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/*
* Copyright (c) Medical Research Council 2001. All rights reserved.
*
* Permission to use, copy, modify and distribute this software and its
* documentation for any purpose is hereby granted without fee, provided that
* this copyright and notice appears in all copies.
*
* This file was written as part of the Staden Package at the MRC Laboratory
* of Molecular Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
*
* MRC disclaims all warranties with regard to this software.
*
*/
#ifndef _MUTLIB_ALIGN_HPP_
#define _MUTLIB_ALIGN_HPP_
#include <cassert>
#include <sp_alignment_structs.h> // For alignment structures
#include <sp_alignment.h> // For alignment constants
#include <matrix.hpp> // For SimpleMatrix<T> object
class Alignment
{
public:
// Algorithms
typedef enum
{
ALGORITHM_NORMAL = SP_ALIGNMENT_ALGORITHM_A,
ALGORITHM_BLOCK_ALIGN = SP_ALIGNMENT_ALGORITHM_B,
ALGORITHM_POISSON = SP_ALIGNMENT_ALGORITHM_C
}algorithm_t;
// Edge scoring
typedef enum
{
EDGE_SCORE_LEFT = SP_ALIGNMENT_LEFT_EDGE_GAPS_COUNT,
EDGE_SCORE_RIGHT = SP_ALIGNMENT_BEST_RIGHT_EDGE
}edge_score_t;
// Support for multiple alignment
enum
{
MAX_INPUT_SEQUENCES = 2
};
public:
// Constructors/destructor
Alignment();
~Alignment();
public:
// Services
void BandSize( int n ) { assert(n>=0); m_nBand=n; }
void PadSymbol( int p ) { assert(p); m_nPadSymbol=p; }
int PadSymbol() const { return m_nPadSymbol; }
void GapPenalty( int nBegin, int nExtend ) { m_nGapPenaltyBegin=nBegin; m_nGapPenaltyExtend=nExtend; }
void EdgeScore( edge_score_t es );
void InputSequence( int n, const char* s, int l=-1 );
void Matrix( int** m, int n, bool AutoDestroy=true );
int Execute( algorithm_t a );
double OutputScore() const;
char* OutputSequence( int n ) const;
int OutputSequenceLength( int n ) const;
int OutputSequenceLeftOverlap( int n ) const;
int OutputSequenceRightOverlap( int n ) const;
void DumpToFile( const char* s, bool AsInteger=false ) const;
private:
// Helpers
void CreateDefaultMatrix();
private:
// Data
int m_nBand;
sp::ALIGN_PARAMS* m_pParams;
sp::OVERLAP* m_pOverlap;
SimpleMatrix<int> m_oMatrix;
int m_nPadSymbol;
int m_nEdgeScore;
int m_nGapPenaltyBegin;
int m_nGapPenaltyExtend;
static bool m_bDNALookupInitialised;
const char* m_pInputSequence[MAX_INPUT_SEQUENCES];
int m_nInputSequenceLength[MAX_INPUT_SEQUENCES];
};
#endif
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