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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/gvf__writer_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/writers/gvf_writer.cpp Source File

47 unsigned int

uFlags ) :

59 unsigned int

uFlags ) :

82 const

list< CRef< CAnnotdesc > > descrs = annot.

GetDesc

().

Get

();

83

list< CRef< CAnnotdesc > >::const_iterator cit = descrs.begin();

85 while

( cit != descrs.end() ) {

88 if

( ! pDesc->IsUser() ) {

91 if

( ! pDesc->GetUser().IsSetType() ) {

94 if

( ! pDesc->GetUser().GetType().IsStr() ) {

97 if

( pDesc->GetUser().GetType().GetStr() ==

"gvf-import-pragmas"

) {

106 if

( ! pDescPragmas ) {

112 for

( CUser_object::TData::const_iterator cit =

data

.begin();

113

cit !=

data

.end(); ++cit )

117 key

= (*cit)->GetLabel().GetStr();

118 value

= (*cit)->GetData().GetStr();

123 if

(

key

"gff-version"

key

"gvf-version"

) {

136 m_Os

"##gff-version 3"

'\n'

;

137 m_Os

"##gvf-version 1.05"

'\n'

;

169 "Processing terminated by user"

);

177 if

(!pRecord->AssignAttributes(mf)) {

235 for

(

; feat_iter; ++feat_iter) {

254

{

"ID"

"Name"

"Alias"

"Parent"

"Target"

"Gap"

"Derives_from"

255 "Note"

"Dbxref"

"Ontology_term"

"Is_circular"

};

258 for

(

const auto

& qual: quals) {

259 if

(!qual->IsSetQual() || !qual->IsSetVal()) {

262 string key

= qual->GetQual();

263 const string

value

= qual->GetVal();

264 if

(

key

"SO_type"

) {

271 if

(

key

"Parent"

) {

276

gff3_attributes.

find

(

key

) == gff3_attributes.

end

()) {

User-defined methods of the data storage class.

unsigned int m_uPendingMrnaId

bool xAssignFeature(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &) override

unsigned int m_uPendingGeneId

virtual string StrType() const

virtual string StrSeqStop() const

virtual string StrAttributes() const

virtual string StrScore() const

virtual string StrPhase() const

bool SetAttribute(const string &, const string &)

virtual string StrSeqStart() const

virtual string StrSeqId() const

virtual string StrStrand() const

virtual string StrMethod() const

virtual bool AssignSource(const CMappedFeat &)

virtual bool AssignType(const CMappedFeat &, unsigned int=0)

virtual bool xWriteFeatureVariationRef(CGffFeatureContext &, const CMappedFeat &)

bool xWriteRecord(const CGffBaseRecord &) override

bool WriteHeader() override

Write a file header.

bool xAssignFeatureAttributes(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &) override

bool x_WriteSeqAnnotHandle(CSeq_annot_Handle) override

bool xWriteFeature(CGffFeatureContext &, const CMappedFeat &) override

bool xAssignFeatureMethod(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &) override

bool xAssignFeatureType(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &) override

CGvfWriter(CScope &, CNcbiOstream &, unsigned int=fNormal)

virtual SAnnotSelector & SetAnnotSelector(void)

const_iterator find(const key_type &key) const

const_iterator end() const

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

CConstRef< CSeq_annot > GetCompleteSeq_annot(void) const

Complete and return const reference to the current seq-annot.

CSeqFeatData::ESubtype GetFeatSubtype(void) const

const CSeq_feat::TQual & GetQual(void) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

static string & ToLower(string &str)

Convert string to lower case â string& version.

const TData & GetData(void) const

Get the Data member data.

vector< CRef< CUser_field > > TData

vector< CRef< CGb_qual > > TQual

const Tdata & Get(void) const

Get the member data.

const TDesc & GetDesc(void) const

Get the Desc member data.

bool IsSetDesc(void) const

used only for stand alone Seq-annots Check if a value has been assigned to Desc data member.

bool IsSet(void) const

Check if a value has been assigned to data member.

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

const GenericPointer< typename T::ValueType > T2 value

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