iroki 0.0.1

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in iroki.gemspec
+gemspec

data/Guardfile

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+# A sample Guardfile
+# More info at https://github.com/guard/guard#readme
+
+## Uncomment and set this to only include directories you want to watch
+# directories %w(app lib config test spec features) \
+#  .select{|d| Dir.exists?(d) ? d : UI.warning("Directory #{d} does not exist")}
+
+## Note: if you are using the `directories` clause above and you are not
+## watching the project directory ('.'), then you will want to move
+## the Guardfile to a watched dir and symlink it back, e.g.
+#
+#  $ mkdir config
+#  $ mv Guardfile config/
+#  $ ln -s config/Guardfile .
+#
+# and, you'll have to watch "config/Guardfile" instead of "Guardfile"
+
+# Note: The cmd option is now required due to the increasing number of ways
+#       rspec may be run, below are examples of the most common uses.
+#  * bundler: 'bundle exec rspec'
+#  * bundler binstubs: 'bin/rspec'
+#  * spring: 'bin/rspec' (This will use spring if running and you have
+#                          installed the spring binstubs per the docs)
+#  * zeus: 'zeus rspec' (requires the server to be started separately)
+#  * 'just' rspec: 'rspec'
+
+guard :rspec, cmd: "bundle exec rspec" do
+  require "guard/rspec/dsl"
+  dsl = Guard::RSpec::Dsl.new(self)
+
+  # Feel free to open issues for suggestions and improvements
+
+  # RSpec files
+  rspec = dsl.rspec
+  watch(rspec.spec_helper) { rspec.spec_dir }
+  watch(rspec.spec_support) { rspec.spec_dir }
+  watch(rspec.spec_files)
+
+  # Ruby files
+  ruby = dsl.ruby
+  dsl.watch_spec_files_for(ruby.lib_files)
+
+  # Rails files
+  rails = dsl.rails(view_extensions: %w(erb haml slim))
+  dsl.watch_spec_files_for(rails.app_files)
+  dsl.watch_spec_files_for(rails.views)
+
+  watch(rails.controllers) do |m|
+    [
+      rspec.spec.("routing/#{m[1]}_routing"),
+      rspec.spec.("controllers/#{m[1]}_controller"),
+      rspec.spec.("acceptance/#{m[1]}")
+    ]
+  end
+
+  # Rails config changes
+  watch(rails.spec_helper)     { rspec.spec_dir }
+  watch(rails.routes)          { "#{rspec.spec_dir}/routing" }
+  watch(rails.app_controller)  { "#{rspec.spec_dir}/controllers" }
+
+  # Capybara features specs
+  watch(rails.view_dirs)     { |m| rspec.spec.("features/#{m[1]}") }
+  watch(rails.layouts)       { |m| rspec.spec.("features/#{m[1]}") }
+
+  # Turnip features and steps
+  watch(%r{^spec/acceptance/(.+)\.feature$})
+  watch(%r{^spec/acceptance/steps/(.+)_steps\.rb$}) do |m|
+    Dir[File.join("**/#{m[1]}.feature")][0] || "spec/acceptance"
+  end
+end

data/README.md

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+# Iroki #
+
+[![Gem Version](https://badge.fury.io/rb/iroki.svg)](https://badge.fury.io/rb/iroki) [![Build Status](https://travis-ci.org/mooreryan/iroki.svg?branch=master)](https://travis-ci.org/mooreryan/iroki) [![Coverage Status](https://coveralls.io/repos/github/mooreryan/iroki/badge.svg?branch=master)](https://coveralls.io/github/mooreryan/iroki?branch=master)
+
+Library code for Iroki, a phylogenetic tree customization program.
+
+## Installation ##
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'iroki'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install iroki
+
+## Development ##
+
+After checking out the repo, run `bin/setup` to install
+dependencies. Then, run `rake spec` to run the tests. You can also run
+`bin/console` for an interactive prompt that will allow you to
+experiment.
+
+To install this gem onto your local machine, run `bundle exec rake
+install`. To release a new version, update the version number in
+`version.rb`, and then run `bundle exec rake release`, which will
+create a git tag for the version, push git commits and tags, and push
+the `.gem` file to [rubygems.org](https://rubygems.org).
+
+## Contributing ##
+
+Bug reports and pull requests are welcome on GitHub at
+https://github.com/mooreryan/iroki. This project is intended to
+be a safe, welcoming space for collaboration, and contributors are
+expected to adhere to the
+[Contributor Covenant](http://contributor-covenant.org) code of
+conduct.

data/Rakefile

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+require "bundler/gem_tasks"
+require "rspec/core/rake_task"
+
+RSpec::Core::RakeTask.new(:spec)
+
+task :default => :spec

data/bin/console

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+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "iroki"
+
+# You can add fixtures and/or initialization code here to make experimenting
+# with your gem easier. You can also use a different console, if you like.
+
+# (If you use this, don't forget to add pry to your Gemfile!)
+# require "pry"
+# Pry.start
+
+require "irb"
+IRB.start

data/bin/setup

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+#!/usr/bin/env bash
+set -euo pipefail
+IFS=$'\n\t'
+set -vx
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/exe/iroki

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+#!/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.
+
+  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(: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)
+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],
+  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]
+)

data/iroki.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'iroki/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "iroki"
+  spec.version       = Iroki::VERSION
+  spec.authors       = ["Ryan Moore"]
+  spec.email         = ["moorer@udel.edu"]
+
+  spec.summary       = %q{Library code for Iroki, a phylogenetic tree customization program.}
+  spec.description   = %q{Library code for Iroki, a phylogenetic tree customization program.}
+  spec.homepage      = "https://github.com/mooreryan/iroki"
+  spec.license       = "GPLv3: http://www.gnu.org/licenses/gpl.txt"
+
+  spec.files         = `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
+  spec.bindir        = "exe"
+  spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
+  spec.require_paths = ["lib"]
+
+  spec.required_ruby_version = ">= 2.2.4"
+
+  spec.add_development_dependency "bundler", "~> 1.11"
+  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "rspec", "~> 3.0"
+  spec.add_development_dependency "guard-rspec", "~> 4.6", ">= 4.6.4"
+  spec.add_development_dependency "yard", "~> 0.8.7.6"
+  spec.add_development_dependency "coveralls", "~> 0.8.11"
+
+  spec.add_runtime_dependency "abort_if", "~> 0.1.0"
+  spec.add_runtime_dependency "bio", "~> 1.5"
+  spec.add_runtime_dependency "trollop", "~> 2.1", ">= 2.1.2"
+end

data/lib/iroki.rb

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+# 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 "abort_if"
+
+require "iroki/version"
+require "iroki/const/const"
+require "iroki/color/color"
+require "iroki/core_ext/hash/hash"
+require "iroki/core_ext/string/string"
+require "iroki/core_ext/file/file"
+require "iroki/utils/utils"
+require "iroki/main/main"
+
+
+include Iroki::Const
+include Iroki::Color
+include Iroki::CoreExt::Hash
+include Iroki::CoreExt::String
+include Iroki::CoreExt::File
+include Iroki::Utils
+
+include AbortIf
+
+
+module Iroki
+end

data/lib/iroki/color/color.rb

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+# 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/>.
+
+module Iroki
+  module Color
+    BASIC =
+      { "1" => "#FF3814",   # red
+        "2" => "#712BFF",   # blue
+        "3" => "#FFDF14",   # yellow
+        "4" => "#14FF63", } # green
+
+    BASIC_LIGHT =
+      { "1" => "#FF8872",
+        "2" => "#A97FFE",
+        "3" => "#FFEC72",
+        "4" => "#71FEA1", }
+
+    BASIC_DARK =
+      { "1" => "#FF2800",
+        "2" => "#4901DD",
+        "3" => "#FFDD00",
+        "4" => "#00E24D", }
+
+    FUNKY =
+      { "1" => "#FF7314",
+        "2" => "#9F23FF",
+        "3" => "#FFF814",
+        "4" => "#14FFD8", }
+
+    FUNKY_LIGHT =
+      { "1" => "#FFAB72",
+        "2" => "#C57AFE",
+        "3" => "#FFFB72",
+        "4" => "#71FEE6", }
+
+    FUNKY_DARK =
+      { "1" => "#FF6700",
+        "2" => "#7C01DC",
+        "3" => "#FFF700",
+        "4" => "#00D7B3", }
+
+  end
+end

data/lib/iroki/const/const.rb

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+# 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/>.
+
+module Iroki
+  module Const
+    COPYRIGHT = "2016 Ryan Moore"
+    CONTACT   = "moorer@udel.edu"
+    WEBSITE   = "https://github.com/mooreryan/color_tree"
+    LICENSE   = "GPLv3"
+
+    VERSION_BANNER = "  # Version: #{Iroki::VERSION}
+  # Copyright #{COPYRIGHT}
+  # Contact: #{CONTACT}
+  # Website: #{WEBSITE}
+  # License: #{LICENSE}"
+
+    FIG = 'begin figtree;
+	set appearance.backgroundColorAttribute="Default";
+	set appearance.backgroundColour=#-1;
+	set appearance.branchColorAttribute="User selection";
+	set appearance.branchLineWidth=1.0;
+	set appearance.branchMinLineWidth=0.0;
+	set appearance.branchWidthAttribute="Fixed";
+	set appearance.foregroundColour=#-16777216;
+	set appearance.selectionColour=#-2144520576;
+	set branchLabels.colorAttribute="User selection";
+	set branchLabels.displayAttribute="Branch times";
+	set branchLabels.fontName="sansserif";
+	set branchLabels.fontSize=8;
+	set branchLabels.fontStyle=0;
+	set branchLabels.isShown=false;
+	set branchLabels.significantDigits=2;
+	set colour.scheme.label="label:InterpolatingContinuous{{false,false,0.0,0.0},#000000,#000000}";
+	set layout.expansion=0;
+	set layout.layoutType="RECTILINEAR";
+	set layout.zoom=0;
+	set legend.attribute=null;
+	set legend.fontSize=10.0;
+	set legend.isShown=false;
+	set legend.significantDigits=2;
+	set nodeBars.barWidth=4.0;
+	set nodeBars.displayAttribute=null;
+	set nodeBars.isShown=false;
+	set nodeLabels.colorAttribute="label";
+	set nodeLabels.displayAttribute="label";
+	set nodeLabels.fontName="sansserif";
+	set nodeLabels.fontSize=8;
+	set nodeLabels.fontStyle=0;
+	set nodeLabels.isShown=true;
+	set nodeLabels.significantDigits=2;
+	set nodeShape.colourAttribute=null;
+	set nodeShape.isShown=false;
+	set nodeShape.minSize=10.0;
+	set nodeShape.scaleType=Width;
+	set nodeShape.shapeType=Circle;
+	set nodeShape.size=4.0;
+	set nodeShape.sizeAttribute=null;
+	set polarLayout.alignTipLabels=false;
+	set polarLayout.angularRange=0;
+	set polarLayout.rootAngle=0;
+	set polarLayout.rootLength=100;
+	set polarLayout.showRoot=true;
+	set radialLayout.spread=0.0;
+	set rectilinearLayout.alignTipLabels=false;
+	set rectilinearLayout.curvature=0;
+	set rectilinearLayout.rootLength=100;
+	set scale.offsetAge=0.0;
+	set scale.rootAge=1.0;
+	set scale.scaleFactor=1.0;
+	set scale.scaleRoot=false;
+	set scaleAxis.automaticScale=true;
+	set scaleAxis.fontSize=8.0;
+	set scaleAxis.isShown=false;
+	set scaleAxis.lineWidth=1.0;
+	set scaleAxis.majorTicks=1.0;
+	set scaleAxis.origin=0.0;
+	set scaleAxis.reverseAxis=false;
+	set scaleAxis.showGrid=true;
+	set scaleBar.automaticScale=true;
+	set scaleBar.fontSize=10.0;
+	set scaleBar.isShown=true;
+	set scaleBar.lineWidth=1.0;
+	set scaleBar.scaleRange=0.0;
+	set tipLabels.colorAttribute="User selection";
+	set tipLabels.displayAttribute="Names";
+	set tipLabels.fontName="sansserif";
+	set tipLabels.fontSize=8;
+	set tipLabels.fontStyle=0;
+	set tipLabels.isShown=true;
+	set tipLabels.significantDigits=2;
+	set trees.order=true;
+	set trees.orderType="increasing";
+	set trees.rooting=false;
+	set trees.rootingType="User Selection";
+	set trees.transform=false;
+	set trees.transformType="cladogram";
+end;
+'
+  end
+end