#include "EXTERN.h"
#include "perl.h"
#include "XSUB.h"

#include "ppport.h"

#include "../pairwise.h"

#include <strings.h>

MODULE = Pairwise		PACKAGE = Pairwise		

void
pairwise (file)
		FILE *file
	PREINIT:
		struct fasta **seqs;
		char **output;
		int i = 0;
	PPCODE:
		/* read the sequences */
		seqs = read_fasta(file);
		check_length(seqs);

		/* do the pairwise comparison */
		output = do_pairwise(seqs);

		/* free the sequences */
		while (seqs[i] != NULL)
			free_fasta(seqs[i++]);
		free(seqs);

		/* find out much output there is */
		while (output[i] != NULL)
			i++;
		EXTEND(SP, i);

		/* convert it to perl and free the output */
		for (i = 0; output[i] != NULL; i++) {
			PUSHs(sv_2mortal( newSVpv(output[i], strlen(output[i])) ));
			free(output[i]);
		}
		free(output);