#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <algo/align/prosplign/prosplign_exception.hpp>
#include <algo/align/prosplign/prosplign.hpp>
#include "Info.hpp"
#include "Ali.hpp"
#include "nucprot.hpp"
#include "NSeq.hpp"
#include "PSeq.hpp"
#include "AliSeqAlign.hpp"
#include <objects/general/general__.hpp>
#include <objects/seqloc/seqloc__.hpp>
#include <objects/seqfeat/seqfeat__.hpp>
#include <objmgr/util/seq_loc_util.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/seq_vector.hpp>
#include <objtools/alnmgr/alntext.hpp>

Include dependency graph for Info.cpp:

Go to the SVN repository for this file.

Classes
class	CProSplignTrimmer

Functions
	USING_SCOPE (ncbi::objects)

list< CNPiece >	FindGoodParts (const CProteinAlignText &alignment_text, CProSplignOutputOptionsExt m_options, const CProSplignScaledScoring &scoring, const CSubstMatrix &matrix)

list< CNPiece >	FindGoodParts (const CNPiece pc, const string &match_all_pos, const string &protein, CProSplignOutputOptionsExt m_options)

list< CNPiece >	ExcludeBadExons (const CNPiece pc, const string &match_all_pos, const string &protein, CProSplignOutputOptionsExt m_options)

bool	TrimNegativeTail (CNPiece &pc, const CProteinAlignText &alignment_text, const CProSplignScaledScoring &scoring, const CSubstMatrix &matrix)

	USING_SCOPE (prosplign)

Variables
const char	GAP_CHAR ='-'

const char	INTRON_CHAR ='.'

const char	SPACE_CHAR =' '

const char	INTRON_OR_GAP [] = {INTRON_CHAR,GAP_CHAR,0}

const char	BAD_PIECE_CHAR ='X'

const char	MISMATCH_CHAR =' '

const char	BAD_OR_MISMATCH [] = {BAD_PIECE_CHAR,MISMATCH_CHAR,0}

const char	MATCH_CHAR ='\|'

const char	POSIT_CHAR ='+'

Function Documentation

◆ ExcludeBadExons()

list<CNPiece> ExcludeBadExons	(	const CNPiece	pc,
		const string &	match_all_pos,
		const string &	protein,
		CProSplignOutputOptionsExt	m_options
	)

Definition at line 388 of file Info.cpp.

References CNPiece::beg, CNPiece::end, CProSplignOutputOptions::GetMinExonId(), CProSplignOutputOptions::GetMinExonPos(), i, INTRON_CHAR, len, match(), MATCH_CHAR, n, and POSIT_CHAR.

Referenced by FindGoodParts().

◆ FindGoodParts() [1/2]

list<CNPiece> FindGoodParts	(	const CNPiece	pc,
		const string &	match_all_pos,
		const string &	protein,
		CProSplignOutputOptionsExt	m_options
	)

◆ FindGoodParts() [2/2]

list<CNPiece> FindGoodParts	(	const CProteinAlignText &	alignment_text,
		CProSplignOutputOptionsExt	m_options,
		const CProSplignScaledScoring &	scoring,
		const CSubstMatrix &	matrix
	)