/* Pairwise identity program.
 *
 * $Id
 *
 * Reads in a gapped alignment sequences in a FASTA file format.
 * Assume gaps are represented by '-' characters.
 *
 * For each pair calculates the sequence percentage identity, see comments
 * for pairwise() for details.
 *
 * Output is in the format for OC to read in, i.e. the number of sequences,
 * followed by the sequence ID's, followed by the pairwise comparisons.
 *
 * Thu Dec  5 14:38:43 GMT 2002 Jon
 * Added checking for eqilength sequences
 *
 * Thu Jul 24 12:14:04 BST 2003 Jon
 * Moved FASTA reading into read_fasta function
 * Checked into CVS
 *
 * */

#include <stdio.h>
#include <stdlib.h>
#include "pairwise.h"

int
main (int argc, char **argv) {
	FILE *fh;
	struct fasta **seqs;
	char **output;
	int i = 0;

	/* Read in the FASTA file */
	if (argc == 2) 
		fh = xfopen(argv[1], "r");
	else
		fh = stdin;

	seqs = read_fasta(fh);
	fclose(fh);

	check_length(seqs);
	output = do_pairwise(seqs);

	for (i = 0; seqs[i] != NULL; i++)
		free_fasta(seqs[i]);
	free(seqs);

	for (i = 0; output[i] != NULL; i++) {
		printf("%s\n", output[i]);
		/*free(output[i]);*/
	}
	/*free(output);*/

	return EXIT_SUCCESS;
}