vienna_rna 0.1.7 → 0.1.9

data/lib/vienna_rna/modules/fold.rb

@@ -4,7 +4,7 @@ module ViennaRna
       "-noPS" => :empty
     }
     
-    attr_reader :structure, :mfe
+    attr_reader :mfe_rna, :structure, :mfe
     
     def post_process
       structure = @response.split(/\n/).last.gsub(Parser::REGEXP[:mfe], "")
@@ -12,7 +12,7 @@ module ViennaRna
       unless data.seq.length == structure.length
         raise "Sequence: '#{data.seq}'\nStructure: '#{structure}'"
       else
-        @structure, @mfe = structure, Parser.mfe(@response)
+        @mfe_rna, @structure, @mfe = ViennaRna::Rna.new(data.seq, structure), structure, Parser.mfe(@response)
       end
     end
     

data/lib/vienna_rna/modules/rna.rb

@@ -3,8 +3,14 @@ module ViennaRna
     attr_reader :sequence, :structure
       
     def initialize(sequence, structure = nil)
-      @sequence  = sequence.upcase
-      @structure = (structure == :mfe ? ViennaRna::Fold.run(seq).structure : structure)
+      if sequence.class == self.class
+        # Too bad you can't do this in a cleaner way without method chaining initialize
+        @sequence  = sequence.sequence
+        @structure = sequence.structure
+      else
+        @sequence  = sequence.upcase
+        @structure = (structure == :mfe ? ViennaRna::Fold.run(seq).structure : structure)
+      end
     end
 
     alias :seq :sequence
@@ -22,6 +28,10 @@ module ViennaRna
       self.class.bp_distance(structure, other_structure)
     end
     
+    def symmetric_bp_distance(other_structure)
+      self.class.symmetric_bp_distance(structure, other_structure)
+    end
+    
     def base_pairs
       self.class.base_pairs(structure)
     end
@@ -49,6 +59,7 @@ module ViennaRna
       end
       
       def bp_distance(structure_1, structure_2)
+        # Takes two structures and calculates the distance between them by |symmetric difference(bp_in_a, bp_in_b)|
         raise "The two structures are not the same length" unless structure_1.length == structure_2.length
         
         bp_set_1, bp_set_2 = base_pairs(structure_1), base_pairs(structure_2)
@@ -56,6 +67,20 @@ module ViennaRna
         ((bp_set_1 - bp_set_2) + (bp_set_2 - bp_set_1)).count
       end
       
+      def symmetric_bp_distance(structure_1, structure_2)
+        # Takes two structures and calculates the distance between them by: sum { ((x_j - x_i) - (y_j - y_i)).abs }
+        raise "The two structures are not the same length" unless structure_1.length == structure_2.length
+  
+        bp_dist = ->(array, i) { array[i] == -1 ? 0 : array[i] - i }
+  
+        structure_1_pairings = get_pairings(structure_1)
+        structure_2_pairings = get_pairings(structure_2)
+  
+        structure_1.length.times.inject(0) do |distance, i|
+          distance + (bp_dist[structure_1_pairings, i] - bp_dist[structure_2_pairings, i]).abs
+        end
+      end
+      
       def base_pairs(structure)
         get_pairings(structure).each_with_index.inject(Set.new) do |set, (j, i)|
           j >= 0 ? set << Set[i, j] : set

data/lib/vienna_rna/modules/utils.rb

@@ -39,9 +39,9 @@ module ViennaRna
               plot.terminal("png size 800,600")
             end
             
-            plot.title(options[:title])
-            plot.xlabel(options[:x_label])
-            plot.ylabel(options[:y_label])
+            options[:plot].keys.each do |option|
+              plot.send(option, options[:plot][option])
+            end
 
             plot.data = data.map do |data_hash|
               Gnuplot::DataSet.new([data_hash[:x], data_hash[:y]]) do |dataset|
@@ -53,14 +53,14 @@ module ViennaRna
         end
       end
       
-      def quick_plot(title, data, filename = false)
-        quick_overlay(title, [{ data: data }], filename)
+      def quick_plot(title, data, options = {})
+        quick_overlay(title, [{ data: data }], options)
       end
       
-      def quick_overlay(title, data, filename = false)
+      def quick_overlay(title, data, options = {})
         # [{ data: [[x_0, y_0], [x_1, y_1], ...], label: "Label" }, { data: [[x_0, y_0], [x_1, y_1], ...] }]
-        options = { title: title }
-        options.merge!(output: "file", filename: filename) if filename
+        options[:plot] = ((options[:plot] || {}).merge(title: title))
+        options.merge!(output: "file") if options[:filename]
         
         plot(data.map { |hash| { title: hash[:label], x: hash[:data].map(&:first), y: hash[:data].map(&:last), style: "linespoints" } }, options)
       end

data/lib/vienna_rna/modules/xbor.rb

@@ -39,10 +39,11 @@ module ViennaRna
       k_p_points.map { |array| array.inject(&:*) }.inject(&:+)
     end
     
-    def quick_plot(title = nil)
+    def quick_plot(options = {})
       ViennaRna::Utils.quick_plot(
-        title || "%s\\n%s\\n%s" % [self.class.name, data.seq, data.safe_structure], 
-        k_p_points
+        options[:title] || "%s\\n%s\\n%s" % [self.class.name, data.seq, data.safe_structure], 
+        k_p_points,
+        options
       )
     end
     

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: vienna_rna
 version: !ruby/object:Gem::Version
-  version: 0.1.7
+  version: 0.1.9
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-09-05 00:00:00.000000000 Z
+date: 2012-09-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio