#include "util.h"#include "seq.h"#include "dna.h"#ifndef __lintstatic const char rcsid[] ="$Id: dna.c,v 1.6 2002/08/12 04:15:32 schwartz Exp $";#endifstatic const uchar nchars[] = "ACGT";static const int HOXD70_sym[4][4] = {  {  91, -114,  -31, -123 },  {-114,  100, -125,  -31 },  { -31, -125,  100, -114 },  {-123,  -31, -114,   91 },};#define CLEN(s) (sizeof((s))-1)/* DNA characters */const uchar dchars[] = "ABCDGHKMNRSTVWXY";/* DNA_scores --------------------------  substitution scoring matrix for DNA */void DNA_scores(ss_t ss){	unsigned int i, j;	int bad, a, b, A, B;	for (i = 0; i < NACHARS; ++i)		for (j = 0; j < NACHARS; ++j)			ss[i][j] = -100;	for (i = 0; i < CLEN(nchars); ++i) {		A = nchars[i];		a = tolower(A);		for (j = 0; j < CLEN(nchars); ++j) {			B = nchars[j];			b = tolower(B);			ss[A][B] = ss[a][B] = ss[A][b] = ss[a][b] =				HOXD70_sym[i][j];		}	}	bad = -1000;	for (i = 0; i < NACHARS; ++i)		ss['X'][i] = ss[i]['X'] = ss['x'][i] = ss[i]['x'] = bad;}int is_dchar(int ch){	return !!strchr((const char*)dchars, toupper(ch));}static int scores_from_fp(FILE *fp, ss_t ss){	char buf[1024];	uchar code[255];	char *p;	int n, i, j, s, a, b, A, B, bad;	while (fgets(buf, sizeof buf, fp) != NULL && buf[0] == '#')		;	/* XXX - strtok isn't thread safe */	for (n=0, p=strtok(buf, " \t\n"); p; p=strtok(0, " \t\n"), ++n)		code[n] = *(uchar*)p;	for (i = 0; i < NACHARS; ++i)		for (j = 0; j < NACHARS; ++j)			ss[i][j] = -100;	/* This alters the values in ss as indicated by the file. */	for (i=0; i < n; ++i) {		for (j=0; j < n; ++j) {			if (fscanf(fp, " %d", &s) == 1) {				A = code[i];				a = tolower(A);				B = code[j];				b = tolower(B);				ss[A][B] = ss[A][b] = ss[a][B] = ss[a][b] = s;			} else {				fatal("cannot read score from file");			}		}	}	bad = -1000;	for (i = 0; i < NACHARS; ++i)		ss['X'][i] = ss[i]['X'] = ss['x'][i] = ss[i]['x'] = bad;			return 1;}int scores_from_file(const char *fname, ss_t ss){	FILE *fp;	int rval;	fp = ckopen(fname, "r");	rval = scores_from_fp(fp, ss);	fclose(fp);	return rval;}