#_ Check for minimum number of command line argument variables
if($#ARGV < 6)
{
    Usage();
    print "NOT ENOUGH COMMAND LINE ARGUMENTS\n";
    exit 0;
}

#_ Command line options & setup filenames
my($alignment_file, $scorecons_file, $image_file, $numbered_model, $csa_file);
foreach my $i (0 .. $#ARGV)
#for ($i=0; $i<=$#ARGV; $i++)
{
    if($ARGV[$i] eq "-a")
    {
        $alignment_file = $ARGV[$i+1];
    }
    if($ARGV[$i] eq "-s")
    {
        $scorecons_file = $ARGV[$i+1];
    }
    if($ARGV[$i] eq "-i")
    {
        $image_file = $ARGV[$i+1];
    }
    if($ARGV[$i] eq "-m")
    {
        $numbered_model = $ARGV[$i+1];
    }
    if($ARGV[$i] eq "-c")
    {
        $csa_file = $ARGV[$i+1];	
    }
}

if (not defined $csa_file) {
    Usage();
    print "No CSA file defined\n";
    exit 0;
}
print "test $csa_file\n";
my $fh_csa = new FileHandle($csa_file, "r")
    or die "Cannot open CSA file: $csa_file ($!)";