From 4d59c18790b6cc5951f7700392018d6ca1e6b411 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Mon, 17 Oct 2011 14:40:37 +0000
Subject: [PATCH] added methods to bitarray.rb

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1582 74ccb610-7750-0410-82ae-013aeee3265d
---
 code_ruby/lib/maasha/bitarray.rb       | 34 +++++++++++++++++++++++++-
 code_ruby/test/maasha/test_bitarray.rb | 31 ++++++++++++++++++++---
 2 files changed, 60 insertions(+), 5 deletions(-)

diff --git a/code_ruby/lib/maasha/bitarray.rb b/code_ruby/lib/maasha/bitarray.rb
index 4cb77b4..e65ab3c 100644
--- a/code_ruby/lib/maasha/bitarray.rb
+++ b/code_ruby/lib/maasha/bitarray.rb
@@ -32,7 +32,7 @@ class BitArrayError < StandardError; end
 # Class containing methods for creating and manipulating a bit array.
 class BitArray
   attr_accessor :byte_array
-  attr_reader :size
+  attr_reader   :size
 
   # Method to initialize a new bit array of a given size in bits.
   def initialize(size)
@@ -41,6 +41,20 @@ class BitArray
     @count_array = init_count_array
   end
 
+  # Method that sets all bits in the bit array.
+  def fill!
+    self.byte_array.fill!(~0)
+
+    self
+  end
+
+  # Method that unsets all bits in the bit array.
+  def clear!
+    self.byte_array.fill!(0)
+
+    self
+  end
+
   # Method to set a bit to 1 at a given position in the bit array.
   def bit_set(pos)
     raise BitArrayError, "Position #{pos} must be an integer."              unless pos.is_a? Fixnum
@@ -49,6 +63,17 @@ class BitArray
     @byte_array[byte_pos(pos)] = @byte_array[byte_pos(pos)] | bit_pos(pos)
   end
 
+  # Method to set a bit to 0 at a given position in the bit array.
+  def bit_unset(pos)
+    raise BitArrayError, "Position #{pos} must be an integer."              unless pos.is_a? Fixnum
+    raise BitArrayError, "Position #{pos} outside of range: 0 ... #{@size}" unless (0 ... @size ).include? pos
+
+    mask = bit_pos(pos)
+    mask = ~mask
+
+    @byte_array[byte_pos(pos)] = @byte_array[byte_pos(pos)] & mask
+  end
+
   # Method to check if a bit at a given position in the bit array is set.
   def bit_set?(pos)
     raise BitArrayError, "Position #{pos} must be an integer."              unless pos.is_a? Fixnum
@@ -106,6 +131,13 @@ class BitArray
     self
   end
 
+  # Method to flip all bits in a bit array. All set bits become unset and visa versa.
+  def ~
+    self.byte_array = ~(self.byte_array)
+
+    self
+  end
+
   # Method to convert a bit array to a string.
   def to_s
     string = ""
diff --git a/code_ruby/test/maasha/test_bitarray.rb b/code_ruby/test/maasha/test_bitarray.rb
index 4745401..182ec27 100755
--- a/code_ruby/test/maasha/test_bitarray.rb
+++ b/code_ruby/test/maasha/test_bitarray.rb
@@ -55,22 +55,38 @@ class TestBitArray < Test::Unit::TestCase
     assert_equal("0000000000", @ba.to_s)
   end
 
+  def test_BitArray_fill_returns_correctly
+    assert_equal("1111111111", @ba.fill!.to_s)
+  end
+
+  def test_BitArray_clear_returns_correctly
+    assert_equal("0000000000", @ba.fill!.clear!.to_s)
+  end
+
   def test_BitArray_bit_set_with_bad_pos_raises
     [-1, 10, 1.1].each do |pos|
       assert_raise(BitArrayError) { @ba.bit_set(pos) }
     end
   end
 
-  def test_BitArray_bit_set
-    str = "0000000000"
+  def test_BitArray_bit_unset
+    @ba.fill!
+
+    str = "1111111111"
 
     (0.upto 9).each do |pos|
-      @ba.bit_set(pos)
-      str[pos] = "1"
+      @ba.bit_unset(pos)
+      str[pos] = "0"
       assert_equal(str, @ba.to_s)
     end
   end
 
+  def test_BitArray_bit_unset_with_bad_pos_raises
+    [-1, 10, 1.1].each do |pos|
+      assert_raise(BitArrayError) { @ba.bit_unset(pos) }
+    end
+  end
+
   def test_BitArray_bit_set_questionmark_with_bad_pos_raises
     [-1, 10, 1.1].each do |pos|
       assert_raise(BitArrayError) { @ba.bit_set?(pos) }
@@ -137,5 +153,12 @@ class TestBitArray < Test::Unit::TestCase
     ba.bit_set(6)
     assert_equal( "0000101000", (@ba ^ ba).to_s)
   end
+
+  def test_BitArray_FLIP_returns_correctly
+    @ba.bit_set(0)
+    @ba.bit_set(9)
+
+    assert_equal( "0111111110", (~@ba).to_s)
+  end
 end
 
-- 
2.39.2