ulla 0.9.6 → 0.9.7

data/lib/ulla/environment.rb

@@ -10,21 +10,25 @@ module Ulla
       :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)
+      @amino_acids        = amino_acids
+      @freq_array         = 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
+      @freq_array[@amino_acids.index(a)] += inc
     end
 
     def label_set
-      label.split("").map_with_index { |l, i| "#{i}#{l}" }.to_set
+      if $direction == 0
+        label.split("").map_with_index { |l, i| "#{i}#{l}" }.to_set
+      else
+        label.gsub('-', '').split("").map_with_index { |l, i| "#{i}#{l}" }.to_set
+      end
     end
 
     def to_s

data/lib/ulla/environment_class_hash.rb

@@ -7,8 +7,12 @@ module Ulla
 
     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|
-          $env_features[i + 1].labels.index(l)
+        env_group[0].gsub('-', '').split('').map_with_index { |l, i|
+          if i < ($env_features.size - 1)
+            $env_features[i + 1].labels.index(l)
+          else
+            $env_features[i + 2 - $env_features.size].labels.index(l)
+          end
         }
       }
     end

data/lib/ulla/environment_feature.rb

@@ -4,11 +4,11 @@ module Ulla
     attr_accessor :name, :symbols, :labels, :constrained, :silent
 
     def initialize(name, symbols, labels, constrained, silent)
-      @name = name
-      @symbols = symbols
-      @labels = labels
-      @constrained = constrained
-      @silent = silent
+      @name         = name
+      @symbols      = symbols
+      @labels       = labels
+      @constrained  = constrained
+      @silent       = silent
     end
 
     def to_s

data/lib/ulla/environment_feature_array.rb

@@ -8,5 +8,13 @@ module Ulla
         pro.product(lb)
       }
     end
+
+    def label_combinations_without_aa_type
+      self[1..-1].inject([]) { |sum, ec|
+        sum << ec.labels
+      }.inject { |pro, lb|
+        pro.product(lb)
+      }
+    end
   end
 end

data/script/console

@@ -5,6 +5,6 @@ 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"
+libs <<  " -r #{File.dirname(__FILE__) + '/../lib/ulla.rb'}"
+puts "Loading ulla gem"
+exec "#{irb} #{libs} --simple-prompt"

data/ulla.gemspec

@@ -6,13 +6,13 @@ Gem::Specification.new do |s|
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Semin Lee"]
-  s.date = %q{2009-03-18}
+  s.date = %q{2009-04-16}
   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", "README.rdoc", "website/index.txt"]
-  s.files = [".autotest", "History.txt", "Manifest.txt", "PostInstall.txt", "README.rdoc", "Rakefile", "bin/ulla", "config/website.yml", "config/website.yml.sample", "lib/.nmatrix_extensions.rb.swp", "lib/math_extensions.rb", "lib/narray_extensions.rb", "lib/nmatrix_extensions.rb", "lib/string_extensions.rb", "lib/ulla.rb", "lib/ulla/.cli.rb.swp", "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 = [".autotest", "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.has_rdoc = true
   s.homepage = %q{http://www-cryst.bioc.cam.ac.uk/ulla}
   s.post_install_message = %q{PostInstall.txt}

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: ulla
 version: !ruby/object:Gem::Version 
-  version: 0.9.6
+  version: 0.9.7
 platform: ruby
 authors: 
 - Semin Lee
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2009-03-18 00:00:00 +00:00
+date: 2009-05-30 00:00:00 +01:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -60,7 +60,7 @@ dependencies:
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        version: 1.3.0
+        version: 1.4.1
     version: 
 - !ruby/object:Gem::Dependency 
   name: hoe
@@ -127,6 +127,8 @@ files:
 - website/template.html.erb
 has_rdoc: true
 homepage: http://www-cryst.bioc.cam.ac.uk/ulla
+licenses: []
+
 post_install_message: PostInstall.txt
 rdoc_options: 
 - --main
@@ -148,9 +150,9 @@ required_rubygems_version: !ruby/object:Gem::Requirement
 requirements: []
 
 rubyforge_project: ulla
-rubygems_version: 1.3.1
+rubygems_version: 1.3.3
 signing_key: 
-specification_version: 2
+specification_version: 3
 summary: "'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."
 test_files: 
 - test/test_math_extensions.rb