#!/usr/bin/env ruby

require_relative '../../lib/ruby/Newick'
require 'optparse'
require 'rubygems'
require 'ostruct'
require_relative '../../lib/ruby/fpdf'

opt = OpenStruct.new
opt.brackets = false
opt.label = false
opt.highlights = nil
opt.file = nil
opt.raw = false
opt.good = 75

# add string->integer method for array access, as fpdf 1.53 fails without it on ruby 1.9 and higher

class Array
  def [](key)
    if key.kind_of?(String)
      self.at(key.to_i)
    else
      self.at(key)
    end
  end
end

ARGV.options {|o|
  o.banner << " tree-file [..tree-file]"
  o.on("-b ", "--opt.brackets ", String, 
          "load list of label brackets") {|b| opt.brackets = b}
  o.on("-h ", "--highlights ", String,
	  "highlight these ids (commas)") {|h| opt.highlights = h} 
  o.on("-f ", "--file ", String,
	  "file with ids to highlight") {|f| opt.file = f} 
  o.on("-l ", "--label ", String, "add label to tree pdf") {|l| opt.label = l}   
  o.on("-r", "--raw", "draw tree with raw names (false)") {opt.raw = true}
  o.on("-g ", "--goodboot ", Float, "minimum level of a good bootstrap (default #{opt.good})") {|l| opt.good = l}
  begin
    o.parse!
  rescue
    STDERR.puts $!.message
    STDERR.puts o
    exit(1)
  end
  if (ARGV.size < 1)
    STDERR.puts o
    exit(1)
  end
}


highlights = Hash.new
if (opt.highlights)
  opt.highlights.split(",").each {|highlight|
    highlights[highlight] = "red"
  }
elsif (opt.file)
  File.new(opt.file).each {|line|
    name, color = line.chomp.split(" ")
    color = "red" if color.nil?
    highlights[name] = color
  }
end

brackets = []
if (opt.brackets)
  File.new(opt.brackets).each {|line|
    x, y1, y2, opt.label, r, p = line.chomp.split(" ")
    opt.brackets.push([x.to_f, y1.to_f, y2.to_f, opt.label, r, p])
  }
end

ARGV.each {|arg|
  tree = NewickTree.fromFile(arg)
  tree.draw(arg + ".pdf", "width", linker = :giLink, opt.label, highlights,
            brackets, opt.raw, opt.good)
}