package Pairwise;

use strict;
use warnings;
use Carp;
use IPC::Open3;
use UNIVERSAL qw(isa);
use File::Temp;
use base qw(Root Common);

use Run qw(check);

sub path {
	my ($self, $path) = @_;
	if (defined $path) { $self->{path}= $path }
	else {
		if (defined $self->{path}) { return $self->{path} }
		else { croak "Path not defined" }
	}
}

sub run {
	my ($self, $fasta) = @_;

	croak "Non FASTA::File object passed to Pairwise::run" unless isa $fasta, 'FASTA::File';

	local ($/, $?) = (undef, 0);

	my $f = File::Temp->new->filename;
	$fasta->write_file($f);

	my $pid = open my $fh, $self->path." $f |" or die $!;

	my @output = join "\n", split "\n", <$fh>;

	waitpid $pid, 0;
	check($self->path, $?) or die "Pairwise was naughty\n";

	return @output;
}

1;