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

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32 #ifndef OBJTOOLS_WRITERS_ALN_WRITER_HPP 33 #define OBJTOOLS_WRITERS_ALN_WRITER_HPP 65 const string

& name =

""

66 const string

& descr=

""

)

override 72 for

(

const auto

& align: alignments) {

82 const string

& name=

""

83 const string

& descr=

""

)

override

;

89 bool

WriteAlignDenseSeg(

const CDense_seg

& denseg);

91 bool

WriteAlignSplicedSeg(

const CSpliced_seg

& spliced_seg);

93 bool

WriteAlignSparseSeg(

const CSparse_seg

& sparse_seg);

107 string

& genomic_seq,

108 string

& product_seq);

117 string

GetSegString(

const string

& seq_plus,

123 void

WriteContiguous(

const string

& defline,

const string

& seqdata);

User-defined methods of the data storage class.

virtual ~CAlnWriter()=default

bool WriteAnnot(const CSeq_annot &annot, const string &name="", const string &descr="") override

Write a raw Seq-annot to the internal output stream.

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

virtual bool WriteAlign(const CSeq_align &, const string &="", const string &="")

Write a raw Seq-align to the internal output stream.

bool GetBestId(CSeq_id_Handle idh, CScope &scope, string &best_id) 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.

#define NCBI_XOBJWRITE_EXPORT

list< CRef< CSpliced_exon_chunk > > TParts

ENa_strand

strand of nucleic acid

const TAlign & GetAlign(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

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