implemented hamming_dist in inline C

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

diff --git a/code_ruby/lib/maasha/seq/ambiguity.rb b/code_ruby/lib/maasha/seq/ambiguity.rb
index 7c21aedb62929837f8f2bb87202c48e71a216e97..4de50ade44ec1c718ee39f8b65a92530c36a6de0 100644 (file)
--- a/code_ruby/lib/maasha/seq/ambiguity.rb
+++ b/code_ruby/lib/maasha/seq/ambiguity.rb
@@ -23,41 +23,12 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 require 'inline'
-#autoload :NArray, 'narray'
 
 module Ambiguity
-  # IUPAC alphabet and binary encoding of the same
-  # http://en.wikipedia.org/wiki/Nucleic_acid_notation
-
-  AMBIGUITY_STR = "ACGTUWSMKRYBDHVNacgtuwsmkrybdhvn"
-  AMBIGUITY_BIN = "\x08\x04\x02\x01\x01\x09\x06\x0c\x03\x0a\x05\x07\x0b\x0d\x0e\x0f\x08\x04\x02\x01\x01\x09\x06\x0c\x03\x0a\x05\x07\x0b\x0d\x0e\x0f"
-
-  # Class method to convert a sequence string to a bit string
-  # where the bit positions in each char corresponds to the following:
-  # A = 1000
-  # C = 0100
-  # G = 0010
-  # T = 0001
-  # And ambiguity codes are expressed using similar bit fields.
-  def self.to_bin(seq)
-    seq.tr(AMBIGUITY_STR, AMBIGUITY_BIN)
-  end
-
-  # Class method to convert a bit string to a NArray.
-  def self.to_na(seq)
-    NArray.to_na(self.to_bin(seq), 'byte')
-  end
-
-  # Class method to calculate the Hamming Distance between
-  # two bit fields encoding in NArrays.
-  def self.hamming_distance(seq1, seq2)
-    (self.to_na(seq1) & self.to_na(seq2)).eq(0).sum
-  end
-
   def add_ambiguity_macro inline_builder
     # Macro for matching nucleotides including ambiguity codes.
     inline_builder.prefix %{
-      #define MATCH(A,B) ((bitmap[A] & bitmap[B]) != 0)
+      #define MATCH(A,B) ((bitmap[(int) A] & bitmap[(int) B]) != 0)
     }
 
     # Bitmap for matching nucleotides including ambiguity codes.