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/* mega.c - MEGA 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/mega.h"
#include "sequence.h"
#include "sequence/utils.h"
/* Functions prototypes */
extern int megay_check(FILE *);
extern align_t *megay_parse(FILE *);
/* Checks MEGA alignment */
int mega_check(FILE *f) {
int i;
i = megay_check(f);
return i; }
/* Parse MEGA alignment */
align_t *mega_parse(FILE *f) {
char *p, *q, *ref;
align_t *ali;
sequence_t **s;
ali = megay_parse(f);
if (ali == NULL) {
return ali; }
/* FIXME: Do not allow identical character in 1st sequence */
/* Replace all "identical" characters in sequences */
s = ali->seq; ref = (*s)->str; s++;
while (s && *s) {
p = (*s)->str; q = ref;
while (p && *p) {
if (*p == '.') { *p = *q; }
p++; q++; }
s++; }
return ali; }
/* Print MEGA alignment */
void mega_print(FILE *f, align_t *ali) {
char *p;
char c;
int j;
sequence_t **s;
if (ali == NULL) { return; }
/* Header */
(void)fprintf(f, "#mega\n");
(void)fprintf(f, "!Title Multiple Sequence Alignment;\n");
(void)fputc('\n', f);
/* Sequences */
s = ali->seq;
while (s && *s) {
/* Name (max 40 chars) */
p = sequence_fixnam((*s)->nam); j = 40;
(void)fprintf(f, "#%-.*s\n", j, p);
free(p);
/* Sequence */
p = (*s)->str; j = 60;
while (*p) {
c = *p;
if (c == '~') { c = '-'; }
if (j == 0) {
(void)fputc('\n', f);
j = 60; }
(void)fputc(c, f);
j--; p++; }
(void)fputc('\n', f);
s++; }
return; }
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