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// $Id: mmdb_math_align.h $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
// functionality in protein crystallography applications.
//
// Copyright (C) Eugene Krissinel 2000-2013.
//
// This library is free software: you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License version 3, modified in accordance with the provisions
// of the license to address the requirements of UK law.
//
// You should have received a copy of the modified GNU Lesser
// General Public License along with this library. If not, copies
// may be downloaded from http://www.ccp4.ac.uk/ccp4license.php
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU Lesser General Public License for more details.
//
// =================================================================
//
// 12.09.13 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
// **** Module : Align <interface>
// ~~~~~~~~~
// **** Classes : mmdb::math::Alignment (char strings alignment)
// ~~~~~~~~~~~~ mmdb::math::Alignment1 (int vectors alignment)
//
// (C) E.Krissinel 2000-2013
//
// =================================================================
//
#ifndef __MMDB_MATH_Align__
#define __MMDB_MATH_Align__
#include "mmdb_io_stream.h"
namespace mmdb {
namespace math {
// ===================== AlignParams ======================
DefineClass(AlignParams);
DefineStreamFunctions(AlignParams);
class AlignParams : public io::Stream {
public :
realtype gapWeight,spaceWeight;
realtype equalScore,nequalScore;
int method;
AlignParams();
AlignParams ( io::RPStream Object );
void write ( io::RFile f );
void read ( io::RFile f );
protected :
void InitAlignParams();
};
// ====================== Alignment =======================
DefineClass(Alignment);
enum ALIGN_METHOD {
ALIGN_GLOBAL = 0,
ALIGN_LOCAL = 1,
ALIGN_GLOBLOC = 2,
ALIGN_FREEENDS = 3
};
class Alignment : public io::Stream {
public :
Alignment ();
Alignment ( io::RPStream Object );
~Alignment ();
void SetAffineModel ( realtype WGap, realtype WSpace );
void SetScores ( realtype SEqual, realtype SNEqual );
void Align ( cpstr S, cpstr T,
ALIGN_METHOD Method=ALIGN_GLOBAL );
inline pstr GetAlignedS() { return AlgnS; }
inline pstr GetAlignedT() { return AlgnT; }
inline realtype GetScore () { return VAchieved; }
inline char GetSpace () { return Space; }
realtype GetSimilarity(); // Score-weighted sequence id
realtype GetSeqId (); // Primitive sequence id
virtual void OutputResults ( io::RFile f, cpstr S, cpstr T );
void read ( io::RFile f );
void write ( io::RFile f );
protected :
char Space;
int AlignKey, SLen,TLen;
rmatrix VT,ET,FT;
pstr AlgnS,AlgnT;
realtype VAchieved;
realtype SEq,SNEq, Wg,Ws;
virtual void InitAlignment();
virtual void FreeMemory ();
virtual realtype Score ( char A, char B );
void BuildGATable ( cpstr S, cpstr T,
bool FreeSEnd, bool FreeTEnd );
void BuildLATable ( cpstr S, cpstr T );
void Backtrace ( cpstr S, cpstr T, int J, int I,
bool StopAtZero );
void AdjustEnds ( cpstr S, cpstr T, int J, int I );
void PrintVT ( cpstr S, cpstr T );
};
// ====================== Alignment1 =======================
DefineClass(Alignment1);
class Alignment1 : public io::Stream {
public :
Alignment1 ();
Alignment1 ( io::RPStream Object );
~Alignment1();
void SetAffineModel ( realtype WGap, realtype WSpace );
void SetScores ( realtype SEqual, realtype SNEqual );
void Align ( ivector S, int SLength,
ivector T, int TLength,
ALIGN_METHOD Method=ALIGN_GLOBAL );
inline ivector GetAlignedS () { return AlgnS; }
inline ivector GetAlignedT () { return AlgnT; }
inline int GetAlignLength() { return AlgnLen; }
inline realtype GetScore () { return VAchieved; }
realtype GetSimilarity(); // Score-weighted sequence id
virtual void OutputResults ( io::RFile f, ivector S, int lenS,
ivector T, int lenT );
void read ( io::RFile f );
void write ( io::RFile f );
protected :
int Space;
int AlignKey, SLen,TLen, AlgnLen;
rmatrix VT,ET,FT;
ivector AlgnS,AlgnT;
realtype VAchieved;
realtype SEq,SNEq, Wg,Ws;
virtual void InitAlignment1();
virtual void FreeMemory ();
virtual realtype Score ( int A, int B );
void BuildGATable ( ivector S, ivector T,
bool FreeSEnds, bool FreeTEnds );
void BuildLATable ( ivector S, ivector T );
void Backtrace ( ivector S, ivector T, int J, int I,
bool StopAtZero );
void AdjustEnds ( ivector S, ivector T, int J, int I );
void PrintVT ( ivector S, ivector T );
};
} // namespace math
} // namespace mmdb
#endif
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