add comments to ambiguity.rb

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2202 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_ruby/lib/maasha/seq/ambiguity.rb b/code_ruby/lib/maasha/seq/ambiguity.rb
index 896edadd5f2b98040ec5dd15e0109b8bf7622515..7c21aedb62929837f8f2bb87202c48e71a216e97 100644 (file)
--- a/code_ruby/lib/maasha/seq/ambiguity.rb
+++ b/code_ruby/lib/maasha/seq/ambiguity.rb
@@ -32,9 +32,26 @@ module Ambiguity
   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)
-    (NArray.to_na(seq1.tr(AMBIGUITY_STR, AMBIGUITY_BIN), 'byte') &
-     NArray.to_na(seq2.tr(AMBIGUITY_STR, AMBIGUITY_BIN), 'byte')).eq(0).sum
+    (self.to_na(seq1) & self.to_na(seq2)).eq(0).sum
   end
 
   def add_ambiguity_macro inline_builder