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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/readfeat_8hpp_source.html below:

NCBI C++ ToolKit: include/objtools/readers/readfeat.hpp Source File

33 #ifndef OBJTOOLS_READERS___READFEAT__HPP 34 #define OBJTOOLS_READERS___READFEAT__HPP 70

fReportBadKey

(

"This flag is redundant. Bad keys are now reported by default" 71 " and fSuppressBadKeyWarning must be specified to silence these warnings."

)

74

fTranslateBadKey = (1<<2),

75

fIgnoreWebComments = (1<<3),

76

fCreateGenesFromCDSs = (1<<4),

77

fCDSsMustBeInTheirGenes = (1<<5),

78

fReportDiscouragedKey = (1<<6),

79

fLeaveProteinIds = (1<<7),

80

fAllIdsAsLocal = (1<<8),

81

fPreferGenbankId = (1<<9),

82

fSuppressBadKeyWarning = (1<<10),

83

fIncludeObjectInMsg = (1<<11),

86 static void

AddStringFlags(

87 const

list<string>& stringFlags,

106 const string

& seqid_prefix =

kEmptyStr

);

113 const string

& seqid_prefix =

kEmptyStr

);

121 const string

& seqid,

122 const string

& annotname,

128 const string

& seqid,

129 const string

& annotname,

136 static void

ReadSequinFeatureTables(

ILineReader

& reader,

142 static void

ReadSequinFeatureTables(

CNcbiIstream

& ifs,

153 unsigned int

line = 0,

159 const string

& feat_name,

180 static bool

ParseInitialFeatureLine (

188 function

void

(

const string

msg

)>* fpReportError=

nullptr

);

200 const string

& seqid_prefix=

kEmptyStr

);

long TFlags

binary OR of EFlags

unique_ptr< CFeatureTableReader_Imp > m_pImpl

Defines and provides stubs for a general interface to a variety of file readers.

EFlags

Customization flags that are relevant to all CReaderBase derived readers.

virtual CRef< CSerialObject > ReadObject(CNcbiIstream &istr, ILineErrorListener *pErrors=nullptr)

Read an object from a given input stream, render it as the most appropriate Genbank object.

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.

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.

Use to give a feature filter to CFeature_table_reader.

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

static const char location[]

#define NCBI_STD_DEPRECATED(message)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

#define NCBI_XOBJREAD_EXPORT

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

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

static SLJIT_INLINE sljit_ins lr(sljit_gpr dst, sljit_gpr src)

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