X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=code_ruby%2Flib%2Fmaasha%2Fseq.rb;h=1d8f3c00594e9208f434251eb23c342413df9506;hb=92dba07b3dd9837ed90212126998a8a1f9e00652;hp=e4b6bfd7c27d5933d0bd9c6b65210bd9a7b32ea0;hpb=b2ea0b5a51a558478af60e9df4c643dd58552086;p=biopieces.git

diff --git a/code_ruby/lib/maasha/seq.rb b/code_ruby/lib/maasha/seq.rb
index e4b6bfd..1d8f3c0 100644
--- a/code_ruby/lib/maasha/seq.rb
+++ b/code_ruby/lib/maasha/seq.rb
@@ -30,7 +30,9 @@ require 'narray'
 autoload :BackTrack,   'maasha/seq/backtrack'
 autoload :Dynamic,     'maasha/seq/dynamic'
 autoload :Homopolymer, 'maasha/seq/homopolymer'
+autoload :Hamming,     'maasha/seq/hamming'
 autoload :Levenshtein, 'maasha/seq/levenshtein'
+autoload :Ambiguity,   'maasha/seq/ambiguity'
 
 # Residue alphabets
 DNA     = %w[a t c g]
@@ -384,8 +386,12 @@ class Seq
 
   # Method to determine the Hamming Distance between
   # two Sequence objects (case insensitive).
-  def hamming_distance(entry)
-    self.seq.upcase.hamming_distance(entry.seq.upcase)
+  def hamming_distance(entry, options = nil)
+    if options and options[:ambiguity]
+      Hamming.distance(self.seq, entry.seq)
+    else
+      self.seq.upcase.hamming_distance(entry.seq.upcase)
+    end
   end
 
   # Method to determine the Edit Distance between