#! /usr/bin/perl -w
use strict;
use Getopt::Long;

my $mode = "global";
my $gap = -2;
my $gif = 0;
my ( $seq1,$seq2);
GetOptions("mode:s"    => \$mode,
           "gap:f"     => \$gap,
           "nogif"    => \$gif,
           "compare:s" => \$seq1,
           "to:s" => \$seq2
          );

die "Usage: $0 -compare 'sequence' -to 'sequence' [options]\n",
  "-mode          : local / global / overlap [default: overlap]\n",
  "-gap penalty   :                           [default:     -2]\n",
  "-nogif         : Do not make gif image     [defauly:      create gif]\n",
    unless ( defined $seq1 && defined $seq2);

$gif = 1-$gif;

die "Wrong alignment mode!\n" unless ($mode eq "local" || $mode eq "global" || $mode eq "overlap");
print "Alignment of $seq1 and $seq2\n";
print "Mode of alignment is $mode with a gap penalty of $gap.\n";
print "Including the gif image of the alignemnt.\n" if ($gif);
