NCBI C++ ToolKit
Classes | Functions | Variables
Info.cpp File Reference
#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 source code of this file.

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Classes

class  CProSplignTrimmer
 

Functions

 USING_SCOPE (ncbi::objects)
 
list< CNPieceFindGoodParts (const CProteinAlignText &alignment_text, CProSplignOutputOptionsExt m_options, const CProSplignScaledScoring &scoring, const CSubstMatrix &matrix)
 
list< CNPieceFindGoodParts (const CNPiece pc, const string &match_all_pos, const string &protein, CProSplignOutputOptionsExt m_options)
 
list< CNPieceExcludeBadExons (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 
)

◆ 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 
)

◆ TrimNegativeTail()

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

◆ USING_SCOPE() [1/2]

USING_SCOPE ( ncbi::objects  )

◆ USING_SCOPE() [2/2]

USING_SCOPE ( prosplign  )

Variable Documentation

◆ BAD_OR_MISMATCH

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

Definition at line 65 of file Info.cpp.

Referenced by FindGoodParts().

◆ BAD_PIECE_CHAR

const char BAD_PIECE_CHAR ='X'

Definition at line 63 of file Info.cpp.

Referenced by CProSplignText::Output().

◆ GAP_CHAR

const char GAP_CHAR ='-'

◆ INTRON_CHAR

const char INTRON_CHAR ='.'

◆ INTRON_OR_GAP

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

◆ MATCH_CHAR

const char MATCH_CHAR ='|'

Definition at line 66 of file Info.cpp.

Referenced by CProSplignTrimmer::CProSplignTrimmer(), ExcludeBadExons(), and FindGoodParts().

◆ MISMATCH_CHAR

const char MISMATCH_CHAR =' '

Definition at line 64 of file Info.cpp.

◆ POSIT_CHAR

const char POSIT_CHAR ='+'

◆ SPACE_CHAR

const char SPACE_CHAR =' '

Definition at line 59 of file Info.cpp.

Referenced by CProSplignTrimmer::CProSplignTrimmer(), and FindGoodParts().

Modified on Mon Jul 15 05:35:43 2024 by modify_doxy.py rev. 669887