vienna_rna 0.1.4 → 0.1.5

data/lib/{modules → vienna_rna/modules}/fftbor.rb

@@ -16,11 +16,11 @@ module ViennaRna
         STDERR.puts "ERROR: The mode requested (%s) is not available" % flags[:mode]
       end
       
-      case flags[:mode]
+      case mode = flags.delete(:mode)
       when :standalone then
         super(flags)
       when :dispatch then
-        "%s -m 6 -tr 0 -s %s -ss '%s'" % [MODES[flags[:mode]], data.seq, data.safe_structure]
+        "%s -m 6 -tr 0 -s %s -ss '%s'" % [MODES[mode], data.seq, data.safe_structure]
       end
     end
     
@@ -38,6 +38,24 @@ module ViennaRna
       self.class.parse(response).map { |row| BigDecimal.new(row[1]) }
     end
     
+    def windows
+      # This is starting to feel pretty hackety.
+      response.gsub(/Sum.*\n+Window size:\s+\d+/) { |match| "[:separator:]" + match }.split("[:separator:]").map do |window_response|
+        window_size  = window_response.match(/Window size:\s+(\d+)/)[1].to_i
+        window_index = window_response.match(/Window starting index:\s+(\d+)/)[1].to_i
+        
+        self.class.new(seq: data.seq[window_index - 1, window_size], str: data.safe_structure[window_index - 1, window_size]).tap do |window_run|
+          class << window_run
+            attr_accessor :response, :window_size, :window_index
+          end
+          
+          window_run.response     = window_response
+          window_run.window_size  = window_size
+          window_run.window_index = window_index
+        end
+      end
+    end
+    
     def compare
       {
         dispatch:   self.class.new(data).run(mode: :dispatch).distribution,

data/lib/{modules → vienna_rna/modules}/utils.rb

@@ -56,9 +56,12 @@ module ViennaRna
         end
       end
       
-      def quick_plot(title, data)
-        # data = [[x_0, y_0], [x_1, y_1], ...]
-        plot([{ x: data.map(&:first), y: data.map(&:last), style: "linespoints" }], title: title)
+      def quick_plot(title, data, filename = false)
+        # data = [[x_0, y_0], [x_1, y_1], ...]        
+        options = { title: title }
+        options.merge!(output: "file", filename: filename) if filename
+        
+        plot([{ x: data.map(&:first), y: data.map(&:last), style: "linespoints" }], options)
       end
     end
   end

data/lib/{modules → vienna_rna/modules}/xbor.rb

@@ -9,7 +9,7 @@ module ViennaRna
     
     self.executable_name = -> { name.demodulize.gsub(/^([A-Z].*)bor$/) { |match| $1.upcase + "bor" } }
     
-    def run_command(flags)
+    def run_command(flags = {})
       file = Tempfile.new("rna")
       file.write("%s\n" % data.seq)
       file.write("%s\n" % data.safe_structure)
@@ -17,7 +17,7 @@ module ViennaRna
       
       "%s %s %s" % [
         exec_name, 
-        stringify_flags(BASE_FLAGS.merge(self.class.const_defined?(:FLAGS) ? self.class.const_get(:FLAGS) : {})), 
+        stringify_flags(BASE_FLAGS.merge(self.class.const_defined?(:FLAGS) ? self.class.const_get(:FLAGS) : {}).merge(flags)), 
         file.path
       ]
     end
@@ -28,13 +28,17 @@ module ViennaRna
     
     def full_distribution
       distribution      = run.distribution
-      full_distribution = distribution + ([0] * (data.seq.length - distribution.length + 1))
+      full_distribution = distribution + ([0.0] * ((differnece = data.seq.length - distribution.length + 1) < 0 ? 0 : differnece))
+    end
+    
+    def k_p_points
+      full_distribution.each_with_index.to_a.map(&:reverse)[0..data.seq.length]
     end
     
     def quick_plot
       ViennaRna::Utils.quick_plot(
         "%s\\n%s\\n%s" % [self.class.name, data.seq, data.safe_structure], 
-        full_distribution.each_with_index.to_a.map(&:reverse)
+        k_p_points
       )
     end
   end

data/lib/vienna_rna.rb

@@ -6,8 +6,9 @@ require "active_support/core_ext/module/aliasing"
 module ViennaRna
   @debug = true
   
-  Dir[File.join(File.dirname(__FILE__), "/modules/*")].each do |file|
-    autoload File.basename(file, ".rb").camelize.to_sym, file
+  Dir[File.join(File.dirname(__FILE__), "vienna_rna", "modules", "*.rb")].each do |file|
+    # Doesn't support autoloading modules that are of the form: TwoWords
+    autoload(File.basename(file, ".rb").camelize.to_sym, "vienna_rna/modules/#{File.basename(file, '.rb')}")
   end
   
   def self.const_missing(name)

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: vienna_rna
 version: !ruby/object:Gem::Version
-  version: 0.1.4
+  version: 0.1.5
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-07-23 00:00:00.000000000 Z
+date: 2012-07-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
@@ -49,15 +49,15 @@ executables: []
 extensions: []
 extra_rdoc_files: []
 files:
-- ./lib/modules/base.rb
-- ./lib/modules/batch.rb
-- ./lib/modules/fftbor.rb
-- ./lib/modules/fold.rb
-- ./lib/modules/heat.rb
-- ./lib/modules/rnabor.rb
-- ./lib/modules/subopt.rb
-- ./lib/modules/utils.rb
-- ./lib/modules/xbor.rb
+- ./lib/vienna_rna/modules/base.rb
+- ./lib/vienna_rna/modules/batch.rb
+- ./lib/vienna_rna/modules/fftbor.rb
+- ./lib/vienna_rna/modules/fold.rb
+- ./lib/vienna_rna/modules/heat.rb
+- ./lib/vienna_rna/modules/rnabor.rb
+- ./lib/vienna_rna/modules/subopt.rb
+- ./lib/vienna_rna/modules/utils.rb
+- ./lib/vienna_rna/modules/xbor.rb
 - ./lib/vienna_rna.rb
 homepage: http://rubygems.org/gems/vienna_rna
 licenses: []