vienna_rna 0.9.0 → 0.9.1

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data/README.md

@@ -1,13 +1,13 @@
 ViennaRna
 ------------------------
 
-A simple gem for facilitating bindings to the ViennaRNA package (http://www.tbi.univie.ac.at/~ivo/RNA/). Note that this gem makes no effort to build and install the ViennaRNA suite locally at this time, and instead relies on its presence on the host machine. Leverages the BioRuby gem (http://bioruby.open-bio.org/) libraries for file parsing.
+A simple gem for facilitating bindings to the ViennaRNA package (http://www.tbi.univie.ac.at/~ivo/RNA/), amongst other RNA packages. Note that this gem makes no effort to build and install the ViennaRNA suite locally at this time, and instead relies on its presence on the host machine. Also includes a lot of utilities surrounding RNA sequence / structure parsing, graphing using R (via RinRuby) and other analysis tools. Used privately as the foundation for much of the research I do at http://bioinformatics.bc.edu/clotelab/
 
 Simple use case:
     
     > require "vienna_rna"
     #=> true 
-    > rna = ViennaRna::Fold.run(seq: "CCUCGAGGGGAACCCGAAAGGGACCCGAGAGG")
+    > rna = ViennaRna::Package::Fold.run(seq: "CCUCGAGGGGAACCCGAAAGGGACCCGAGAGG")
     #=> #<ViennaRna::Fold:0x007f9c48839dc0>
     > rna.structure
     #=> "((((..(((...(((....))).)))..))))" 

data/lib/vienna_rna/global/rna.rb

@@ -95,7 +95,7 @@ module ViennaRna
       end
 
       def run(module_name, options = {})
-        if rna_module = ViennaRna.const_missing("#{module_name}".camelize)
+        if rna_module = ViennaRna::Package.const_missing("#{module_name}".camelize)
           rna_module.run(self, options)
         else
           raise ArgumentError.new("#{module_name} can't be resolved as an executable")

data/lib/vienna_rna.rb

@@ -30,7 +30,9 @@ module ViennaRna
     end
     
     def self.const_missing(name)
-      if Base.exec_exists?(name)
+      if const_defined?(name)
+        const_get(name)
+      elsif Base.exec_exists?(name)
         module_eval do
           const_set(name, Class.new(Base))
         end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: vienna_rna
 version: !ruby/object:Gem::Version
-  version: 0.9.0
+  version: 0.9.1
 platform: ruby
 authors:
 - Evan Senter