geneSynonym.empty()) {

gene.

().push_back(geneSynonym);

locusTag =

.ValueOf(

);

(!locusTag.empty()) {

(!locus.empty()) {

proteinId =

.ValueOf(

);

(!proteinId.empty()) {

ribosomalSlippage =

.ValueOf(

);

(!ribosomalSlippage.empty()) {

transTable =

.ValueOf(

);

(!transTable.empty()) {

cdr.

().Set().push_back(pGc);

(

: values) {

vector< string > tags;

(

it = tags.begin(); it != tags.end(); ++it ) {

(

& pQual : feature.

()) {

(pQual->GetQual() ==

) {

existingVals.

(pQual->GetVal());

(

: values) {

(existingVals.

(

) == existingVals.

()) {

(

itLocation:

->LocationMap()) {

= itLocation.first;

featSubType, itLocation.second);

(

itLocation:

->LocationMap()) {

= itLocation.first;

parentRnaFeatId =

(

) + pFeature->

(

) +

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

void xSetXrefFromTo(CSeq_feat &, CSeq_feat &)

virtual bool xAddFeatureToAnnot(CRef< CSeq_feat >, CSeq_annot &)

void xPostProcessAnnot(CSeq_annot &) override

bool x_GetFeatureById(const CTempString &, CRef< CSeq_feat > &)

IdToFeatureMap m_MapIdToFeature

virtual bool xParseFeature(const CTempString &, CSeq_annot &, ILineErrorListener *)

static CRef< CDbtag > x_ParseDbtag(const CTempString &)

virtual bool xParseStructuredComment(const CTempString &)

unsigned int mCurrentFeatureCount

static string xNormalizedAttributeValue(const CTempString &)

bool xSplitGffAttributes(const string &, vector< string > &) const

static string xNormalizedAttributeKey(const CTempString &)

const string & Type() const

const string & NormalizedType() const

void AddValue(const string &key, const string &value)

string ValueOf(const string &key) const

void GetValues(const string &key, MultiValue &values) const

const MultiAttributes & Get() const

bool HasValue(const string &key, const string &value="") const

string TranscriptId() const

CGtfAttributes mAttributes

bool xAssignAttributesFromGff(const string &, const string &)

const CGtfAttributes & GtfAttributes() const

void xFeatureAddQualifiers(const string &key, const CGtfAttributes::MultiValue &, CSeq_feat &)

void xFeatureSetQualifiersRna(const CGtfAttributes &attribs, CSeq_feat &)

void xCheckForGeneIdConflict(const CGtfReadRecord &record)

void xCreateParent(const CGtfReadRecord &record, const string &parentType, CSeq_annot &annot)

void xAssignFeatureId(const string &stub, CSeq_feat &feat)

bool xUpdateAnnotFeature(const CGff2Record &, CSeq_annot &, ILineErrorListener *=nullptr) override

unique_ptr< CGtfLocationMerger > mpLocations

void xCreateGene(const CGtfReadRecord &, CSeq_annot &)

void xFeatureSetQualifiersGene(const CGtfAttributes &attribs, CSeq_feat &)

void xFeatureSetDataCds(const CGtfReadRecord &, CSeq_feat &)

void xPostProcessAnnot(CSeq_annot &) override

void xCreateRna(const CGtfReadRecord &record, CSeq_annot &annot)

void xAddQualsToParent(const string &recType, const CGtfAttributes &attribs, const string &parentType, CSeq_feat &parent)

void xAddQualToFeat(const CGtfAttributes &attribs, const string &qualName, CSeq_feat &feat)

CRef< CSeq_feat > xFindFeatById(const string &)

CRef< CSeq_annot > ReadSeqAnnot(ILineReader &lr, ILineErrorListener *pErrors=nullptr) override

Read an object from a given line reader, render it as a single Seq-annot, if possible.

void xUpdateAnnotCds(const CGtfReadRecord &, CSeq_annot &)

CGtfReader(unsigned int=0, const string &="", const string &="", SeqIdResolver=CReadUtil::AsSeqId, CReaderListener *=nullptr)

void xFeatureSetDataGene(const CGtfReadRecord &, CSeq_feat &)

void xUpdateGeneAndMrna(const CGtfReadRecord &, CSeq_annot &)

bool xIsCommentLine(const CTempString &line) override

void xUpdateAnnotParent(const CGtfReadRecord &record, const string &parentType, CSeq_annot &annot)

map< string, string > m_TranscriptToGeneMap

TParentChildQualMap m_ParentChildQualMap

void xCreateCds(const CGtfReadRecord &, CSeq_annot &)

void xFeatureSetQualifiersCds(const CGtfAttributes &attribs, CSeq_feat &)

bool xProcessQualifierSpecialCase(const string &, const CGtfAttributes::MultiValue &, CSeq_feat &)

void xSetAncestorXrefs(CSeq_feat &, CSeq_feat &) override

void xFeatureSetQualifiers(const CGtfAttributes &attribs, const set< string > &ignoredAttrs, CSeq_feat &)

void xProcessData(const TReaderData &, CSeq_annot &) override

Common file reader utility functions.

virtual bool xParseBrowserLine(const CTempString &, CSeq_annot &)

unique_ptr< CReaderMessageHandler > m_pMessageHandler

SeqIdResolver mSeqIdResolve

unsigned int m_uLineNumber

vector< TReaderLine > TReaderData

virtual CRef< CSeq_annot > ReadSeqAnnot(CNcbiIstream &istr, ILineErrorListener *pErrors=nullptr)

Read an object from a given input stream, render it as a single Seq-annot.

virtual bool xIsTrackTerminator(const CTempString &)

ESubtype GetSubtype(void) const

namespace ncbi::objects::

const string & GetNamedQual(const CTempString &qual_name) const

Return a named qualifier.

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

Add a qualifier to this feature.

static bool SoTypeToFeature(std::string_view, CSeq_feat &, bool=false)

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

Abstract base class for lightweight line-by-line reading.

const_iterator begin() const

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator find(const key_type &key) const

const_iterator end() const

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

static const struct attribute attributes[]

@ eDiag_Error

Error message.

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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 list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static string Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

bool empty(void) const

Return true if the represented string is empty (i.e., the length is zero)

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static bool SplitInTwo(const CTempString str, const CTempString delim, string &str1, string &str2, TSplitFlags flags=0)

Split a string into two pieces using the specified delimiters.

static unsigned int StringToUInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to unsigned int.

TSyn & SetSyn(void)

Assign a value to Syn data member.

void SetLocus(const TLocus &value)

Assign a value to Locus data member.

void SetLocus_tag(const TLocus_tag &value)

Assign a value to Locus_tag data member.

EType

type of RNA feature

TDbxref & SetDbxref(void)

Assign a value to Dbxref data member.

void SetLocation(TLocation &value)

Assign a value to Location data member.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

void SetComment(const TComment &value)

Assign a value to Comment data member.

void SetProduct(TProduct &value)

Assign a value to Product data member.

const TQual & GetQual(void) const

Get the Qual member data.

void SetCode(TCode &value)

Assign a value to Code data member.

void SetExcept(TExcept value)

Assign a value to Except data member.

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.

void SetPseudo(TPseudo value)

Assign a value to Pseudo data member.

void SetExcept_text(const TExcept_text &value)

Assign a value to Except_text data member.

TQual & SetQual(void)

Assign a value to Qual data member.

bool IsRna(void) const

Check if variant Rna is selected.

bool IsGenbank(void) const

Check if variant Genbank is selected.

static bool s_IsCDSType(const string &recType)

static string s_GetTranscriptBiotype(const CGtfAttributes &attrs)

static CRNA_ref::EType s_RnaTypeFromRecType(const string &rec_type)

static CGtfAttributes s_GetIntersection(const CGtfAttributes &x, const CGtfAttributes &y)

static void s_TrimFeatQuals(const CGtfAttributes &prevAttributes, const CGtfAttributes &attributes, CSeq_feat &feature)

static bool s_IsExonOrUTR(const string &recType)

Lightweight interface for getting lines of data with minimal memory copying.

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

const GenericPointer< typename T::ValueType > T2 value

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

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