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NCBI C++ ToolKit: src/algo/align/prosplign/Info.hpp Source File

(string::size_type obeg, string::size_type oend,

oposit,

oefflen);

(

efflen,

posit, list<prosplign::CNPiece>::iterator it);

(list<prosplign::CNPiece>::iterator it, list<prosplign::CNPiece>::iterator

);

(list<prosplign::CNPiece>::iterator it,

efflen,

posit, list<prosplign::CNPiece>::iterator

);

(list<prosplign::CNPiece>::iterator it);

(list<prosplign::CNPiece>::iterator it1, list<prosplign::CNPiece>::iterator it2);

(list<prosplign::CNPiece>::iterator it1, list<prosplign::CNPiece>::iterator it2);

(objects::CScope& scope, objects::CSeq_align& seq_align,

list<CNPiece>& good_parts);

(objects::CSeq_align& seq_align, objects::CScope& scope,

& matrix_name =

);

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

void RefineAlignment(objects::CScope &scope, objects::CSeq_align &seq_align, const list< CNPiece > &good_parts)

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

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

void SetScores(objects::CSeq_align &seq_align, objects::CScope &scope, const string &matrix_name="BLOSUM62")

Extended output filtering parameters deprecated, used in older programs.

CProSplignOutputOptionsExt(const CProSplignOutputOptions &options)

bool Perc(list< prosplign::CNPiece >::iterator it, int efflen, int posit, list< prosplign::CNPiece >::iterator last)

bool ForwCheck(list< prosplign::CNPiece >::iterator it1, list< prosplign::CNPiece >::iterator it2)

void Join(list< prosplign::CNPiece >::iterator it, list< prosplign::CNPiece >::iterator last)

bool Bad(list< prosplign::CNPiece >::iterator it)

bool BackCheck(list< prosplign::CNPiece >::iterator it1, list< prosplign::CNPiece >::iterator it2)

bool Dropof(int efflen, int posit, list< prosplign::CNPiece >::iterator it)

Output filtering parameters.

Text representation of ProSplign alignment.

Substitution Matrix for Scoring Amino-Acid Alignments.

static DLIST_TYPE *DLIST_NAME() last(DLIST_LIST_TYPE *list)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

The NCBI C++/STL use hints.

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