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NCBI C++ ToolKit: src/objtools/readers/gff3_reader.cpp Source File

(recordType ==

) {

cdsId = parentId;

& strRawInput )

(! parent.empty() && parent ==

) {

+ parent +

);

(

==

||

(

==

) {

& strRawKey )

;

;

& title,

(

& lineData: readerData) {

& line = lineData.mData;

annot.

().SetAlign().push_back(pAlign);

(!pRecord->AssignFromGff(line)) {

= pRecord->GetOneAttribute(

);

parent = pRecord->GetOneAttribute(

);

(! parent.empty()) {

cerr <<

<< parent <<

<<

<< endl;

(!

.

()) {

(pRecord->IsMultiParent()) {

));

& strLine)

( !pRecord->AssignFromGff(strLine) ) {

( !pRecord->GetAttribute(

,

) ) {

(alignments.find(

) == alignments.end()) {

alignments[id].push_back(alignment);

(recType ==

|| recType ==

|| recType ==

) {

(recType ==

) {

(recType ==

) {

(recType ==

) {

& mrnaId,

message =

;

message += exon.

();

message +=

;

& containingInt = cit->second.GetObject();

containedInt.

() > containingInt.

()) {

message =

;

message += exon.

();

message +=

;

(!parentId.empty()) {

(!parentId.empty()) {

& parent,

&grandParentsStr = pParent->

(

);

list<string> grandParents;

(grandParentsStr,

, grandParents, 0);

(list<string>::const_iterator gpcit = grandParents.begin();

gpcit != grandParents.end(); ++gpcit) {

pGrandParentXref->SetId(*pGrandParentId);

pFeature->

().push_back(pGrandParentXref);

pGrandChildXref->SetId(*pGrandChildId);

pGrandParent->

().push_back(pGrandChildXref);

& parent,

pParentXref->SetId(*pParentId);

pChild->

().push_back(pParentXref);

pChildXref->SetId(*pChildId);

pParent->

().push_back(pChildXref);

+

+

);

underConstruction = it->second;

featType = record.

();

(featType ==

|| featType ==

) {

);

);

pCodeBreak->

().SetNcbieaa(

(featType ==

) ?

:

);

list< CRef< CCode_break > >& codeBreaks = cdRegion.

();

codeBreaks.push_back(pCodeBreak);

list<string> parents;

(list<string>::const_iterator cit = parents.begin();

cit != parents.end();

);

);

annot.

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

(it->second == parentId) {

);

(mCdsParents.find(

) != mCdsParents.end());

*

ignoredTypesAlways_[] = {

STRINGARRAY::const_iterator cit = ignoredTypesAlways.find(ftype);

(cit != ignoredTypesAlways.end()) {

*

specialTypesGenbank_[] = {

,

,

,

*

ignoredTypesGenbank_[] = {

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

cit = specialTypesGenbank.find(ftype);

(cit != specialTypesGenbank.end()) {

cit = ignoredTypesGenbank.find(ftype);

(cit != ignoredTypesGenbank.end()) {

it = attrs.

(

);

(it != attrs.end()) {

(featData.

()) {

subtype = featData.

();

(

itLocation :

->LocationMap()) {

= itLocation.first;

& locs = itLocation.second;

list<CGff3LocationRecord> exonLocs;

(

record : locs) {

(record.mType ==

) {

exonLocs.push_back(record);

(! exonLocs.empty()) {

->MergeLocation(pNewLoc, frame, exonLocs);

list<CGff3LocationRecord> geneLocs;

(

record : locs) {

(record.mType ==

) {

geneLocs.push_back(record);

(! geneLocs.empty()) {

->MergeLocation(pNewLoc, frame, geneLocs);

->MergeLocation(pNewLoc, frame, itLocation.second);

& cdrData = pFeature->

().SetCdregion();

vector<string> tokens;

(tokens.size() < 2) {

);

(tokens.size() >= 4) {

(exception&) {

);

->SetSequenceSize(tokens[1], sequenceSize);

->SetSequenceSize(resolvedId, sequenceSize);

& seqId)

mpLocations->GetSequenceSize(seqId);

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.

User-defined methods of the data storage class.

static bool IsAlignmentData(const CTempString &)

virtual bool x_CreateAlignment(const CGff2Record &gff, CRef< CSeq_align > &pAlign)

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

CRef< CAnnotdesc > m_CurrentBrowserInfo

void xPostProcessAnnot(CSeq_annot &) override

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

IdToFeatureMap m_MapIdToFeature

bool x_MergeAlignments(const list< CRef< CSeq_align >> &alignment_list, CRef< CSeq_align > &processed)

virtual bool xParseStructuredComment(const CTempString &)

virtual bool xIsIgnoredFeatureId(const CTempString &)

unsigned int mCurrentFeatureCount

bool IsInGenbankMode() const

bool GetAttribute(const string &, string &) const

virtual bool UpdateFeature(TReaderFlags, CRef< CSeq_feat >, SeqIdResolver=nullptr) const

virtual bool AssignFromGff(const string &)

virtual bool InitializeFeature(TReaderFlags, CRef< CSeq_feat >, SeqIdResolver=nullptr) const

const TAttributes & Attributes() const

static string xNormalizedAttributeKey(const CTempString &)

string GetOneAttribute(const string &)

string x_NormalizedAttributeKey(const string &)

bool AssignFromGff(const string &) override

static string xNextGenericId()

void xPostProcessAnnot(CSeq_annot &) override

bool xIsIgnoredFeatureType(const CTempString &) override

set< string > mIDsAlreadySeen

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.

virtual bool xFindFeatureUnderConstruction(const CGff2Record &, CRef< CSeq_feat > &)

virtual bool xUpdateAnnotCds(const CGff2Record &, CRef< CSeq_feat >, CSeq_annot &, ILineErrorListener *)

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

virtual bool xUpdateAnnotGeneric(const CGff2Record &, CRef< CSeq_feat >, CSeq_annot &, ILineErrorListener *)

virtual bool xUpdateAnnotRegion(const CGff2Record &, CRef< CSeq_feat >, CSeq_annot &, ILineErrorListener *)

map< string, string > mIdToSeqIdMap

void xProcessSequenceRegionPragma(const CTempString &pragma) override

CGff3ReadRecord * x_CreateRecord() override

virtual bool xUpdateAnnotExon(const CGff2Record &, CRef< CSeq_feat >, CSeq_annot &, ILineErrorListener *)

void xVerifyExonLocation(const string &, const CGff2Record &)

virtual bool xFeatureSetXrefParent(const string &, CRef< CSeq_feat >)

void xProcessAlignmentData(CSeq_annot &pAnnot)

TSeqPos SequenceSize() const

virtual bool xUpdateAnnotRna(const CGff2Record &, CRef< CSeq_feat >, CSeq_annot &, ILineErrorListener *)

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

map< string, string > mCdsParentMap

virtual bool xInitializeFeature(const CGff2Record &, CRef< CSeq_feat >)

bool xReadInit() override

CGff3Reader(TReaderFlags uFlags, const string &name="", const string &title="", SeqIdResolver resolver=CReadUtil::AsSeqId, CReaderListener *=nullptr)

SAlignmentData mAlignmentData

shared_ptr< CGff3LocationMerger > mpLocations

set< string > mCdsParents

TSeqPos GetSequenceSize(const string &) const

virtual void xValidateAnnot(const CSeq_annot &) override

string xMakeRecordId(const CGff2Record &record)

map< string, CRef< CSeq_interval > > mMrnaLocs

bool xHasCdsChild(const string &id) const

static unsigned int msGenericIdCounter

void xVerifyCdsParents(const CGff2Record &)

virtual bool xParseAlignment(const string &strLine)

virtual bool xUpdateAnnotGene(const CGff2Record &, CRef< CSeq_feat >, CSeq_annot &, ILineErrorListener *)

virtual bool xFeatureSetXrefGrandParent(const string &, CRef< CSeq_feat >)

void xProcessData(const TReaderData &, CSeq_annot &) override

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

CRef< CSeq_loc > GetSeqLoc(TReaderFlags, SeqIdResolver seqidresolve=nullptr) const

const string & Type() const

ENa_strand Strand() const

const string & Id() const

virtual void SetType(const string &recType)

const string & NormalizedType() const

static CObjReaderLineException * Create(EDiagSev eSeverity, unsigned int uLine, const std::string &strMessage, EProblem eProblem=eProblem_GeneralParsingError, const std::string &strSeqId=string(""), const std::string &strFeatureName=string(""), const std::string &strQualifierName=string(""), const std::string &strQualifierValue=string(""), CObjReaderLineException::EErrCode eErrCode=eFormat, const TVecOfLines &vecOfOtherLines=TVecOfLines())

Please use this instead of the constructor because the ctor is protected.

Common file reader utility functions.

virtual bool xParseBrowserLine(const CTempString &, CSeq_annot &)

SeqIdResolver mSeqIdResolve

unsigned int m_uLineNumber

void ProcessError(CObjReaderLineException &, ILineErrorListener *)

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.

ESubtype GetSubtype(void) const

void SetNameDesc(const string &name)

void SetTitleDesc(const string &title)

namespace ncbi::objects::

const string & GetNamedQual(const CTempString &qual_name) const

Return a named qualifier.

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

static string ResolveSoAlias(std::string_view)

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.

container_type::iterator iterator

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

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

static void fatal(const char *msg,...)

static bool s_TreatAsRna(const CSeqFeatData &featData)

unsigned int TSeqPos

Type for sequence locations and lengths.

@ eDiag_Error

Error message.

@ eDiag_Warning

Warning message.

@ eDiag_Fatal

Fatal error – guarantees exit(or abort)

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

Set object to copy of another one.

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 StringToNonNegativeInt(const CTempString str, TStringToNumFlags flags=0)

Convert string to non-negative integer value.

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

Check if a string starts with a specified prefix value.

@ fSplit_MergeDelimiters

Merge adjacent delimiters.

void SetAa(TAa &value)

Assign a value to Aa data member.

TXref & SetXref(void)

Assign a value to Xref data member.

const TKey & GetKey(void) const

Get the Key member data.

void SetLocation(TLocation &value)

Assign a value to Location data member.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

bool IsImp(void) const

Check if variant Imp is selected.

bool IsSetKey(void) const

Check if a value has been assigned to Key data member.

const TId & GetId(void) const

Get the Id 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 SetData(TData &value)

Assign a value to Data data member.

TCode_break & SetCode_break(void)

Assign a value to Code_break data member.

void SetLoc(TLoc &value)

Assign a value to Loc data member.

bool IsRna(void) const

Check if variant Rna is selected.

const TImp & GetImp(void) const

Get the variant data.

@ eFrame_not_set

not set, code uses one

void SetTo(TTo value)

Assign a value to To data member.

void SetId(TId &value)

Assign a value to Id data member.

TFrom GetFrom(void) const

Get the From member data.

E_Choice Which(void) const

Which variant is currently selected.

void SetFrom(TFrom value)

Assign a value to From data member.

TTo GetTo(void) const

Get the To member data.

const TInt & GetInt(void) const

Get the variant data.

void SetStrand(TStrand value)

Assign a value to Strand data member.

E_Choice

Choice variants.

void SetData(TData &value)

Assign a value to Data data member.

void SetDesc(TDesc &value)

Assign a value to Desc data member.

@ e_not_set

No variant selected.

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

constexpr bool empty(list< Ts... >) noexcept

static SLJIT_INLINE sljit_ins lr(sljit_gpr dst, sljit_gpr src)

#define DEFINE_STATIC_ARRAY_MAP(Type, Var, Array)

MAP_ID_TO_ALIGN mAlignments

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