#_ Command line options & setup filenames
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];	
    }

print "test $csa_file\n";
    
#_ Check for minimum number of command line argument variables
    if($#ARGV < 6)
    {
	Usage();
	print "NOT ENOUGH COMMAND LINE ARGUMENTS\n";
	exit 0;
    }
    
    $fh_csa = new FileHandle($csa_file, "r") || die "Cannot open CSA file: $csa_file ($!)";