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/* msf.c - MSF alignment functions */
#ifdef HAVE_CONFIG_H
# include <config.h>
#endif
#include <stdio.h>
#ifdef STDC_HEADERS
# include <stdlib.h>
# include <string.h>
#endif
#include <ctype.h>
#include <time.h>
#include "align.h"
#include "align/msf.h"
#include "sequence.h"
#include "sequence/utils.h"
#define crc_t unsigned long
/* Functions prototypes */
extern int msfy_check(FILE *);
extern align_t *msfy_parse(FILE *);
extern crc_t gcg_crc(char *);
crc_t msf_crc(align_t *);
/* Checks MSF alignment */
int msf_check(FILE *f) {
int i;
i = msfy_check(f);
return i; }
/* Parse MSF alignment */
align_t *msf_parse(FILE *f) {
align_t *ali;
ali = msfy_parse(f);
return ali; }
/* Print MSF alignment */
void msf_print(FILE *f, align_t *ali) {
char *p, *b, *e, *nam, c, d[255];
const char *q;
float v;
size_t l, i, j, n, len, nlen;
time_t tt;
struct tm ts;
crc_t crc;
sequence_t **s;
seqtyp_t t;
if (ali == NULL) { return; }
s = ali->seq; t = sequence_type((*s)->str);
len = (*s)->strlen;
crc = msf_crc(ali);
d[0] = '\0'; tt = time(NULL);
(void)localtime_r(&tt, &ts);
(void)strftime(d, 100, "%B %e, %Y %H:%M", &ts);
/* Header */
v = 1.0; c = (t == SEQTYP_PRO) ? 'A' : 'N';
(void)fprintf(f, "!!%cA_MULTIPLE_ALIGNMENT %.1f\n", c, v);
c = (t == SEQTYP_PRO) ? 'P' : 'N'; q = "unknown";
(void)fprintf(f, " %s MSF: %lu", q, len);
(void)fprintf(f, " Type: %c %s Check: %04lu", c, d, crc);
(void)fprintf(f, " ..\n");
/* Names */
(void)fputc('\n', f);
s = ali->seq; nlen = 0;
while (s && *s) {
l = strlen((*s)->nam);
if (l > nlen) { nlen = l; }
s++; }
if (nlen > 39) { nlen = 39; }
l = (nlen < 15) ? 15 : nlen;
s = ali->seq;
while (s && *s) {
crc = gcg_crc((*s)->str); nam = sequence_fixnam((*s)->nam);
(void)fprintf(f, " Name: %-*.*s", (int)l, (int)l, nam);
(void)fprintf(f, " Len: %5lu", len);
(void)fprintf(f, " Check: %4lu", crc);
(void)fprintf(f, " Weight: %2.2f\n", 1.0);
free(nam); s++; }
(void)fputc('\n', f);
(void)fprintf(f, "//\n");
/* Sequences */
i = 0; n = len / 50; if (len % 50) { n++; }
while (n--) {
(void)fputc('\n', f);
s = ali->seq;
p = (*s)->str + i; j = 50;
while (j && *p) { j--; p++; }
(void)fprintf(f, "%*s ", (int)nlen, "");
if (j != 0) {
(void)fprintf(f, "%lu\n", i+1); }
else {
(void)fprintf(f, "%-27lu%27lu\n", i+1, i+50);
}
while (s && *s) {
/* Name */
p = sequence_fixnam((*s)->nam); l = strlen(p); j = nlen;
(void)fprintf(f, "%*s%s ", (int)(j - l), "", p);
free(p);
/* Sequence */
b = (*s)->str; while (*b && (*b == '-' || *b == '?')) b++;
e = p = (*s)->str; while (*e) e++; e--;
while (e > p && (*e == '-' || *e == '?')) e--;
p = (*s)->str + i; j = 0;
while (*p && j < 50) {
if (j && j % 10 == 0) { (void)fputc(' ', f); }
c = *p;
if (c == '-' || c == '?') {
c = '.'; if (p < b || p > e) c = '~'; }
(void)fputc(c, f);
p++; j++; }
(void)fputc(' ', f);
(void)fputc('\n', f);
s++; }
i += 50; }
(void)fputc('\n', f);
return; }
/* MSF sequence CRC */
crc_t msf_crc(align_t *ali) {
crc_t crc;
sequence_t **s;
crc = 0;
if (ali == NULL) { return crc; }
s = ali->seq;
while (s && *s) {
crc += gcg_crc((*s)->str);
s++; }
crc %= 10000;
return crc; }
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