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/* fasta2.c - FASTA alignment functions */
#ifdef HAVE_CONFIG_H
# include <config.h>
#endif
#include <stdio.h>
#include <stdlib.h>
#include "align.h"
#include "align/fasta2.h"
#include "sequence/fasta.h"
/* Functions prototypes */
extern int fastay_check(FILE *);
extern sequence_t *fastay_parse(FILE *);
/* Checks FASTA alignment */
int fasta2_check(FILE *f) {
int i, nb;
nb = 0;
while ((i = fastay_check(f)) == 0) { nb++; }
if (i == -1 && nb > 1) { i = 0; }
return i; }
/* Parse FASTA alignment */
align_t *fasta2_parse(FILE *f) {
int i;
size_t len;
align_t *ali;
sequence_t **s, *seq;
if ((ali = align_new()) == NULL) {
return NULL; }
while ((seq = fastay_parse(f)) != NULL) {
s = ali->seq; i = (int)(ali->cur - ali->seq);
len = sizeof(*s) * (i + 1 + 1);
if ((ali->seq = realloc(ali->seq, len)) == NULL) {
align_free(ali); return NULL; }
s = ali->seq + i; *s = seq; *(s+1) = NULL;
ali->cur = s + 1; }
return ali; }
/* Print FASTA alignment */
void fasta2_print(FILE *f, align_t *ali) {
sequence_t **s;
if (ali == NULL) { return; }
s = ali->seq;
while (s && *s) {
fasta_print(f, *s);
s++; }
return; }
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