From 124ad80bd42309d1e6ea7d10dcffb86938c29069 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Thu, 28 Feb 2013 10:21:22 +0000
Subject: [PATCH] added Seq.shuffle method and tests

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2105 74ccb610-7750-0410-82ae-013aeee3265d
---
 code_ruby/lib/maasha/seq.rb       |  7 ++++++-
 code_ruby/test/maasha/test_seq.rb | 16 +++++++++++++++-
 2 files changed, 21 insertions(+), 2 deletions(-)

diff --git a/code_ruby/lib/maasha/seq.rb b/code_ruby/lib/maasha/seq.rb
index 577d51a..e72250d 100644
--- a/code_ruby/lib/maasha/seq.rb
+++ b/code_ruby/lib/maasha/seq.rb
@@ -390,7 +390,12 @@ class Seq
     seq_new
   end
 
-  # Method to shuffle a sequence readomly inline.
+  # Method to return a new Seq object with shuffled sequence.
+  def shuffle
+    Seq.new(self.seq_name, self.seq.split('').shuffle!.join, self.type, self.qual)
+  end
+
+  # Method to shuffle a sequence randomly inline.
   def shuffle!
     self.seq = self.seq.split('').shuffle!.join
     self
diff --git a/code_ruby/test/maasha/test_seq.rb b/code_ruby/test/maasha/test_seq.rb
index a7145ef..f966a5f 100755
--- a/code_ruby/test/maasha/test_seq.rb
+++ b/code_ruby/test/maasha/test_seq.rb
@@ -9,7 +9,8 @@ class TestSeq < Test::Unit::TestCase
     @entry = Seq.new
   end
 
-  #  def test_Seq# autoremoves whitespace, newlines, and carriage returns
+  #  # autoremoves whitespace, newlines, and carriage returns
+  #  def test_Seq_strip
   #    dna = Seq.new
   #    dna.seq = "A\tT\r\tC\nG  "
   #    assert_equal(dna.seq, "ATCG")
@@ -277,6 +278,19 @@ class TestSeq < Test::Unit::TestCase
     end
   end
 
+  def test_Seq_shuffle_returns_correctly
+    orig       = "actgactgactgatcgatcgatcgatcgtactg" 
+    @entry.seq = "actgactgactgatcgatcgatcgatcgtactg"
+    entry_shuf = @entry.shuffle
+    assert_equal(orig, @entry.seq)
+    assert_not_equal(@entry.seq, entry_shuf.seq)
+  end
+
+  def test_Seq_shuffle_bang_returns_correctly
+    @entry.seq = "actgactgactgatcgatcgatcgatcgtactg"
+    assert_not_equal(@entry.seq, @entry.shuffle!.seq)
+  end
+
   def test_Seq_subseq_with_start_lt_0_raises
     @entry.seq = "ATCG"
     assert_raise(SeqError) { @entry.subseq(-1, 1) }
-- 
2.39.2