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NCBI C++ ToolKit: src/app/convert_seq/gff_reader.hpp Source File

1 #ifndef OBJTOOLS_READERS___GFF_READER__HPP 2 #define OBJTOOLS_READERS___GFF_READER__HPP 85

fMergeOnyCdsMrna = 0x08,

92

fCreateGeneFeats = 0x20,

95

fNumericIdsAsLocal = 0x40,

98

fAllIdsAsLocal = 0x80,

101

fSetVersion3 = 0x100,

156 size_t

min_values = 1)

const

;

170 virtual void

x_Info(

const string

& message,

171 unsigned int

line = 0);

173 virtual void

x_Warn(

const string

& message,

174 unsigned int

line = 0);

176 virtual void

x_Error(

const string

& message,

177 unsigned int

line = 0);

180 virtual void

x_Reset(

void

);

185 virtual bool

x_ParseStructuredComment(

const

TStr& line);

186 virtual void

x_ParseDateComment(

const

TStr& date);

187 virtual void

x_ParseTypeComment(

const

TStr& moltype,

188 const

TStr& seqname);

191 virtual CRef<SRecord>

x_ParseFeatureInterval(

const

TStr& line);

197 virtual void

x_ParseV2Attributes(SRecord& record,

200 virtual void

x_ParseV3Attributes(SRecord& record,

203 virtual void

x_AddAttribute(SRecord& record,

204

vector<string>& attr);

209 virtual string

x_FeatureID(

const

SRecord& record);

211 virtual void

x_MergeRecords(SRecord& dest,

const

SRecord& src);

212 virtual void

x_MergeAttributes(SRecord& dest,

214 virtual void

x_PlaceFeature(

CSeq_feat

& feat,

215 const

SRecord& record);

216 virtual void

x_PlaceAlignment(

CSeq_align

& align,

217 const

SRecord& record);

218 virtual void

x_ParseAndPlace(

const

SRecord& record);

221 virtual CRef<CSeq_id>

x_ResolveSeqName(

const string

& name);

223 virtual CRef<CSeq_id>

x_ResolveNewSeqName(

const string

& name);

233 virtual void

x_PlaceSeq(

CBioseq

& seq);

235 virtual bool

x_IsLineUcscMetaInformation(

const

TStr&);

237 virtual bool

x_SplitKeyValuePair(

const string

string

& );

namespace ncbi::objects::

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.

parent_type::const_iterator const_iterator

void Read(CObjectIStream &in, TObjectPtr object, const CTypeRef &type)

TDelayedRecords m_DelayedRecords

TLoc loc

from accession, start, stop, strand

unsigned int x_GetLineNumber(void)

set< vector< string > > TAttrs

virtual CRef< SRecord > x_NewRecord(void)

map< string, CRef< SRecord >, PNocase > TDelayedRecords

TFlags x_GetFlags(void) const

set< TSeqRange > merge_ranges

a subsidiary set of ranges that is merged into ranges after parsing.

unsigned int m_LineNumber

TSeqNameCache m_SeqNameCache

map< string, CRef< CSeq_id >, PNocase > TSeqNameCache

map< CConstRef< CSeq_id >, CRef< CBioseq >, PPtrLess< CConstRef< CSeq_id > > > TSeqCache

set< TSeqRange > ranges

the set of ranges that make up this location this allows us to separately assign frame even if the ra...

map< string, CRef< CGene_ref > > TGeneRefs

ILineReader * m_LineReader

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

NCBI_NS_STD::string::size_type SIZE_TYPE

ENa_strand

strand of nucleic acid

Useful/utility classes and methods.

std::istream & in(std::istream &in_, double &x_)

Compare objects pointed to by (smart) pointer.

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