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/////////////////////////////////////////////////////////////////
// ReadMatrix.cc
//
// routines for reading substitution matrix
/////////////////////////////////////////////////////////////////
#include "SafeVector.h"
#include <string.h>
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "Matrix.h"
#define TRACE 0
////////////////////////////////////////////////////////////
// extern variables for scoring matrix data
////////////////////////////////////////////////////////////
extern float g_gap_open1, g_gap_open2, g_gap_ext1, g_gap_ext2;
extern char *aminos, *bases, matrixtype[20];
extern int subst_index[26];
extern float sub_matrix[26][26];
extern float scorez_matrix[26][26];
extern float TEMPERATURE;
extern int MATRIXTYPE;
extern float GAPOPEN;
extern float GAPEXT;
typedef struct {
char input[30];
int matrix;
int N;
float T;
float beta;
char opt; //can be 'P' or 'M'
float gapopen;
float gapext;
} argument_decl;
//argument support
extern argument_decl argument;
/////////////////////////////////////////////////////////
//sets substitution matrix type
////////////////////////////////////////////////////////
void setmatrixtype(int le)
{
switch (le)
{
case 160:
strcpy(matrixtype, "gonnet_160");
break;
case 4:
strcpy(matrixtype, "nuc_simple");
break;
default:
strcpy(matrixtype, "CUSTOM");
break;
};
}
///////////////////////////////////////////////////////////////////
//sets matrix flag
///////////////////////////////////////////////////////////////////
inline int matrixtype_to_int()
{
if (!strcmp(matrixtype, "nuc_simple"))
return 4;
else if (!strcmp(matrixtype, "gonnet_160"))
return 160;
else
return 1000;
}
/////////////////////////////////////////////////////////////////
//
// Can read any scoring matrix as long as it is defined in Matrix.h
// AND it is a lower triangular
// AND the order of amino acids/bases is mentioned
/////////////////////////////////////////////////////////////////
inline void read_matrix(score_matrix matrx)
{
int i, j, basecount,position=0;
bases=(char *)matrx.monomers;
basecount = strlen(bases);
for (i = 0; i < basecount; i++)
subst_index[i] = -1;
for (i = 0; i < basecount; i++)
subst_index[bases[i] - 'A'] = i;
if (TRACE == 1)
printf("\nbases read: %d\n", basecount);
for (i = 0; i < basecount; i++)
for (j = 0; j <= i; j++)
{
sub_matrix[i][j]=matrx.matrix[position++];
sub_matrix[j][i] = sub_matrix[i][j];
scorez_matrix[i][j]= exp(sub_matrix[i][j]*argument.beta);
scorez_matrix[j][i] = exp(sub_matrix[j][i]*argument.beta);
}
if (TRACE)
for (i = 0; i < basecount; i++)
{
for (j = 0; j < basecount; j++)
printf(" %f ", sub_matrix[i][j]);
printf("\n");
}
}
//////////////////////////////////////////////////////////////////////////////////
//intialize the arguments (default values)
//////////////////////////////////////////////////////////////////////////////////
void init_arguments()
{
float gap_open = 0, gap_ext = 0;
int le;
le = matrixtype_to_int();
argument.N = 1;
strcpy(argument.input, "tempin");
argument.matrix = le;
argument.gapopen = GAPOPEN;
argument.gapext = GAPEXT;
argument.T = TEMPERATURE;
argument.beta = 1.0 / TEMPERATURE;
argument.opt = 'P';
if (le == 4) //NUC OPTION :default is nuc_simple
{
read_matrix(nuc_simple);
gap_open = -4;
gap_ext = -0.25;
}
else if (le == 160) //PROT option: default is gonnet_160
{
if (TRACE)
printf("read matrix\n");
read_matrix(gonnet_160);
gap_open = -22;
gap_ext = -1;
}
else if (le == 1000) //Error handling
{
printf("Error: enter a valid matrix type\n");
exit(1);
//additional matrices can only be lower triangular
}
//now override the gapopen and gapext
if (argument.gapopen != 0.0 || argument.gapext != 0.00)
{
gap_open = -argument.gapopen;
gap_ext = -argument.gapext;
}
if (TRACE)
printf("%f %f %f %d\n",argument.T, gap_open, gap_ext, le);
argument.gapopen = gap_open;
argument.gapext = gap_ext;
argument.opt = 'P';
} //end of init
/////////////////////////////////////////////////////////////////////////////////
//END OF MATRIX MODULE
///////////////////////////////////////////////////////////////////////////////
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