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/* parse.c - Alignment parsing helper functions */
#ifdef HAVE_CONFIG_H
# include <config.h>
#endif
#include <err.h>
#ifdef STDC_HEADERS
# include <stdlib.h>
# include <string.h>
#endif
#include <ctype.h>
#include "align.h"
#include "align/parse.h"
#include "sequence.h"
#include "sequence/parse.h"
#include "extern/text.h"
/* Update sequence name in temporary buffer */
int parse_tmpupd(align_t *ali, char *nam) {
if (nam == NULL) { return 0; }
if (ali == NULL) { free(nam); return 0; }
ali->_tmp = text_strupd(ali->_tmp, nam);
free(nam);
return (ali->_tmp == NULL); }
/* Add new sequence ... */
int parse_seqnew(align_t *ali) {
char *q, *r;
int i, d;
size_t len;
sequence_t **p;
if (ali == NULL || ali->_tmp == NULL) { return 0; }
d = (getenv("SQUIZZ_DEBUG") != NULL) ? 1 : 0;
/* Cleanup leading spaces */
q = ali->_tmp; while (*q && isspace((unsigned char)*q)) { q++; }
if (q != ali->_tmp) { r = strdup(q); free(ali->_tmp); ali->_tmp = r; }
/* Search if sequence already exist */
p = ali->cur;
if (p && *p) {
i = strcmp((*p)->nam, ali->_tmp);
if (d && i) {
fprintf(stderr, "%s: unexpected sequence name\n", ali->_tmp); }
free(ali->_tmp);
ali->_tmp = NULL;
return i; }
/* Check for reallocation */
p = ali->seq; i = 0; while (p && *p) { i++; p++; }
len = sizeof(*p) * (i + 1 + 1);
if ((ali->seq = realloc(ali->seq, len)) == NULL) {
err(EXIT_FAILURE, "memory"); }
/* Add new sequence & NULL byte */
p = ali->seq + i;
*p = sequence_new();
*(p+1) = NULL;
(*p)->nam = ali->_tmp;
ali->_tmp = NULL;
/* Set current sequence */
ali->cur = p;
return 0; }
/* Update sequence string */
int parse_sequpd(align_t *ali, char *str) {
sequence_t **p;
if (str == NULL) { return 0; }
if (ali == NULL) { free(str); return 0; }
p = ali->cur;
if (*p == NULL) { return -1; }
parse_stradd(*p, str);
return 0; }
/* Set current sequence pointer at the begginning */
int parse_seqrst(align_t *ali) {
if (ali == NULL || ali->seq == NULL) { return 0; }
if (*ali->cur != NULL && ali->cur != ali->seq) { return -1; }
ali->cur = ali->seq;
return 0; }
/* Update current sequence pointer to the next one */
int parse_seqnxt(align_t *ali) {
if (ali == NULL || ali->seq == NULL) { return 0; }
if (*ali->cur == NULL) { return -1; }
ali->cur += 1;
return 0; }
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