vienna_rna 0.1.3 → 0.1.4

data/lib/modules/base.rb

@@ -82,14 +82,18 @@ module ViennaRna
     end
     
     def run_with_hooks(flags = {})
-      tap do
-        @runtime = Benchmark.measure do
-          pre_run_check unless respond_to?(:run_command)
-          @response = run_without_hooks(flags)
-          post_process if respond_to?(:post_process)
-        end
+      unless @response
+        tap do
+          @runtime = Benchmark.measure do
+            pre_run_check unless respond_to?(:run_command)
+            @response = run_without_hooks(flags)
+            post_process if respond_to?(:post_process)
+          end
         
-        debugger { "Total runtime: %.3f sec." % runtime.real }
+          debugger { "Total runtime: %.3f sec." % runtime.real }
+        end
+      else
+        self
       end
     end
     

data/lib/modules/rnabor.rb

@@ -3,12 +3,16 @@ require "bigdecimal"
 
 module ViennaRna
   class Rnabor < Xbor
+    FLAGS = {
+      nodangle: :empty
+    }
+    
     def partition
-      non_zero_shells.sum
+      non_zero_shells.inject(&:+)
     end
     
     def total_count
-      counts.sum
+      counts.inject(&:+)
     end
     
     def counts

data/lib/modules/utils.rb

@@ -34,24 +34,32 @@ module ViennaRna
       end
       
       def plot(data, options = {})
-        options = { title: "Title", x_label: "X Axis", y_label: "Y Axis" }.merge(options)
-        
         Gnuplot.open do |gnuplot|
           Gnuplot::Plot.new(gnuplot) do |plot|
-
+            case options[:output]
+            when /file/i then
+              plot.output(options[:filename])
+              plot.terminal("png size 800,600")
+            end
+            
             plot.title(options[:title])
             plot.xlabel(options[:x_label])
             plot.ylabel(options[:y_label])
 
             plot.data = data.map do |data_hash|
               Gnuplot::DataSet.new([data_hash[:x], data_hash[:y]]) do |dataset|
-                dataset.with = "points"
+                dataset.with = data_hash[:style] || "points"
                 data_hash[:title] ? dataset.title = data_hash[:title] : dataset.notitle
               end
             end
           end
         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)
+      end
     end
   end
 end

data/lib/modules/xbor.rb

@@ -3,6 +3,10 @@ require "bigdecimal"
 
 module ViennaRna
   class Xbor < Base
+    BASE_FLAGS = {
+      E: "/usr/local/bin/energy.par"
+    }
+    
     self.executable_name = -> { name.demodulize.gsub(/^([A-Z].*)bor$/) { |match| $1.upcase + "bor" } }
     
     def run_command(flags)
@@ -11,11 +15,27 @@ module ViennaRna
       file.write("%s\n" % data.safe_structure)
       file.close
       
-      "%s -nodangle -E /usr/local/bin/energy.par %s" % [exec_name, file.path]
+      "%s %s %s" % [
+        exec_name, 
+        stringify_flags(BASE_FLAGS.merge(self.class.const_defined?(:FLAGS) ? self.class.const_get(:FLAGS) : {})), 
+        file.path
+      ]
     end
     
     def self.parse(response)
       response.split(/\n/).select { |line| line =~ /^\d+\t-?\d+/ }.map { |line| line.split(/\t/) }
     end
+    
+    def full_distribution
+      distribution      = run.distribution
+      full_distribution = distribution + ([0] * (data.seq.length - distribution.length + 1))
+    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)
+      )
+    end
   end
 end

data/lib/vienna_rna.rb

@@ -3,12 +3,6 @@ require "active_support/inflector"
 require "active_support/core_ext/class"
 require "active_support/core_ext/module/aliasing"
 
-module Enumerable
-  def sum
-    inject(&:+)
-  end
-end
-
 module ViennaRna
   @debug = true
   

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: vienna_rna
 version: !ruby/object:Gem::Version
-  version: 0.1.3
+  version: 0.1.4
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-07-11 00:00:00.000000000 Z
+date: 2012-07-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio