#!/usr/perl/perl580/bin/perl 

use Algorithm::Cluster;

#$|++;

#$^W = 1;
#use strict;

my $i = 0;
my $firstline;
my $i;

open (DATA, "$ARGV[0]");

$firstline = <DATA>;  # Skip the title line

while(my $line = <DATA>) {
	chomp $line;
#	print ("$line\n");
	@field = split /\t/, $line;
	$orfname[$i] = $field[0];
#	print ("$orfname[$i]\n");
	$orfdata[$i] = join (",", @field[2..5]); #this is the field where we'll find the data
	print ("$orfdata[$i]\n"); #this is the field where we'll find the data
#	$mask[$i] = [ 1,1,1,1 ];
#	print ("$mask[$i]\n");
# 	$a = <STDIN>;
	$i++;
}
close(DATA);


#my @weight = [1,1,1,1];

print "--------------[pairwise average linkage]-------\n";
my %params = (

	applyscale =>		0,
	transpose  =>		1,
	method     =>		'a',
	dist       =>		'e',
	data      =>		\@orfdata,
	mask      =>		\@mask,
	weight    =>		\@weight,
);

my ($result, $linkdist);
my ($i,$j);

($result, $linkdist) = Algorithm::Cluster::treecluster(%params);

$i=0;
foreach(@{$result}) {
	printf("%3d: %3d %3d %7.3f\n",-1-$i,$_->[0],$_->[1],$linkdist->[$i]);
	++$i;
}

print "--------------[pairwise single linkage]-------\n";
$params{method} = 's';

($result, $linkdist) = Algorithm::Cluster::treecluster(%params);

$i=0;
foreach(@{$result}) {
	printf("%3d: %3d %3d %7.3f\n",-1-$i,$_->[0],$_->[1],$linkdist->[$i]);
	++$i;
}

print "--------------[pairwise centroid linkage]-------\n";
$params{method} = 'c';

($result, $linkdist) = Algorithm::Cluster::treecluster(%params);

$i=0;
foreach(@{$result}) {
	printf("%3d: %3d %3d %7.3f\n",-1-$i,$_->[0],$_->[1],$linkdist->[$i]);
	++$i;
}

print "--------------[pairwise maximum linkage]-------\n";
$params{method} = 'm';

($result, $linkdist) = Algorithm::Cluster::treecluster(%params);

$i=0;
foreach(@{$result}) {
	printf("%3d: %3d %3d %7.3f\n",-1-$i,$_->[0],$_->[1],$linkdist->[$i]);
	++$i;
}
__END__