src/algo/align/splign/splign_formatter.cpp File Reference

#include <ncbi_pch.hpp>
#include <algo/align/nw/align_exception.hpp>
#include <algo/align/splign/splign_formatter.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seqalign/Score.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
#include <objects/seqalign/Dense_seg.hpp>
#include <objects/seqalign/Spliced_seg.hpp>
#include <objects/seqalign/Spliced_exon.hpp>
#include <objects/seqalign/Product_pos.hpp>
#include <objects/seqalign/Score_set.hpp>
#include <objects/seqalign/Splice_site.hpp>
#include <objects/seqalign/Spliced_exon_chunk.hpp>
#include <objects/general/Object_id.hpp>
#include <objmgr/seq_vector.hpp>
#include <objmgr/util/sequence.hpp>
#include <algorithm>
#include "splign_util.hpp"
#include "messages.hpp"

Include dependency graph for splign_formatter.cpp:

Go to the source code of this file.

Functions
	USING_SCOPE (objects)
void	MakeLeftHeader (size_t x, string *ps)
double	CalcIdentity (const string &transcript)
CRef< CSpliced_exon_chunk >	CreateSplicedExonChunk (char cur, size_t count)

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Function Documentation

double CalcIdentity (  const string &  transcript  )

Definition at line 511 of file splign_formatter.cpp. References ITERATE. Referenced by CSplignFormatter::x_Compartment2SeqAlign().

CRef<CSpliced_exon_chunk> CreateSplicedExonChunk (  char  cur, size_t  count )

Definition at line 596 of file splign_formatter.cpp. References g_msg_UnknownTranscriptSymbol, and NCBI_THROW. Referenced by CSplignFormatter::AsSeqAlignSet().

void MakeLeftHeader (  size_t  x, string *  ps )

Definition at line 209 of file splign_formatter.cpp. References NStr::IntToString(). Referenced by CSplignFormatter::AsAlignmentText().

USING_SCOPE (  objects   )

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