# args=-supermax -d -l 50 -h 7 -seedlength 7 -evalue 0.0001 -s 60 /home/anonymous_monk/clusters/all/all_clusters
   140     8778      333   D   140     8778      334  -7    3.60e-56   -259    95.00
Sbjct: AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA         393
       !    
                                                       
Sbjct: -AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA         394

Sbjct: AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGCCTT         453
Sbjct: AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGCCTT         454

Sbjct: TTAAAATTCCCCCC-GGGGGG                                                474
                     !      
Sbjct: TTAAAATTCCCCCCGGGGGGG                                                475

##</code><code>##

sub _parse_paired {
	my $this = shift;
	my $pkey = 1;
	my $c = { comments => '',
		  left_instance => '',
		  right_instance => '',
		  match => '' };	
	
	### build up each record and place in the collection ###
	$INPUT_RECORD_SEPARATOR = "\n\n\n";
	while (my $record = $this->{handle}->getline()) {
		my ($lt, $rt, $lseq, $rseq) = ();
		my @rows = split /\n/, $record;
		for (my $i = 0; $i < $#rows; $i++) {
			if ($rows[$i] =~ m/^\n?$/) { next; }
			elsif ($rows[$i] =~ m/^#/) {
				$c->{$pkey}->{comments} .= "$rows[$i]\n";
			}
			elsif ($rows[$i] =~ m/^\s+\d+/) {
				_load_stats($pkey, $rows[$i], $c);
			}
			elsif ($rows[$i] =~ m/^Sbjct/ &&
				 $rows[$i+1] =~ m/^Sbjct/) {
				(undef, $lt, undef) = split /\s+/, $rows[$i];
				(undef, $rt, undef) = split /\s+/, $rows[$i+1];
				$lseq .= $lt; $rseq .= $rt;
			}
			elsif ($rows[$i] =~ m/^Sbjct/ &&
				 $rows[$i+1] =~ m/!/) {
				(undef, $lt, undef) = split /\s+/, $rows[$i];
				(undef, $rt, undef) = split /\s+/, $rows[$i+2];
				$lseq .= $lt; $rseq .= $rt;
			}
		}
		$c->{$pkey}->{left_instance}->{sequence} = $lseq;
		$c->{$pkey}->{right_instance}->{sequence} = $rseq;
		++$pkey;
	}

	return $c;
}