From be88ef5821b5b0d3fa297ff10d2f7e17500db1d7 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Mon, 5 Sep 2011 13:23:08 +0000
Subject: [PATCH] speedup of bits.rb

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1513 74ccb610-7750-0410-82ae-013aeee3265d
---
 code_ruby/lib/maasha/bits.rb | 58 ++++++++++++++----------------------
 1 file changed, 23 insertions(+), 35 deletions(-)

diff --git a/code_ruby/lib/maasha/bits.rb b/code_ruby/lib/maasha/bits.rb
index b976c88..1ed9e56 100644
--- a/code_ruby/lib/maasha/bits.rb
+++ b/code_ruby/lib/maasha/bits.rb
@@ -22,65 +22,53 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
+require 'narray'
+
 # Error class for all exceptions to do with String.
 class StringError < StandardError; end
 
 # Monkey patching Class String to add bitwise operators.
-# Behaviour matching Perl's:
-# http://perldoc.perl.org/perlop.html#Bitwise-String-Operators
 class String
   # Method to that returns the case senstive Hamming Distance between two strings.
   # http://en.wikipedia.org/wiki/Hamming_distance
-  def self.hamming_dist(str1, str2)
-    raise StringError, "Uneven string lengths: #{str1.length} != #{str2.length}" if str1.length != str2.length
-    (str1 ^ str2 ).count("\x01-\xff")
+  def hamming_distance(str)
+    (self ^ str).tr("\x00",'').length
   end
 
   # Method that performs bitwise AND operation where bits
-  # are copied if they exists in BOTH operands. If the operand
-  # sizes are different, the & operator methods acts as though
-  # the longer operand were truncated to the length of the shorter.
+  # are copied if they exists in BOTH operands.
   def &(str)
-    new = ""
-
-    (0 ... [self.length, str.length].min).each do |i|
-      new << (self[i].ord & str[i].ord)
-    end
+    narray1, narray2 = to_narray(self, str)
 
-    new
+    (narray1 & narray2).to_s
   end
 
   # Method that performs bitwise OR operation where bits
-  # are copied if they exists in EITHER operands. If the operand
-  # sizes differ, the shorter operand is extended with the terminal
-  # part of the longer operand.
+  # are copied if they exists in EITHER operands.
   def |(str)
-    new = ""
-
-    min = [self.length, str.length].min
-
-    (0 ... min).each do |i|
-      new << (self[i].ord | str[i].ord)
-    end
+    narray1, narray2 = to_narray(self, str)
 
-    if self.length > str.length
-      new << self[min ... self.length]
-    elsif self.length < str.length
-      new << str[min ... str.length]
-    end
-
-    new
+    (narray1 | narray2).to_s
   end
 
   # Method that performs bitwise XOR operation where bits
   # are copied if they exists in ONE BUT NOT BOTH operands.
   def ^(str)
-    new = ""
+    narray1, narray2 = to_narray(self, str)
+
+    (narray1 ^ narray2).to_s
+  end
+
+  private
 
-    (0 ... [self.length, str.length].min).each do |i|
-      new << (self[i].ord ^ str[i].ord)
+  def to_narray(str1, str2)
+    if str1.length != str2.length
+      raise StringError, "Uneven string lengths: #{str1.length} != #{str2.length}"
     end
 
-    new
+    narray1 = NArray.to_na(str1, "byte")
+    narray2 = NArray.to_na(str2, "byte")
+
+    [narray1, narray2]
   end
 end
-- 
2.39.5