vienna_rna 0.4.3 → 0.4.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 5b692c3183ad74aff60eef165837c3009a3d6bff
+  metadata.gz: 7d9804f2f40ec0ae56690e373c7f9a3e6e37e2c9
+  data.tar.gz: 8e0513d28b214658a90f1c0000aa09457c0dc568
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+  data.tar.gz: 6c64233272aa7cf6188a467f65e965bd589f4a15a122d8730ad3ee430ee851bb75c3152fa3584c19a03e300900cec8bf6f00050d4bbf3eaca195e9254d71dcc1

data/README.md

@@ -16,4 +16,4 @@ Simple use case:
     > mfe_rna = RNA("CCUCGAGGGGAACCCGAAAGGGACCCGAGAGG").run(:fold).mfe_rna
     #=> echo CCUCGAGGGGAACCCGAAAGGGACCCGAGAGG | rnafold --noPS
     #=> Total runtime: 0.013 sec.
-    #=> #<ViennaRna::ViennaRna::Rna CCUCGAGGGGAACCCGAAAG... ((((..(((...(((....) [truncated]>
+    #=> #<ViennaRna::Rna CCUCGAGGGGAACCCGAAAG... ((((..(((...(((....) [truncated]>

data/lib/vienna_rna/modules/fold.rb

@@ -12,7 +12,7 @@ module ViennaRna
       unless data.seq.length == structure.length
         raise "Sequence: '#{data.seq}'\nStructure: '#{structure}'"
       else
-        @mfe_rna, @structure, @mfe = ViennaRna::Rna.init_from_string(data.seq, structure), structure, Parser.rnafold_mfe(@response)
+        @mfe_rna, @structure, @mfe = Rna.init_from_string(data.seq, structure), structure, Parser.rnafold_mfe(@response)
       end
     end
     

data/lib/vienna_rna/modules/rna.rb

@@ -32,7 +32,7 @@ module ViennaRna
       
       @structure = case structure
       when :empty then empty_structure
-      when :mfe   then ViennaRna::Fold.run(ViennaRna::Rna.init_from_string(seq)).structure
+      when :mfe   then ViennaRna::Fold.run(Rna.init_from_string(seq)).structure
       when String then structure
       end
     end
@@ -44,11 +44,11 @@ module ViennaRna
     def inspect
       case [sequence.present?, structure.present?]
       when [true, true] then
-        "#<ViennaRna::#{self.class.name} #{seq[0, 20] + (seq.length > 20 ? '...' : '')} #{str[0, 20] + (str.length > 20 ? ' [truncated]' : '')}>"
+        "#<#{self.class.name} #{seq[0, 20] + (seq.length > 20 ? '...' : '')} #{str[0, 20] + (str.length > 20 ? ' [truncated]' : '')}>"
       when [true, false] then
-        "#<ViennaRna::#{self.class.name} #{seq[0, 20] + (seq.length > 20 ? '...' : '')}>"
+        "#<#{self.class.name} #{seq[0, 20] + (seq.length > 20 ? '...' : '')}>"
       when [false, false] then
-        "#<ViennaRna::#{self.class.name}>"
+        "#<#{self.class.name}>"
       end
     end
     

data/lib/vienna_rna/modules/subopt.rb

@@ -3,7 +3,7 @@ module ViennaRna
     attr_reader :structures
     
     def post_process
-      @structures = @response.split(/\n/)[1..-1].map { |output| ViennaRna::Rna.init_from_string(data.seq, output.split(/\s+/).first) }
+      @structures = @response.split(/\n/)[1..-1].map { |output| Rna.init_from_string(data.seq, output.split(/\s+/).first) }
     end
     
     def bin(count = 1)

data/lib/vienna_rna/modules/xbor.rb

@@ -29,7 +29,7 @@ module ViennaRna
       sequence  = log.split(/\n/).first.split(/\s+/)[1]
       structure = log.split(/\n/).first.split(/\s+/)[2]
       
-      klass.bootstrap(ViennaRna::Rna.init_from_string(sequence, structure), log)
+      klass.bootstrap(Rna.init_from_string(sequence, structure), log)
     end
     
     def self.parse(response)

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: vienna_rna
 version: !ruby/object:Gem::Version
-  version: 0.4.3
+  version: 0.4.4
 platform: ruby
 authors:
 - Evan Senter