ulla 0.9.3

data/lib/ulla/environment.rb

@@ -0,0 +1,34 @@
+module Ulla
+  class Environment
+
+    attr_accessor :amino_acids,
+      :number,
+      :label,
+      :freq_array,
+      :prob_array,
+      :logo_array,
+      :smooth_prob_array
+
+    def initialize(number, label, amino_acids = "ACDEFGHIKLMNPQRSTVWYJ".split(''))
+      @amino_acids        = amino_acids
+      @number             = number
+      @label              = label
+      @freq_array         = $noweight ? NArray.int(@amino_acids.size) : NArray.float(@amino_acids.size)
+      @prob_array         = NArray.float(@amino_acids.size)
+      @logo_array         = NArray.float(@amino_acids.size)
+      @smooth_prob_array  = NArray.float(@amino_acids.size)
+    end
+
+    def increase_residue_count(a, inc = 1.0)
+      @freq_array[@amino_acids.index(a.upcase)] += inc
+    end
+
+    def label_set
+      label.split("").map_with_index { |l, i| "#{i}#{l}" }.to_set
+    end
+
+    def to_s
+      "#{number}-#{label}"
+    end
+  end
+end

data/lib/ulla/environment_class_hash.rb

@@ -0,0 +1,20 @@
+module Ulla
+  class EnvironmentClassHash < Hash
+
+    def group_by_non_residue_labels
+      self.values.group_by { |env| env.label[1..-1] }
+    end
+
+    def groups_sorted_by_residue_labels
+      group_by_non_residue_labels.to_a.sort_by { |env_group|
+        env_group[0].split('').map_with_index { |l, i|
+          $env_features[i + 1].labels.index(l)
+        }
+      }
+    end
+
+    def group_size
+      group_by_non_residue_labels.size
+    end
+  end
+end

data/lib/ulla/environment_feature.rb

@@ -0,0 +1,26 @@
+module Ulla
+  class EnvironmentFeature
+
+    attr_accessor :name, :symbols, :labels, :constrained, :silent
+
+    def initialize(name, symbols, labels, constrained, silent)
+      @name = name
+      @symbols = symbols
+      @labels = labels
+      @constrained = constrained
+      @silent = silent
+    end
+
+    def to_s
+      [name, symbols.join, labels.join, constrained, silent].join(";")
+    end
+
+    def constrained?
+      constrained == "T"
+    end
+
+    def silent?
+      silent == "T"
+    end
+  end
+end

data/lib/ulla/environment_feature_array.rb

@@ -0,0 +1,12 @@
+module Ulla
+  class EnvironmentFeatureArray < Array
+
+    def label_combinations
+      self.inject([]) { |sum, ec|
+        sum << ec.labels
+      }.inject { |pro, lb|
+        pro.product(lb)
+      }
+    end
+  end
+end

data/lib/ulla/heatmap_array.rb

@@ -0,0 +1,111 @@
+require 'rubygems'
+require 'facets'
+
+begin
+  require 'RMagick'
+  include Magick
+rescue
+  $logger.warn "A RubyGems package, 'rmagick' is not found, so heat maps cannot be generated."
+  $no_rmagick = true
+end
+
+
+
+module Ulla
+  class HeatmapArray < Array
+
+    def heatmap(options = {})
+      if $no_rmagick
+        return nil
+      end
+
+      opts = {:columns                => 4,
+              :rvg_width              => nil,
+              :dpi                    => 100,
+              :title                  => '',
+              :max_val                => nil,
+              :mid_val                => nil,
+              :min_val                => nil,
+              :print_gradient         => true,
+              :gradient_beg_color     => '#FFFFFF',
+              :gradient_mid_color     => nil,
+              :gradient_end_color     => '#FF0000',
+              :gradient_border_width  => 1,
+              :gradient_border_color  => '#000000'}.merge(options)
+
+      row_images = ImageList.new
+
+      self.each_by(opts[:columns]) { |maps|
+        images = ImageList.new
+        maps.each { |m| images << m }
+        row_images << images.append(false)
+      }
+
+      tbl_img = row_images.append(true)
+
+      unless opts[:print_gradient]
+        return tbl_img
+      else
+        RVG::dpi    = opts[:dpi]
+        rvg_width   = opts[:rvg_width] * opts[:columns]
+        rvg_height  = rvg_width / 10.0
+
+        rvg = RVG.new(rvg_width, rvg_height) do |canvas|
+          canvas.viewbox(0, 0, rvg_width, rvg_height)
+          canvas.background_fill = 'white'
+          canvas.desc = 'gradient key'
+
+          gradient_width = rvg_width / 2.0
+          gradient_height = gradient_width / 15.0
+
+          if opts[:gradient_mid_color]
+            img1  = Image.new(gradient_width / 2,
+                              gradient_height,
+                              GradientFill.new(0, 0, 0, gradient_width / 2,
+                                               opts[:gradient_beg_color], opts[:gradient_mid_color]))
+
+            img2  = Image.new(gradient_width / 2,
+                              gradient_height,
+                              GradientFill.new(0, 0, 0, gradient_width / 2,
+                                               opts[:gradient_mid_color], opts[:gradient_end_color]))
+
+            img3  = ImageList.new
+            img3  << img1 << img2
+            img   = img3.append(false)
+          else
+            img = Image.new(gradient_width,
+                            gradient_height,
+                            GradientFill.new(0, 0, 0, gradient_width,
+                                             opts[:gradient_beg_color], opts[:gradient_end_color]))
+          end
+
+          img.border!(opts[:gradient_border_width],
+                      opts[:gradient_border_width],
+                      opts[:gradient_border_color])
+
+          gradient_x = (rvg_width - gradient_width) / 2.0
+          gradient_y = (rvg_height - gradient_height) / 2.0
+          gradient_font_size = rvg_width / 45.0
+
+          canvas.image(img,
+                       gradient_width,
+                       gradient_height,
+                       gradient_x,
+                       gradient_y)
+
+          canvas.text(gradient_x,
+                      gradient_y + gradient_height + gradient_font_size * 1.1,
+                      "#{'%.1f' % opts[:min_val]}").styles(:font_size => gradient_font_size)
+
+          canvas.text(gradient_x + gradient_width,
+                      gradient_y + gradient_height + gradient_font_size * 1.1,
+                      "#{'%.1f' % opts[:max_val]}").styles(:font_size => gradient_font_size)
+        end
+
+        fin_img = ImageList.new
+        fin_img << tbl_img << rvg.draw
+        fin_img.append(true)
+      end
+    end
+  end
+end

data/lib/ulla.rb

@@ -0,0 +1,6 @@
+$:.unshift(File.dirname(__FILE__)) unless
+  $:.include?(File.dirname(__FILE__)) || $:.include?(File.expand_path(File.dirname(__FILE__)))
+
+module Ulla
+  VERSION = '0.9.3'
+end

data/script/console

@@ -0,0 +1,10 @@
+#!/usr/bin/env ruby
+# File: script/console
+irb = RUBY_PLATFORM =~ /(:?mswin|mingw)/ ? 'irb.bat' : 'irb'
+
+libs =  " -r irb/completion"
+# Perhaps use a console_lib to store any extra methods I may want available in the cosole
+# libs << " -r #{File.dirname(__FILE__) + '/../lib/console_lib/console_logger.rb'}"
+libs <<  " -r #{File.dirname(__FILE__) + '/../lib/egor.rb'}"
+puts "Loading egor gem"
+exec "#{irb} #{libs} --simple-prompt"

data/script/destroy

@@ -0,0 +1,14 @@
+#!/usr/bin/env ruby
+APP_ROOT = File.expand_path(File.join(File.dirname(__FILE__), '..'))
+
+begin
+  require 'rubigen'
+rescue LoadError
+  require 'rubygems'
+  require 'rubigen'
+end
+require 'rubigen/scripts/destroy'
+
+ARGV.shift if ['--help', '-h'].include?(ARGV[0])
+RubiGen::Base.use_component_sources! [:rubygems, :newgem, :newgem_theme, :test_unit]
+RubiGen::Scripts::Destroy.new.run(ARGV)

data/script/generate

@@ -0,0 +1,14 @@
+#!/usr/bin/env ruby
+APP_ROOT = File.expand_path(File.join(File.dirname(__FILE__), '..'))
+
+begin
+  require 'rubigen'
+rescue LoadError
+  require 'rubygems'
+  require 'rubigen'
+end
+require 'rubigen/scripts/generate'
+
+ARGV.shift if ['--help', '-h'].include?(ARGV[0])
+RubiGen::Base.use_component_sources! [:rubygems, :newgem, :newgem_theme, :test_unit]
+RubiGen::Scripts::Generate.new.run(ARGV)

data/script/txt2html

@@ -0,0 +1,71 @@
+#!/usr/bin/env ruby
+
+load File.dirname(__FILE__) + "/../Rakefile"
+require 'rubyforge'
+require 'redcloth'
+require 'syntax/convertors/html'
+require 'erb'
+
+download = "http://rubyforge.org/projects/#{$hoe.rubyforge_name}"
+version  = $hoe.version
+
+def rubyforge_project_id
+  RubyForge.new.configure.autoconfig["group_ids"][$hoe.rubyforge_name]
+end
+
+class Fixnum
+  def ordinal
+    # teens
+    return 'th' if (10..19).include?(self % 100)
+    # others
+    case self % 10
+    when 1: return 'st'
+    when 2: return 'nd'
+    when 3: return 'rd'
+    else    return 'th'
+    end
+  end
+end
+
+class Time
+  def pretty
+    return "#{mday}#{mday.ordinal} #{strftime('%B')} #{year}"
+  end
+end
+
+def convert_syntax(syntax, source)
+  return Syntax::Convertors::HTML.for_syntax(syntax).convert(source).gsub(%r!^<pre>|</pre>$!,'')
+end
+
+if ARGV.length >= 1
+  src, template = ARGV
+  template ||= File.join(File.dirname(__FILE__), '/../website/template.html.erb')
+else
+  puts("Usage: #{File.split($0).last} source.txt [template.html.erb] > output.html")
+  exit!
+end
+
+template = ERB.new(File.open(template).read)
+
+title = nil
+body = nil
+File.open(src) do |fsrc|
+  title_text = fsrc.readline
+  body_text_template = fsrc.read
+  body_text = ERB.new(body_text_template).result(binding)
+  syntax_items = []
+  body_text.gsub!(%r!<(pre|code)[^>]*?syntax=['"]([^'"]+)[^>]*>(.*?)</\1>!m){
+    ident = syntax_items.length
+    element, syntax, source = $1, $2, $3
+    syntax_items << "<#{element} class='syntax'>#{convert_syntax(syntax, source)}</#{element}>"
+    "syntax-temp-#{ident}"
+  }
+  title = RedCloth.new(title_text).to_html.gsub(%r!<.*?>!,'').strip
+  body = RedCloth.new(body_text).to_html
+  body.gsub!(%r!(?:<pre><code>)?syntax-temp-(\d+)(?:</code></pre>)?!){ syntax_items[$1.to_i] }
+end
+stat = File.stat(src)
+created = stat.ctime
+modified = stat.mtime
+
+$stdout << template.result(binding)

data/test/test_helper.rb

@@ -0,0 +1,2 @@
+require 'test/unit'
+require File.dirname(__FILE__) + '/../lib/ulla'

data/test/test_math_extensions.rb

@@ -0,0 +1,11 @@
+$:.unshift File.join(File.dirname(__FILE__), "..", "lib")
+
+require 'test/unit'
+require 'math_extensions'
+
+class TestMathExtensions < Test::Unit::TestCase
+
+  def test_log2
+    assert_equal(1, Math::log2(2))
+  end
+end

data/test/test_narray_extensions.rb

@@ -0,0 +1,14 @@
+$:.unshift File.join(File.dirname(__FILE__), "..", "lib")
+
+require "test/unit"
+require "narray_extensions"
+
+class TestArrayExtensions < Test::Unit::TestCase
+
+  def test_pretty_string(opts={})
+    m = NArray.float(3).indgen
+    result ="#        A      B      C\n" +
+            "VAL   0.00   1.00   2.00"
+    assert_equal(result, m.pretty_string(:col_header => %w[A B C], :row_header => 'VAL'))
+  end
+end

data/test/test_nmatrix_extensions.rb

@@ -0,0 +1,16 @@
+$:.unshift File.join(File.dirname(__FILE__), "..", "lib")
+
+require "test/unit"
+require "nmatrix_extensions"
+
+class TestNmatrixExtensions < Test::Unit::TestCase
+
+  def test_pretty_string(opts={})
+    m = NMatrix.float(3,3).indgen
+    result ="#        A      B      C\n" +
+            "VAL   0.00   1.00   2.00\n" +
+            "      3.00   4.00   5.00\n" +
+            "      6.00   7.00   8.00"
+    assert_equal(result, m.pretty_string(:col_header => %w[A B C], :row_header => %w[VAL]))
+  end
+end

data/test/test_string_extensions.rb

@@ -0,0 +1,11 @@
+$:.unshift File.join(File.dirname(__FILE__), "..", "lib")
+
+require "test/unit"
+require "string_extensions"
+
+class TestStringExtensions < Test::Unit::TestCase
+
+  def test_remove_internal_spaces
+    assert_equal("hellosemin", "he ll o\r\n sem in\r \n".remove_internal_spaces)
+  end
+end

data/test/test_ulla.rb

@@ -0,0 +1,11 @@
+require File.dirname(__FILE__) + '/test_helper.rb'
+
+class TestUlla < Test::Unit::TestCase
+
+  def setup
+  end
+  
+  def test_truth
+    assert true
+  end
+end

data/test/ulla/test_cli.rb

@@ -0,0 +1,9 @@
+require File.join(File.dirname(__FILE__), "..", "test_helper.rb")
+require 'ulla/cli'
+
+class TestUllaCli < Test::Unit::TestCase
+  def test_execute
+    #Ulla::CLI.execute
+    assert(true)
+  end
+end

data/test/ulla/test_environment_class_hash.rb

@@ -0,0 +1,25 @@
+$:.unshift File.join(File.dirname(__FILE__), '..', '..', 'lib', 'ulla')
+
+require 'test/unit'
+require 'environment_class_hash'
+
+class TestEnvironmentClassHash < Test::Unit::TestCase
+
+  include Ulla
+
+  def setup
+    @env_cls = EnvironmentClassHash.new
+  end
+
+  def test_group_by_non_residue_labels
+    assert(true)
+  end
+
+  def test_groups_sorted_by_residue_labels
+    assert(true)
+  end
+
+  def group_size
+    assert(true)
+  end
+end

data/test/ulla/test_environment_feature.rb

@@ -0,0 +1,29 @@
+$:.unshift File.join(File.dirname(__FILE__), '..', '..', 'lib', 'ulla')
+
+require 'test/unit'
+require 'environment_feature'
+
+class TestEnvironmentFeature < Test::Unit::TestCase
+
+  include Ulla
+
+  def setup
+    @env_ftr = EnvironmentFeature.new('Secondary Structure',
+                                      'HEPC'.split(''),
+                                      'HEPC'.split(''),
+                                      'T',
+                                      'F')
+  end
+
+  def test_to_s
+    assert_equal('Secondary Structure;HEPC;HEPC;T;F', @env_ftr.to_s)
+  end
+
+  def test_constrained?
+    assert(@env_ftr.constrained?)
+  end
+
+  def silent?
+    assert(!@env_ftr.silent?)
+  end
+end

data/website/index.html

@@ -0,0 +1,16 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+  <meta http-equiv="Refresh" content="5; URL=http://github.com/semin/ulla">
+  <title>
+      ulla: a program for calculating environment-specific substitution tables
+  </title>
+</head>
+<body>
+    <p>
+    Egor has been renamed to Ulla, and an official web site for Ulla will be available when our new web contents management system is ready. Until then, this page will be redirected to its Git repository, <a href="http://http://github.com/semin/ulla/">http://github.com/semin/ulla</a> in 5 seconds.
+    </p>
+    - Semin
+</body>
+</html>