#!/usr/bin/env ruby

require 'Newick'
require 'optparse'
require 'ostruct'

opt = OpenStruct.new
opt.verbose = false

ARGV.options {|opts|
  opts.banner << " tree-file"
  opts.on("-v", "--verbose", "show progress") {|t| opt.verbose = t} 
  begin
    opts.parse!
  rescue
    STDERR.puts $!.message
    STDERR.puts opts
    exit(1)
  end
  if (ARGV.size < 1)
    STDERR.puts opts
    exit(1)
  end
}


file = ARGV.pop

tree = NewickTree.fromFile(file)
dMatrix = tree.distanceMatrix(opt.verbose)

printf("    %d\n", dMatrix.keys.size)
dMatrix.keys.each {|key1|
  printf("%-16s ", key1)
  dMatrix.keys.each {|key2|
    printf("%f  ", dMatrix[key1][key2])
  }
  printf("\n")
}