vienna_rna 0.9.1 → 0.9.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 61102bfc0d277cdb89da81c7114f2f4a1a370eff
+  metadata.gz: 75269157e25be08827f08546fffdb90af43be397
+  data.tar.gz: a8b2094c492af287894e3219e3328233ecf31340
 SHA512:
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+  data.tar.gz: bd6799d8ca85f2ddf712fac00e97eb17700b01218e2a99579a0aba94ee2d0fd7a899bff56a473b8b719f7eec8112ab110dd02372a43f5326b19d107aac4ea829

data/lib/vienna_rna/global/rna.rb

@@ -46,7 +46,7 @@ module ViennaRna
       end
     
       def initialize(sequence: "", structure: "", second_structure: "", raw_data: {})
-        @sequence, @raw_data = sequence, raw_data
+        @sequence, @raw_data = sequence.kind_of?(Rna) ? sequence.seq : sequence, raw_data
       
         [:structure, :second_structure].each do |structure_symbol|
           instance_variable_set(
@@ -55,6 +55,12 @@ module ViennaRna
             when :empty then empty_structure
             when :mfe   then RNA(sequence).run(:fold).mfe_rna.structure
             when String then structure_value
+            when Hash   then 
+              if structure_value.keys.count > 1
+                ViennaRna.debugger { "The following options hash has more than one key. This will probably produce unpredictable results: %s" % structure_value.inspect }
+              end
+              
+              RNA(sequence).run(*structure_value.keys, *structure_value.values).mfe_rna.structure
             end
           )
         end

data/lib/vienna_rna/graphing/r.rb

@@ -26,7 +26,7 @@ module ViennaRna
             
             r.assign("legend.titles", data.each_with_index.map { |hash, index| hash[:legend] || "Line #{index + 1}" })
             r.eval("line.colors <- rainbow(%d)" % data.size)
-            r.eval("plot(0, 0, type = 'n', cex = .75, xlab = '', ylab = '', xlim = c(%d, %d), ylim = c(%d, %d))" % [
+            r.eval("plot(0, 0, type = 'n', cex = .75, cex.axis = .9, xlab = '', ylab = '', xlim = c(%d, %d), ylim = c(%d, %d))" % [
               x_range.min, x_range.max, y_range.min, y_range.max
             ])
             
@@ -47,9 +47,11 @@ module ViennaRna
             
             r.eval <<-STR
               title(
-                xlab = "#{x_label}", 
-                ylab = "#{y_label}", 
-                main = "#{title || 'Line Graph'}"
+                xlab     = "#{x_label}", 
+                ylab     = "#{y_label}", 
+                main     = "#{title || 'Line Graph'}",
+                cex.main = .9,
+                cex.lab  = .9
               )
             STR
               
@@ -61,7 +63,8 @@ module ViennaRna
                   bty = "n",
                   col = line.colors,
                   lty = rep(1, #{data.size}),
-                  pch = 0:#{data.size}
+                  pch = 0:#{data.size},
+                  cex = .9
                 )
               STR
             end
@@ -74,10 +77,10 @@ module ViennaRna
           overlay([{ data: data }], title: title, type: type, x_label: x_label, y_label: y_label, legend: false, filename: filename)
         end
         
-        def histogram(data, title: nil, x_label: "Bins", bin_size: 1, relative: false, filename: false)
+        def histogram(data, title: nil, x_label: "Bins", num_bins: false, bin_size: 1, x_arrow: false, relative: false, filename: false)
           half     = bin_size / 2.0
           range    = Range.new((data.min - half).floor, (data.max + half).ceil)
-          breaks   = (range.min + half).step(range.max + half, bin_size).to_a
+          breaks   = num_bins ? num_bins : (range.min + half).step(range.max + half, bin_size).to_a
           
           graph do |r|
             r.assign("histogram.data", data)
@@ -91,13 +94,18 @@ module ViennaRna
             r.eval <<-STR
               hist(
                 histogram.data, 
-                breaks = histogram.breaks, 
-                xlab   = "#{x_label} (width: #{bin_size})", 
-                main   = "#{title || 'Histogram'}", 
-                freq   = #{relative ? 'FALSE' : 'TRUE'}
+                breaks   = histogram.breaks, 
+                xlab     = "#{x_label}", 
+                main     = "#{title || 'Histogram'}", 
+                freq     = #{relative ? 'F' : 'T'},
+                cex.main = 0.9,
+                cex.lab  = 0.9,
+                cex.axis = 0.9
               )
             STR
             
+            r.eval("abline(v = #{x_arrow}, lty = 'dashed')") if x_arrow
+            
             r.eval("dev.off()") if writing_file?(filename)
           end
         end

metadata

@@ -1,83 +1,83 @@
 --- !ruby/object:Gem::Specification
 name: vienna_rna
 version: !ruby/object:Gem::Version
-  version: 0.9.1
+  version: 0.9.2
 platform: ruby
 authors:
 - Evan Senter
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-09-19 00:00:00.000000000 Z
+date: 2013-10-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.4.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.4.2
 - !ruby/object:Gem::Dependency
   name: activesupport
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '3.2'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '3.2'
 - !ruby/object:Gem::Dependency
   name: shuffle
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.1.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.1.0
 - !ruby/object:Gem::Dependency
   name: rinruby
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 2.0.3
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 2.0.3
 - !ruby/object:Gem::Dependency
   name: rroc
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.1.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.1.1
 description: A Ruby 2.0 API for interacting with command line tools involving RNA
@@ -113,17 +113,17 @@ require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.1.2
+rubygems_version: 2.1.4
 signing_key: 
 specification_version: 4
 summary: Bindings to the Vienna RNA package, and other major command line utilities