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/* align.c - Generic alignment functions */
#ifdef HAVE_CONFIG_H
# include <config.h>
#endif
#include <err.h>
#include <stdio.h>
#include <sys/types.h>
#ifdef STDC_HEADERS
# include <stdlib.h>
# include <string.h>
#endif
#ifndef HAVE_FSEEKO
# define fseeko fseek
# define ftello ftell
#endif
#include "align.h"
#include "align/clustal.h"
#include "align/fasta2.h"
#include "align/mega.h"
#include "align/msf.h"
#include "align/nexusi.h"
#include "align/phylipi.h"
#include "align/phylips.h"
#include "align/stock.h"
static int namcmp(const void *a, const void *b) {
const char * const *p = a, * const *q = b;
return strcmp(*p, *q); }
/* Create a new alignment object */
align_t *align_new(void) {
size_t len;
align_t *ali;
/* Allocate */
len = sizeof(*ali);
if ((ali = malloc(len)) == NULL) { return NULL; }
/* Initialise */
ali->seq = NULL;
ali->cur = ali->seq;
ali->_tmp = NULL;
return ali; }
/* Delete an alignment object */
void align_free(align_t *ali) {
sequence_t **p;
if (ali == NULL) { return; }
p = ali->seq;
while (p && *p) {
sequence_free(*p);
p++; }
free(ali->seq);
free(ali->_tmp);
free(ali);
return; }
/* Parse a formatted alignment from file */
align_t *align_parse(FILE *f, alifmt_t fmt) {
align_t *ali;
ali = NULL;
switch (fmt) {
case ALIFMT_CLUSTAL:
ali = clustal_parse(f); break;
case ALIFMT_FASTA:
ali = fasta2_parse(f); break;
case ALIFMT_MEGA:
ali = mega_parse(f); break;
case ALIFMT_MSF:
ali = msf_parse(f); break;
case ALIFMT_NEXUSI:
ali = nexusi_parse(f); break;
case ALIFMT_PHYLIPI:
ali = phylipi_parse(f); break;
case ALIFMT_PHYLIPS:
ali = phylips_parse(f); break;
case ALIFMT_STOCK:
ali = stock_parse(f); break;
default: break; }
return ali; }
/* Check alignment format */
int align_check(FILE *f, alifmt_t fmt) {
int i;
switch (fmt) {
case ALIFMT_CLUSTAL:
i = clustal_check(f); break;
case ALIFMT_FASTA:
i = fasta2_check(f); break;
case ALIFMT_MEGA:
i = mega_check(f); break;
case ALIFMT_MSF:
i = msf_check(f); break;
case ALIFMT_NEXUSI:
i = nexusi_check(f); break;
case ALIFMT_PHYLIPI:
i = phylipi_check(f); break;
case ALIFMT_PHYLIPS:
i = phylips_check(f); break;
case ALIFMT_STOCK:
i = stock_check(f); break;
default:
i = 1; break; }
return i; }
/* Check aligment file format */
alifmt_t align_format(FILE *f) {
int i;
off_t off;
alifmt_t fmt;
if ((off = ftello(f)) == -1) {
err(EXIT_FAILURE, "file position"); }
for (fmt = ALIFMT_UNKWN + 1; fmt != ALIFMT_NONE; fmt++) {
i = align_check(f, fmt);
if (fseeko(f, off, SEEK_SET) != 0) {
err(EXIT_FAILURE, "file position"); }
if (i == 0) { break; }
}
return fmt; }
/* Check for alignment strict conditions */
int align_strict(align_t *ali) {
int i, d, n, num;
size_t len;
char **x, **buf;
sequence_t **p;
if (ali == NULL || ali->seq == NULL) { return 1; }
d = (getenv("SQUIZZ_DEBUG") != NULL) ? 1 : 0;
/* Need more than 1 sequence */
p = ali->seq; n = 0;
while (p && *p) { n++; p++; }
if (d) { fprintf(stderr, "Found %d sequence(s)\n", n); }
if (n < 2) { return 1; }
num = n;
/* All sequences must have the same length */
p = ali->seq; n = 0; len = (*p)->strlen;
while (p && *p) {
if ((*p)->strlen != len) { n++; }
p++; }
if (d) { fprintf(stderr, "Found %d sequence(s) with bad lengths\n", n); }
if (n > 0) { return 1; }
/* Sequence names must exists */
p = ali->seq; n = 0;
while (p && *p) {
if ((*p)->nam == NULL) { n++; }
p++; }
if (d) { fprintf(stderr, "Found %d unnamed sequence(s)\n", n); }
if (n > 0) { return 1; }
/* Sequence names must be unique */
len = num * sizeof(*buf);
if ((buf = malloc(len)) == NULL) { return 1; }
p = ali->seq; x = buf; n = 0;
while (p && *p) {
*x = (*p)->nam; x++; p++; }
qsort(buf, num, sizeof(*buf), namcmp);
for (i = 0, x = buf; i < num - 1; i++, x++) {
if (strcmp(*x, *(x+1)) != 0) { continue; }
n++; }
free(buf);
if (d) { fprintf(stderr, "Found %d identical sequence name pair(s)\n", n); }
if (n > 0) { return 1; }
return 0; }
/* Print alignment */
void align_print(FILE *f, align_t *ali, alifmt_t fmt) {
switch (fmt) {
case ALIFMT_CLUSTAL:
clustal_print(f, ali); break;
case ALIFMT_FASTA:
fasta2_print(f, ali); break;
case ALIFMT_MEGA:
mega_print(f, ali); break;
case ALIFMT_MSF:
msf_print(f, ali); break;
case ALIFMT_NEXUSI:
nexusi_print(f, ali); break;
case ALIFMT_PHYLIPI:
phylipi_print(f, ali); break;
case ALIFMT_PHYLIPS:
phylips_print(f, ali); break;
case ALIFMT_STOCK:
stock_print(f, ali); break;
default:
break; }
return; }
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