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NCBI C++ ToolKit: include/objtools/writers/gtf_writer.hpp Source File

32 #ifndef OBJTOOLS_WRITERS___GTF_WRITER__HPP 33 #define OBJTOOLS_WRITERS___GTF_WRITER__HPP 70 return

prefix +

"_1"

;

84

fStructibutes = 1<<16,

85

fNoGeneFeatures = 1<<17,

86

fNoExonNumbers = 1<<18

120 virtual bool

xAssignFeatureAttributeGeneId(

124 virtual bool

xAssignFeatureAttributeTranscriptId(

128 virtual bool

xAssignFeatureAttributeTranscriptBiotype(

157 virtual bool

xWriteRecordsGene(

160 virtual bool

xWriteRecordsTranscript(

163 const string

& =

""

);

164 virtual bool

xWriteRecordsCds(

167 const string

& =

""

);

168 virtual bool

xWriteFeatureExons(

171 const string

& =

""

);

173 virtual bool

xAssignFeaturesGene(

177 virtual bool

xAssignFeaturesTranscript(

182 virtual bool

xAssignFeaturesCds(

186 const string

& =

""

);

User-defined methods of the data storage class.

CWriterBase implementation that formats Genbank objects as plain GFF files.

virtual bool xAssignFeatureAttributeNote(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

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

virtual bool xAssignFeatureAttributeDbxref(CGffFeatureRecord &, CGffFeatureContext &, const string &label, const CMappedFeat &)

virtual bool xWriteFeature(CGffFeatureContext &, const CMappedFeat &)

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

virtual bool xAssignFeatureAttributesQualifiers(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

bool WriteHeader() override

Write a file header identifying the file content as GFF version 2.

virtual bool xAssignFeatureAttributesFormatSpecific(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool x_WriteBioseqHandle(CBioseq_Handle)

map< string, int > mLastSuffixes

string NextId(const string prefix)

map< CMappedFeat, string > mMapFeatToGeneId

bool WriteHeader(const CSeq_annot &annot) override

Write a file header, using annotation information.

CGtfIdGenerator mIdGenerator

const_iterator end() const

const_iterator find(const key_type &key) const

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

#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 enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

#define NCBI_XOBJWRITE_EXPORT

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