#!/usr/bin/env ruby

# Copyright 2016 Ryan Moore
# Contact: moorer@udel.edu
#
# This file is part of Iroki.
#
# Iroki is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Iroki is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
# General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Iroki.  If not, see <http://www.gnu.org/licenses/>.

require "iroki"
require "trollop"

opts = Trollop.options do
  version Iroki::VERSION_BANNER

  banner <<-EOS

#{Iroki::VERSION_BANNER}

  Iroki command line program.

  See https://github.com/mooreryan/iroki/wiki for the Iroki manual.

  Options:
  EOS

  opt(:color_branches,
      "Color branches?",
      short: "-b")

  opt(:color_taxa_names,
      "Color label names?",
      short: "-t")

  opt(:exact,
      "Exact pattern matching")

  # opt(:remove_bootstraps_below,
  #     "Remove bootstrap values below given value",
  #     type: :float)

  opt(:color_map,
      "File with color mappings",
      type: :string)

  opt(:biom,
      "Biom file to make color gradient",
      type: :string)

  opt(:single_color,
      "Use single color gradient for single group biom files")

  opt(:name_map,
      "File with name mappings",
      type: :string)

  opt(:auto_color,
      "Specify color scheme for auto coloring",
      type: :string)

  opt(:display_auto_color_options,
      "Display options for auto coloring")

  opt(:infile,
      "Name of input newick file",
      type: :string)

  opt(:outfile,
      "Name of outfile",
      type: :string)

  opt(:default_color,
      "Default color",
      type: :string,
      default: "black")

    opt(:min_lumin,
      "Min luminosity (only used for gradients)",
      type: :int,
      default: 35)

    opt(:max_lumin,
      "Max luminosity (only used for gradients)",
      type: :int,
      default: 70)

end

Iroki::Main.main(
  color_branches:             opts[:color_branches],
  color_taxa_names:           opts[:color_taxa_names],
  exact:                      opts[:exact],
  remove_bootstraps_below:    opts[:remove_bootstraps_below],
  color_map_f:                opts[:color_map],
  biom_f:                     opts[:biom],
  single_color:               opts[:single_color],
  name_map_f:                 opts[:name_map],
  auto_color:                 opts[:auto_color],
  display_auto_color_options: opts[:display_auto_color_options],
  newick_f:                   opts[:infile],
  out_f:                      opts[:outfile],
  default_color:              opts[:default_color],
  min_lumin:                  opts[:min_lumin],
  max_lumin:                  opts[:max_lumin]
)