#!/usr/local/bin/perl

use strict;
use English;
use Data::Dumper;
use UNIVERSAL qw(isa);
use FileHandle;
use Exception;

my $alignment = shift;

if (!$alignment || ! -e $alignment) {
	die new Exception("couldnt open names file $alignment $!");
}

warn "# Reading alignment data";
my $alignData = getAlignData($alignment);
warn "# Got data: ".scalar (keys %$alignData);

#################################################

sub getAlignData {
	my ($fIn) = @ARG;

	my $fh = new FileHandle($fIn)
		or die "";

	my $count = 0;

        my $hData = {};

	while (my $line = $fh->getline)
	{
	    my @cols = split /\s+/, $line;

	    # search only for lines with identifier

	    my $field = $cols[0];

	    my $test = substr($field, 0, 1);

	    if("$test" eq ">")
	    {
                 $count++;
		 my $hEntry = {
		    'identifier' => $cols[0],
		    'line' => $count,
		};

		my ($record) = sort ($hEntry->{identifier});
		$hData->{$record} = $hEntry;
        }
    }

	foreach my $k ( keys %{$hData} )
	{
	    printf "%s -> %s\n", $k, $hData->{$k};
	}

	return $hData;
}