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#include <stdlib.h> /* free */
#include <string.h> /* strlen */
#include "util.h"
#include "alignment.h"
int aln_same_lengths(const alignment *a) {
const size_t len = strlen(a->key_positions);
size_t i;
for (i = 0; i != a->seq_num; ++i)
if (strlen(a->seqs[i].seq) != len)
return 0;
return 1;
}
static char *next_word(const char *cs) {
return skipws(skipnw(cs));
}
void aln_read(alignment *a, FILE *stream) {
char *line = NULL;
size_t line_size = 0;
int state = 0;
a->seq_num = 0;
a->seqs = NULL;
a->key_positions = NULL;
while (xgetline(&line, &line_size, stream)) {
if (state == 0) {
char *beg = skipws(line);
char *end = skipnw(beg);
if (*beg == '*' && *(end-1) == '*') {
*end = 0;
a->key_positions = xstrdup(beg);
state = 1;
}
} else {
char *name = line;
char *start = next_word(name);
char *seq = next_word(start);
if (*seq == 0)
break;
*skipnw(name) = 0;
*skipnw(start) = 0;
*skipnw(seq) = 0;
++a->seq_num;
/* slow but simple linear reallocation for now: */
a->seqs = XREALLOC(a->seqs, a->seq_num);
a->seqs[a->seq_num-1].name = xstrdup(name);
a->seqs[a->seq_num-1].seq = xstrdup(seq);
a->seqs[a->seq_num-1].start = xstrdup(start);
}
}
free(line);
}
static void seq_free(aligned_seq *s) {
free(s->name);
free(s->seq);
free(s->start);
}
void aln_free(alignment *a) {
size_t i;
for (i = 0; i != a->seq_num; ++i)
seq_free(&a->seqs[i]);
free(a->seqs);
free(a->key_positions);
}
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