From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Fri, 14 Jan 2011 20:30:41 +0000 (+0000)
Subject: fixed license text
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=a688871b29335f089aecc6888080b7f34c9624fc;p=biopieces.git

fixed license text

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1205 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/code_ruby/Maasha/lib/align.rb b/code_ruby/Maasha/lib/align.rb
index 5c0b9f5..a494b4d 100644
--- a/code_ruby/Maasha/lib/align.rb
+++ b/code_ruby/Maasha/lib/align.rb
@@ -1,6 +1,6 @@
 raise "Ruby 1.9 or later required" if RUBY_VERSION < "1.9"
 
-# Copyright (C) 2007-2010 Martin A. Hansen.
+# Copyright (C) 2007-2011 Martin A. Hansen.
 
 # This program is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
diff --git a/code_ruby/Maasha/lib/bitarray.rb b/code_ruby/Maasha/lib/bitarray.rb
index 5533c52..e3f1a12 100644
--- a/code_ruby/Maasha/lib/bitarray.rb
+++ b/code_ruby/Maasha/lib/bitarray.rb
@@ -1,3 +1,27 @@
+# Copyright (C) 2007-2011 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
 BitsInChar = 8
 
 # Error class for all exceptions to do with BitArray.
@@ -11,7 +35,7 @@ class BitArray
   def initialize(size)
     @size        = size
     @byte_array  = init_byte_array
-    @count_table = init_count_table
+    @count_array = init_count_array
   end
 
   # Method to set a bit to 1 at a given position in the bit array.
@@ -30,23 +54,12 @@ class BitArray
     (@byte_array[byte_pos(pos)].ord & bit_pos(pos)) != 0
   end
 
-  # Method that returns the number of bits set "on" in a bit array.
-  def bits_on1
-    bits_on = 0
-
-    (0 ... @size).each do |pos|
-      bits_on += 1 if bit_set?(pos)
-    end
-
-    bits_on
-  end
-
   # Method that returns the number of bits set "on" in a bit array.
   def bits_on 
     bits_on = 0
 
     (0 ... self.byte_array.size).each do |byte|
-      bits_on += @count_table[byte]
+      bits_on += @count_array[self.byte_array[byte].ord]
     end
 
     bits_on
@@ -130,19 +143,27 @@ class BitArray
     byte_array
   end
 
-  # Method that creates a table with number of bits set.
-  def init_count_table
-    count_table = []
+  # Method that returns an array where the element index value is
+  # the number of bits set for that index value.
+  def init_count_array
+    count_array = []
 
+    (0 ... (2 ** BitsInChar)).each do |i|
+      count_array << bits_in_char(i)
+    end
+
+    count_array
+  end
+
+  # Method that returns the number of set bits in a byte.
+  def bits_in_char(char)
     bits = 0
 
-    (0 ... BitsInChar).each do |i|
-      (0 ... BitsInChar).each do |c|
-        bits += 1
-      end
+    (0 ... BitsInChar).each do |pos|
+      bits += 1 if ((char & bit_pos(pos)) != 0)
     end
 
-    puts bits
+    bits
   end
 
   # Method that returns the byte position in the byte array for a given bit position.
diff --git a/code_ruby/Maasha/lib/fasta.rb b/code_ruby/Maasha/lib/fasta.rb
index bd551be..26e6d73 100644
--- a/code_ruby/Maasha/lib/fasta.rb
+++ b/code_ruby/Maasha/lib/fasta.rb
@@ -1,3 +1,5 @@
+# Copyright (C) 2007-2011 Martin A. Hansen.
+
 # This program is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
 # as published by the Free Software Foundation; either version 2
diff --git a/code_ruby/Maasha/lib/fastq.rb b/code_ruby/Maasha/lib/fastq.rb
index b8ce35e..fc2863a 100644
--- a/code_ruby/Maasha/lib/fastq.rb
+++ b/code_ruby/Maasha/lib/fastq.rb
@@ -1,3 +1,5 @@
+# Copyright (C) 2007-2011 Martin A. Hansen.
+
 # This program is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
 # as published by the Free Software Foundation; either version 2
diff --git a/code_ruby/Maasha/lib/genbank.rb b/code_ruby/Maasha/lib/genbank.rb
index f52505f..f83e8b7 100644
--- a/code_ruby/Maasha/lib/genbank.rb
+++ b/code_ruby/Maasha/lib/genbank.rb
@@ -1,3 +1,5 @@
+# Copyright (C) 2007-2010 Martin A. Hansen.
+
 # This program is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
 # as published by the Free Software Foundation; either version 2
diff --git a/code_ruby/Maasha/lib/seq.rb b/code_ruby/Maasha/lib/seq.rb
index 04dfdeb..893b854 100644
--- a/code_ruby/Maasha/lib/seq.rb
+++ b/code_ruby/Maasha/lib/seq.rb
@@ -1,3 +1,26 @@
+# Copyright (C) 2007-2011 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 # Residue alphabets
 DNA     = %w[a t c g]