#ifndef MATRIX_H
#define MATRIX_H

#include "helix.h"

/* parameter representations used in matrix */
#define u 1.0
#define w1_m -10.0
#define w_m  -20.0
#define vN_m -30.0
#define vC_m -40.0

/* maximum dimension of the matrices */
#define MAXDIM 27

struct matrix {int nRow; int nCol; float Wi[MAXDIM][MAXDIM];};

struct matrix ClearMatrix (struct matrix W, float type);
float MtplyMatrix (struct matrix W,
                   int nIndx, 
                   int nResidue,
                   float type,
                   struct sequence *Seqence);

static struct matrix W[]={
1,3,{u,u,u},
3,4,{{vN_m,0.,0.,0.},{0.,u,0.,0.},{0.,0.,u,u}},
4,6,{{w1_m,w1_m,0.,0.,0.,0.},{0.,0.,vN_m,0.,0.,0.},{0.,0.,0.,u,0.,0.},{0.,0.,0.,0.,u,u}},
6,10,{{w1_m,w1_m,0.,0.,0.,0.,0.,0.,0.,0.},{0.,0.,vC_m,vC_m,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,w1_m,w1_m,0.,0.,0.,0.},{0.,0.,0.,0.,0.,0.,vN_m,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,u,0.,0.},{0.,0.,0.,0.,0.,0.,0.,0.,u,u}},
10,17,{{w1_m,w1_m,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,vC_m,vC_m,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,u,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,u,u,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,w1_m,w1_m,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,vC_m,vC_m,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,w1_m,w1_m,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,vN_m,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,u,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,u,u}},
17,21,{{w_m,w_m,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,vC_m,vC_m,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,u,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,u,u,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,vN_m,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,u,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,u,u,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{w1_m,w1_m,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,vC_m,vC_m,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,u,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,u,u,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,w1_m,w1_m,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,vC_m,vC_m,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,w1_m,w1_m,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,vN_m,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,u,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,u,u}},
21,27,{{w_m,w_m,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,vC_m,vC_m,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,u,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,u,u,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,vN_m,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,u,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,u,u,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,w1_m,w1_m,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,vN_m,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,u,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,u,u,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{w1_m,w1_m,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,vC_m,vC_m,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,u,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,u,u,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,w1_m,w1_m,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,vC_m,vC_m,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,w1_m,w1_m,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,vN_m,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,u,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,u,u}},
27,27,{{w_m,w_m,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,vC_m,vC_m,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,u,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,u,u,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,vN_m,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,u,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,u,u,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,w1_m,w1_m,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,vN_m,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,u,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,u,u,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,w1_m,w1_m,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,vC_m,vC_m,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,w1_m,w1_m,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,vN_m,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,u,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,u,u},
{w1_m,w1_m,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,vC_m,vC_m,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,u,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,u,u,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,w1_m,w1_m,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,vC_m,vC_m,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,w1_m,w1_m,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,vN_m,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,u,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,u,u}},
27,21,{{w_m,w_m,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,vC_m,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,u,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,u,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,vN_m,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,u,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,u,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,w1_m,w1_m,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,vN_m,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,u,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,u,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,w1_m,w1_m,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,vC_m,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,w1_m,w1_m,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,vN_m,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,u,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,u},
{w1_m,w1_m,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,vC_m,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,u,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,u,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,w1_m,w1_m,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,vC_m,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,w1_m,w1_m,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,vN_m,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,u,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,u}},
21,17,{{w_m,w_m,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,vC_m,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,u,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,vN_m,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,u,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,w1_m,w1_m,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,vN_m,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,u,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,w1_m,w1_m,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,vC_m,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,w1_m,w1_m,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,vN_m,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,u},
{w1_m,w1_m,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,vC_m,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,u,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,w1_m,w1_m,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,vC_m,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,w1_m,w1_m,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,vN_m,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,u}},
17,10,{{w_m,0.,0.,0.,0.,0.,0.,0.,0.,0.},{0.,vC_m,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,u,0.,0.,0.,0.,0.,0.,0.},{0.,0.,0.,u,0.,0.,0.,0.,0.,0.},
{0.,0.,0.,0.,w1_m,0.,0.,0.,0.,0.},{0.,0.,0.,0.,0.,u,0.,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,w1_m,0.,0.,0.},{0.,0.,0.,0.,0.,0.,0.,vC_m,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,w1_m,0.},{0.,0.,0.,0.,0.,0.,0.,0.,0.,u},
{w1_m,0.,0.,0.,0.,0.,0.,0.,0.,0.},{0.,vC_m,0.,0.,0.,0.,0.,0.,0.,0.},
{0.,0.,u,0.,0.,0.,0.,0.,0.,0.},{0.,0.,0.,0.,0.,0.,w1_m,0.,0.,0.},
{0.,0.,0.,0.,0.,0.,0.,vC_m,0.,0.},{0.,0.,0.,0.,0.,0.,0.,0.,w1_m,0.},
{0.,0.,0.,0.,0.,0.,0.,0.,0.,u}},
10,6,{{vC_m,0.,0.,0.,0.,0.},{0.,u,0.,0.,0.,0.},
{0.,0.,u,0.,0.,0.},{0.,0.,0.,u,0.,0.},{0.,0.,0.,0.,vC_m,0.},
{0.,0.,0.,0.,0.,u},{vC_m,0.,0.,0.,0.,0.},{0.,u,0.,0.,0.,0.},
{0.,0.,0.,0.,vC_m,0.},{0.,0.,0.,0.,0.,u}},
6,1,{{u},{u},{u},{u},{u},{u}}
};

#endif