added edit_distance method to seq.rb

[biopieces.git] / code_ruby / lib / maasha / seq.rb

diff --git a/code_ruby/lib/maasha/seq.rb b/code_ruby/lib/maasha/seq.rb
index 2788e5dcc02d78cdb9e3fd38ef83749bad158b79..e4b6bfd7c27d5933d0bd9c6b65210bd9a7b32ea0 100644 (file)
--- a/code_ruby/lib/maasha/seq.rb
+++ b/code_ruby/lib/maasha/seq.rb
@@ -27,9 +27,10 @@ require 'maasha/seq/digest'
 require 'maasha/seq/trim'
 require 'narray'
 
-autoload :BackTrack,   'maasha/seq/backtrack.rb'
-autoload :Dynamic,     'maasha/seq/dynamic.rb'
-autoload :Homopolymer, 'maasha/seq/homopolymer.rb'
+autoload :BackTrack,   'maasha/seq/backtrack'
+autoload :Dynamic,     'maasha/seq/dynamic'
+autoload :Homopolymer, 'maasha/seq/homopolymer'
+autoload :Levenshtein, 'maasha/seq/levenshtein'
 
 # Residue alphabets
 DNA     = %w[a t c g]
@@ -68,7 +69,6 @@ TRANS_TAB11 = {
   "GTG" => "V", "GCG" => "A", "GAG" => "E", "GGG" => "G"
 }
 
-
 # Error class for all exceptions to do with Seq.
 class SeqError < StandardError; end
 
@@ -384,8 +384,14 @@ class Seq
 
   # Method to determine the Hamming Distance between
   # two Sequence objects (case insensitive).
-  def hamming_distance(seq)
-    self.seq.upcase.hamming_distance(seq.seq.upcase)
+  def hamming_distance(entry)
+    self.seq.upcase.hamming_distance(entry.seq.upcase)
+  end
+
+  # Method to determine the Edit Distance between
+  # two Sequence objects (case insensitive).
+  def edit_distance(entry)
+    Levenshtein.distance(self.seq, entry.seq)
   end
 
   # Method that generates a random sequence of a given length and type.