ulla 0.9.9 → 0.9.9.1

data/History.txt

@@ -1,3 +1,8 @@
+== 0.9.9.1 26/08/2009
+
+* Removed dependency on the Ruby Facets library
+* Total -> total for compativility with melody
+
 == 0.9.9 09/08/2009
 
 * Changed default value for --classdef option from 'classdef.dat' to nil

data/Manifest.txt

@@ -6,6 +6,7 @@ Rakefile
 bin/ulla
 config/website.yml
 config/website.yml.sample
+lib/array_extensions.rb
 lib/math_extensions.rb
 lib/narray_extensions.rb
 lib/nmatrix_extensions.rb

data/README.rdoc

@@ -24,8 +24,8 @@ http://www-cryst.bioc.cam.ac.uk/ulla
 Following RubyGems will be automatically installed if you have rubygems installed on your machine
 
 * narray (http://narray.rubyforge.org)
-* facets (http://facets.rubyforge.org)
 * bio (http://bioruby.open-bio.org)
+* Active Support (http://as.rubyonrails.org)
 * RMagick (http://rmagick.rubyforge.org)
 
 

data/Rakefile

@@ -14,10 +14,9 @@ $hoe = Hoe.spec 'ulla' do
   self.post_install_message = 'PostInstall.txt' # TODO remove if post-install message not required
   self.rubyforge_name       = self.name # TODO this is default value
   self.extra_deps           = [
-    ['narray',  '>= 0.5.9.5'],
-    ['bio',     '>= 1.2.1'],
-    ['facets',  '>= 2.4.5'],
-    ['rmagick', '>= 2.9.1'],
+    ['narray',        '>= 0.5.9.5'],
+    ['bio',           '>= 1.2.1'],
+    ['rmagick',       '>= 2.9.1'],
   ]
 end
 

data/lib/array_extensions.rb

@@ -0,0 +1,16 @@
+module ArrayExtensions
+
+  # from Active Support library
+  def sum(identity = 0, &block)
+    return identity unless size > 0
+
+    if block_given?
+      map(&block).sum
+    else
+      inject { |sum, element| sum + element }
+    end
+  end
+
+end
+
+Array.send :include, ArrayExtensions

data/lib/math_extensions.rb

@@ -1,7 +1,9 @@
 module MathExtensions
+
   def log2(val)
     log(val) / log(2)
   end
+
 end
 
 Math.extend(MathExtensions)

data/lib/narray_extensions.rb

@@ -1,6 +1,5 @@
 require 'rubygems'
 require 'narray'
-require 'facets'
 
 module NArrayExtensions
 

data/lib/nmatrix_extensions.rb

@@ -1,6 +1,5 @@
 require 'rubygems'
 require 'narray'
-require 'facets'
 
 begin
   require 'rvg/rvg'
@@ -19,7 +18,7 @@ module NMatrixExtensions
 
     ("%-3s" % "#") + opts[:col_header].inject("") { |s, a|
       s + ("%#{opts[:col_size]}s" % a)
-    } + "\n" + self.to_a.map_with_index { |a, i|
+    } + "\n" + self.to_a.each_with_index.map { |a, i|
       ("%-3s" % opts[:row_header][i]) + a.inject("") { |s, v|
         if v.is_a? Float
           s + ("%#{opts[:col_size]}.2f" % v)

data/lib/string_extensions.rb

@@ -1,5 +1,19 @@
 module StringExtensions
 
+  unless method_defined?(:blank?)
+    # from Active Support library
+    def blank?
+      self !~ /\S/
+    end
+  end
+
+  unless method_defined?(:start_with?)
+    # from Ruby Facets library
+    def start_with?(prefix)
+      self.index(prefix) == 0
+    end
+  end
+
   def remove_internal_spaces
     gsub(/[\n|\r|\s]+/, '')
   end
@@ -14,4 +28,3 @@ module StringExtensions
 end
 
 String.send :include, StringExtensions
-

data/lib/ulla.rb

@@ -2,5 +2,5 @@ $:.unshift(File.dirname(__FILE__)) unless
   $:.include?(File.dirname(__FILE__)) || $:.include?(File.expand_path(File.dirname(__FILE__)))
 
 module Ulla
-  VERSION = '0.9.9'
+  VERSION = '0.9.9.1'
 end

data/lib/ulla/cli.rb

@@ -4,7 +4,6 @@ require 'logger'
 require 'narray'
 require 'bio'
 require 'set'
-require 'facets'
 
 # This is a module for an actual command line interpreter for Ulla
 # ---
@@ -368,6 +367,7 @@ Options:
         end
 
 	require 'math_extensions'
+	require 'array_extensions'
 	require 'string_extensions'
 	require 'narray_extensions'
 	require 'nmatrix_extensions'
@@ -535,7 +535,7 @@ Options:
               ff.rewind
               ff.each_entry do |pir|
                 if (pir.entry_id == key) && (pir.definition == ec.name)
-                  labels = pir.data.remove_internal_spaces.split('').map_with_index do |sym, pos|
+                  labels = pir.data.remove_internal_spaces.split('').each_with_index.map do |sym, pos|
                     if sym == '-'
                       '-'
                     elsif sym == 'X' || sym == 'x'
@@ -562,13 +562,13 @@ Options:
           if $noweight
             ali.each_pair do |id1, seq1|
               if $environment == 1
-                seq1 = seq1.split('').map_with_index { |aa, pos| aa == $gap ? $ext_gap : env_labels[id1][pos] }.join
+                seq1 = seq1.split('').each_with_index.map { |aa, pos| aa == $gap ? $ext_gap : env_labels[id1][pos] }.join
               end
 
               ali.each_pair do |id2, seq2|
                 if id1 != id2
                   if $environment == 1
-                    seq2 = seq2.split('').map_with_index { |aa, pos| aa == $gap ? $ext_gap : env_labels[id2][pos] }.join
+                    seq2 = seq2.split('').each_with_index.map { |aa, pos| aa == $gap ? $ext_gap : env_labels[id2][pos] }.join
                   end
 
                   pid = calculate_pid(seq1, seq2, $col_size)
@@ -639,7 +639,7 @@ Options:
             ali.each_pair do |key, seq|
               clusters << [key]
               if $environment == 1
-                ext_seq = seq.split('').map_with_index { |aa, pos| aa == $gap ? $ext_gap : env_labels[key][pos] }.join
+                ext_seq = seq.split('').each_with_index.map { |aa, pos| aa == $gap ? $ext_gap : env_labels[key][pos] }.join
                 ext_ali.add_seq(ext_seq, key)
               end
             end
@@ -988,7 +988,7 @@ HEADER
           end
 
           # total
-          $outfh.puts '>Total'
+          $outfh.puts '>total'
           $outfh.puts $tot_cnt_mat.pretty_string(:col_header => $amino_acids,
                                                  :row_header => $amino_acids,
                                                  :col_size   => mat_col_size > 7 ? mat_col_size : 7)
@@ -1132,7 +1132,7 @@ HEADER
           end
 
           if $output == 1
-            $outfh.puts '>Total'
+            $outfh.puts '>total'
             $outfh.puts $tot_prob_mat.pretty_string(:col_header => $amino_acids,
                                                     :row_header => $amino_acids)
             $outfh.close
@@ -1197,10 +1197,10 @@ HEADER
           #
           # p2 and above
           #
-          env_labels = $env_features.map_with_index { |ef, ei| ef.labels.map { |l| "#{ei}#{l}" } }
+          env_labels = $env_features.each_with_index.map { |ef, ei| ef.labels.map { |l| "#{ei}#{l}" } }
 
           if $environment == 1
-            env_labels += $env_features[1..-1].map_with_index { |ef, ei| ef.labels.map { |l| "#{ei + $env_features.size}#{l}" } }
+            env_labels += $env_features[1..-1].each_with_index.map { |ef, ei| ef.labels.map { |l| "#{ei + $env_features.size}#{l}" } }
           end
 
           if $smooth == :partial
@@ -1337,7 +1337,7 @@ HEADER
                   entropies       = priors.map { |prior| -1.0 * prior.to_a.inject(0.0) { |s, p| p == 0 ? s : s + p * Math::log(p) } }
                   mod_entropies   = entropies.map { |entropy| (entropy_max - entropy) / entropy_max }
                   weights         = mod_entropies.map { |mod_entropy| mod_entropy / mod_entropies.sum }
-                  weighted_priors = priors.map_with_index { |prior, i| prior * weights[i] }.sum
+                  weighted_priors = priors.each_with_index.map { |prior, i| prior * weights[i] }.sum
 
                   # actual smoothing step
                   smooth_prob_arr = NArray.float($amino_acids.size)
@@ -1432,9 +1432,9 @@ HEADER
                   # entropy based weighting priors step
                   entropy_max     = NMath::log($amino_acids.size)
                   entropies       = priors.map { |prior| -1.0 * prior.to_a.inject(0.0) { |s, p| p == 0 ? s : s + p * Math::log(p) } }
-                  mod_entropies   = entropies.map_with_index { |entropy, i| (entropy_max - entropies[i]) / entropy_max }
+                  mod_entropies   = entropies.each_with_index.map { |entropy, i| (entropy_max - entropies[i]) / entropy_max }
                   weights         = mod_entropies.map { |mod_entropy| mod_entropy / mod_entropies.sum }
-                  weighted_priors = priors.map_with_index { |prior, i| prior * weights[i] }.sum
+                  weighted_priors = priors.each_with_index.map { |prior, i| prior * weights[i] }.sum
 
                   # smoothing step
                   smooth_prob_arr = NArray.float($amino_acids.size)
@@ -1548,7 +1548,7 @@ HEADER
           end
 
           if $output == 1
-            $outfh.puts '>Total'
+            $outfh.puts '>total'
             $outfh.puts $tot_prob_mat.pretty_string(:col_header => $amino_acids,
                                                     :row_header => $amino_acids)
             $outfh.close
@@ -1810,7 +1810,7 @@ HEADER
             $tot_logo_mat = $tot_logo_mat.round
           end
 
-          $outfh.puts ">Total #{grp_logo_mats.size}"
+          $outfh.puts ">total #{grp_logo_mats.size}"
           $outfh.puts $tot_logo_mat.pretty_string(:col_header => $amino_acids,
                                                   :row_header => row_header)
 

data/lib/ulla/environment.rb

@@ -25,9 +25,9 @@ module Ulla
 
     def label_set
       if $direction == 0
-        label.split("").map_with_index { |l, i| "#{i}#{l}" }.to_set
+        label.split("").each_with_index.map { |l, i| "#{i}#{l}" }.to_set
       else
-        label.gsub('-', '').split("").map_with_index { |l, i| "#{i}#{l}" }.to_set
+        label.gsub('-', '').split("").each_with_index.map { |l, i| "#{i}#{l}" }.to_set
       end
     end
 

data/lib/ulla/environment_class_hash.rb

@@ -7,7 +7,7 @@ module Ulla
 
     def groups_sorted_by_residue_labels
       group_by_non_residue_labels.to_a.sort_by { |env_group|
-        env_group[0].gsub('-', '').split('').map_with_index { |l, i|
+        env_group[0].gsub('-', '').split('').each_with_index.map { |l, i|
           if i < ($env_features.size - 1)
             $env_features[i + 1].labels.index(l)
           else

data/lib/ulla/heatmap_array.rb

@@ -1,5 +1,4 @@
 require 'rubygems'
-require 'facets'
 
 begin
   require 'RMagick'

data/ulla.gemspec

@@ -2,17 +2,17 @@
 
 Gem::Specification.new do |s|
   s.name = %q{ulla}
-  s.version = "0.9.9"
+  s.version = "0.9.9.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Semin Lee"]
-  s.date = %q{2009-08-09}
+  s.date = %q{2009-08-26}
   s.default_executable = %q{ulla}
   s.description = %q{'ulla' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes.}
   s.email = ["seminlee@gmail.com"]
   s.executables = ["ulla"]
   s.extra_rdoc_files = ["History.txt", "Manifest.txt", "PostInstall.txt", "website/index.txt"]
-  s.files = ["History.txt", "Manifest.txt", "PostInstall.txt", "README.rdoc", "Rakefile", "bin/ulla", "config/website.yml", "config/website.yml.sample", "lib/math_extensions.rb", "lib/narray_extensions.rb", "lib/nmatrix_extensions.rb", "lib/string_extensions.rb", "lib/ulla.rb", "lib/ulla/cli.rb", "lib/ulla/environment.rb", "lib/ulla/environment_class_hash.rb", "lib/ulla/environment_feature.rb", "lib/ulla/environment_feature_array.rb", "lib/ulla/heatmap_array.rb", "script/console", "script/destroy", "script/generate", "script/txt2html", "test/test_helper.rb", "test/test_math_extensions.rb", "test/test_narray_extensions.rb", "test/test_nmatrix_extensions.rb", "test/test_string_extensions.rb", "test/test_ulla.rb", "test/ulla/test_cli.rb", "test/ulla/test_environment_class_hash.rb", "test/ulla/test_environment_feature.rb", "ulla.gemspec", "website/index.html", "website/index.txt", "website/javascripts/rounded_corners_lite.inc.js", "website/stylesheets/screen.css", "website/template.html.erb"]
+  s.files = ["History.txt", "Manifest.txt", "PostInstall.txt", "README.rdoc", "Rakefile", "bin/ulla", "config/website.yml", "config/website.yml.sample", "lib/array_extensions.rb", "lib/math_extensions.rb", "lib/narray_extensions.rb", "lib/nmatrix_extensions.rb", "lib/string_extensions.rb", "lib/ulla.rb", "lib/ulla/cli.rb", "lib/ulla/environment.rb", "lib/ulla/environment_class_hash.rb", "lib/ulla/environment_feature.rb", "lib/ulla/environment_feature_array.rb", "lib/ulla/heatmap_array.rb", "script/console", "script/destroy", "script/generate", "script/txt2html", "test/test_helper.rb", "test/test_math_extensions.rb", "test/test_narray_extensions.rb", "test/test_nmatrix_extensions.rb", "test/test_string_extensions.rb", "test/test_ulla.rb", "test/ulla/test_cli.rb", "test/ulla/test_environment_class_hash.rb", "test/ulla/test_environment_feature.rb", "ulla.gemspec", "website/index.html", "website/index.txt", "website/javascripts/rounded_corners_lite.inc.js", "website/stylesheets/screen.css", "website/template.html.erb"]
   s.homepage = %q{http://www-cryst.bioc.cam.ac.uk/ulla}
   s.post_install_message = %q{PostInstall.txt}
   s.rdoc_options = ["--main", "README.rdoc"]
@@ -29,20 +29,17 @@ Gem::Specification.new do |s|
     if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<narray>, [">= 0.5.9.5"])
       s.add_runtime_dependency(%q<bio>, [">= 1.2.1"])
-      s.add_runtime_dependency(%q<facets>, [">= 2.4.5"])
       s.add_runtime_dependency(%q<rmagick>, [">= 2.9.1"])
       s.add_development_dependency(%q<hoe>, [">= 2.3.3"])
     else
       s.add_dependency(%q<narray>, [">= 0.5.9.5"])
       s.add_dependency(%q<bio>, [">= 1.2.1"])
-      s.add_dependency(%q<facets>, [">= 2.4.5"])
       s.add_dependency(%q<rmagick>, [">= 2.9.1"])
       s.add_dependency(%q<hoe>, [">= 2.3.3"])
     end
   else
     s.add_dependency(%q<narray>, [">= 0.5.9.5"])
     s.add_dependency(%q<bio>, [">= 1.2.1"])
-    s.add_dependency(%q<facets>, [">= 2.4.5"])
     s.add_dependency(%q<rmagick>, [">= 2.9.1"])
     s.add_dependency(%q<hoe>, [">= 2.3.3"])
   end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: ulla
 version: !ruby/object:Gem::Version 
-  version: 0.9.9
+  version: 0.9.9.1
 platform: ruby
 authors: 
 - Semin Lee
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2009-08-09 00:00:00 +01:00
+date: 2009-08-26 00:00:00 +01:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -32,16 +32,6 @@ dependencies:
       - !ruby/object:Gem::Version 
         version: 1.2.1
     version: 
-- !ruby/object:Gem::Dependency 
-  name: facets
-  type: :runtime
-  version_requirement: 
-  version_requirements: !ruby/object:Gem::Requirement 
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        version: 2.4.5
-    version: 
 - !ruby/object:Gem::Dependency 
   name: rmagick
   type: :runtime
@@ -83,6 +73,7 @@ files:
 - bin/ulla
 - config/website.yml
 - config/website.yml.sample
+- lib/array_extensions.rb
 - lib/math_extensions.rb
 - lib/narray_extensions.rb
 - lib/nmatrix_extensions.rb