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/* phylips.c - PHYLIPS alignment functions */
#ifdef HAVE_CONFIG_H
# include <config.h>
#endif
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "align.h"
#include "align/phylip.h"
#include "align/phylips.h"
#include "compat.h"
/* Functions prototypes */
extern int phylipsy_check(FILE *);
extern align_t *phylipsy_parse(FILE *);
/* Check PHYLIPS alignment */
int phylips_check(FILE *f) {
int i;
i = phylipsy_check(f);
return i; }
/* Parse PHYLIPS alignment */
align_t *phylips_parse(FILE *f) {
align_t *ali;
ali = phylipsy_parse(f);
return ali; }
/* Print PHYLIPS alignment */
void phylips_print(FILE *f, align_t *ali) {
const char *p;
char *q, c;
int i, j;
size_t n, len;
sequence_t **s;
if (ali == NULL) { return; }
s = ali->seq; len = (*s)->strlen; n = 0;
while (s && *s) { n++; s++; }
/* Print alignment header */
(void)fprintf(f, " %5"PRIsiz" %5"PRIsiz"\n", n, len);
/* Process all sequences */
s = ali->seq;
while (s && *s) {
n = len / 60; if (len % 60) { n++; }
i = 0;
while (n--) {
/* Name */
q = (i == 0) ? phylip_fixnam((*s)->nam) : "";
(void)fprintf(f, "%-10.10s", q);
if (*q) { free(q); }
/* Sequence */
p = (*s)->str + i; j = 60;
while (j && *p) {
c = *p;
if (c == '~' || c == '.') { c = '-'; }
(void)fputc(c, f);
j--; p++; }
(void)fputc('\n', f);
i += 60; }
s++; }
return; }
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