#!/usr/bin/env ruby
def binary_available(name)
  available = false
  ENV['PATH'].split(':').each do |folder|
    available = true if File.exists?(File.join folder, name)
  end
  available
end

class NewickString
  attr_reader :str
  def initialize(str)
    @str=String.new(str)
  end
  def support_values
    @str.gsub("0.0;","").scan(/\[([0-9]+)\]/).map{|n| n[0].to_i}
  end
  def multifurcations
    # TODO find the multifurcations and show their support (guess it is 100 cause bifurcations were lower than 50)
    # maybe try to resolve them on the fly?
  end
  def branch_lengths
    @str.gsub("0.0;","").scan(/:([0-9]+\.[0-9]+)/).map{|n| n[0].to_f}
  end
  def str_with_scaled_branch_lengths(factor)
    newt = @str.gsub(/:([0-9]+\.[0-9]+)/) do |bl|
      newval = bl.gsub(":","").to_f * factor
      ":" + "%.9f" % newval 
    end
    newt
  end
  def str_with_numeric_branch_lengths
    newt = @str.gsub(/:([0-9]+\.[0-9]+)e-([0-9]+)/) do |bl|
      newval = bl.gsub(":","").to_f  
      ":" + "%.9f" % newval 
    end
    newt
  end
  def treelength
    self.branch_lengths.inject(0){|acc,i| acc+i}
  end
  def rawtopology
    @str.gsub(/[0-9]+\.[0-9]+/,'').gsub(':','')
  end
  def taxanames
    self.rawtopology.gsub("(", " ").gsub(")", " ").gsub(",", " ").gsub(";", " ").strip.split
  end
  def numtaxa
    @str.count(",").to_i + 1
  end
  def clean
    newstr = @str.gsub('(,)',"").gsub('(,(','((').gsub('),)','))')
    newstr = newstr.gsub('(,)',"").gsub('(,(','((').gsub('),)','))')
    newstr.gsub(',)',")").gsub('(,','(').gsub("e-06","")
  end
end
class NewickFile
  attr_reader :newickStrings
  def initialize(filename)
    @newickStrings = File.open(filename).readlines.map{|line| NewickString.new(line)}
    @filename = filename 
  end
  def size
    @newickStrings.size
  end
  def save_each_newick_as(newfile_basename, ending)
    @newickStrings.each_with_index do |newick, i|
      File.open(newfile_basename + "_#{i}.#{ending}" , "w") do |f|
        f.puts newick.str
      end
    end
  end
  def remove_taxa(taxa, pruned_tree, verbose = false)
    # assume nw_prune and nw_reroot are in the PATH
    nw_pruner = "nw_prune"
    nw_unrooter = "nw_reroot"
    #required_utils = [nw_pruner, nw_unrooter] 
    required_utils = [nw_pruner] 
    required_utils.each do |nw_util|
      raise "#{nw_util} from newick utilities not available" unless binary_available(nw_util)
    end
    # prune a list of taxa and unroot resulting tree with these nice and fast newick utilities
    # on the first tree of the file or all of them?
    #system "#{nw_pruner} #{@filename} #{taxa.join ' '} | #{nw_unrooter} -d - > #{pruned_tree}"
    system "#{nw_pruner} #{@filename} #{taxa.join ' '} > #{pruned_tree}"
    puts "removed #{taxa.join ','} and saved in #{pruned_tree}" if verbose
  end
end

=begin
if __FILE__ == $0 then
  # test usage
  tree = NewickFile.new(tree_topology).newickStrings[0]
  puts tree.numtaxa
end
=end