#ifndef __W_MATRIX_POS_H__
#define __W_MATRIX_POS_H__

#include "w_matrix.h"

//#define   Matrix_scale       1000
//#define   Max_num_letters    22
//#define   Unknown_letter     (Max_num_letters-1)


class Weight_matrix_pos : public Weight_matrix 
{
/**
public :
	int    elem[ Max_num_letters ][ Max_num_letters ];
	double diag_average;
	double covariation;

	double mean, dispersion, mdisp;
	int    type;
	int    orig_elem[ Max_num_letters ][ Max_num_letters ];
**/
public :
	//+TMatrix* duplicate() { return new Weight_matrix( *this ); }

	Weight_matrix_pos( ) : Weight_matrix() {};

/**
	uc ord (char c) const {
		return nalpha[ ( unsigned char )c ];
	}

	int _weight( uc ia, uc ib ) const {
		return elem[ ia ][ ib ];
	}

	int weight( char a, char b ) const {
		return _weight( ord( a ), ord( b ) );
	}

	void	   print();
	void	   setPenal( int gap );
	void     makeDiag( );
	void     makeBlos62( );

	//_________________________ The successors of the TMatrix abstaract class
	int	   recalcSum( int len, const char *sq1, const char *sq2, int sum, int base0, double& mult, double& add ) const;
	int		fread( FILE *mfile );
	int    	normalize( double *freq1, double *freq2 );
	// double*	makeFreq( int len, const char *seq ) const;
	void   	recast( double *freq1, double *freq2 );
	int 		rescale( double homology_factor ) const {
		return int ( homology_factor * diag_average * Matrix_scale );
	}
	void	   getWeight( const BankSeq &shCurr, const BankSeq &shBank, int *weight, int homFact, int base0 ) const;
	void		getWeight( int ishSeq, const BankSeq &seq, int ishAli, WorkAli& ali, int len, int* weight, int homFac ) const;
**/

	void	   getWeight( const BankSeq &shCurr, int left1, const BankSeq &shBank, int left2, int len, int *weight, int homFact, int base0 ) const;

};


/*================================================================
	Fill given array with the weights for the two given sequences
================================================================*/
/**
void	Weight_matrix::getWeight( const BankSeq &shCurr, const BankSeq &shBank,
										  int *wei, int homFact, int )	const
{
	int  len = shCurr.len();
	for( int i = 0; i < len; i++ )
		wei[ i ] = elem[ nalpha[ shCurr[ i ] ] ][ nalpha[ shBank[ i ] ] ] - homFact;
}
**/

void	Weight_matrix_pos::getWeight( const BankSeq &shCurr, int left1, const BankSeq &shBank,
                         int left2, int len, int *wei, int homFact, int )	const
{
	//int  len = shCurr.len();
	for( int i = 0; i < len; i++ )
		wei[ i ] = elem[ nalpha[ shCurr[ i + left1 ] ] ][ nalpha[ shBank[ i + left2 ] ] ] - homFact;
}

#endif