From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Fri, 8 Mar 2013 10:09:02 +0000 (+0000)
Subject: added << method to Seq.rb
X-Git-Url: https://git.donarmstrong.com/?p=biopieces.git;a=commitdiff_plain;h=80706855913e8607239241fd2938f47d1fb76799

added << method to Seq.rb

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2113 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/code_ruby/lib/maasha/seq.rb b/code_ruby/lib/maasha/seq.rb
index c8cc9f1..cf4b6e6 100644
--- a/code_ruby/lib/maasha/seq.rb
+++ b/code_ruby/lib/maasha/seq.rb
@@ -420,6 +420,17 @@ class Seq
     self
   end
 
+  # Method to concatenate sequence entries.
+  def <<(entry)
+    raise SeqError, "sequences of different types" unless self.type == entry.type
+    raise SeqError, "qual is missing in one entry" unless self.qual.class == entry.qual.class
+
+    self.seq  << entry.seq
+    self.qual << entry.qual unless entry.qual.nil?
+
+    self
+  end
+
   # Method that returns a subsequence of from a given start position
   # and of a given length.
   def subseq(start, length = self.length - start)
diff --git a/code_ruby/test/maasha/test_seq.rb b/code_ruby/test/maasha/test_seq.rb
index 8ec6f97..4a68d67 100755
--- a/code_ruby/test/maasha/test_seq.rb
+++ b/code_ruby/test/maasha/test_seq.rb
@@ -333,6 +333,46 @@ class TestSeq < Test::Unit::TestCase
     assert_not_equal(@entry.seq, @entry.shuffle!.seq)
   end
 
+  test "#<< with different types raises" do
+    @entry.seq = "atcg"
+    assert_raise(SeqError) { @entry << Seq.new("test", "atcg", "dna") }
+  end
+
+  test "#<< with missing qual in one entry raises" do
+    @entry.seq  = "atcg"
+    @entry.type = "dna"
+    assert_raise(SeqError) { @entry << Seq.new("test", "atcg", "dna", "IIII") }
+    @entry.qual = "IIII"
+    assert_raise(SeqError) { @entry << Seq.new("test", "atcg", "dna") }
+  end
+
+  test "#<< with nil qual in both entries dont raise" do
+    @entry.seq = "atcg"
+    assert_nothing_raised { @entry << Seq.new("test", "atcg") }
+  end
+
+  test "#<< with qual in both entries dont raise" do
+    @entry.seq  = "atcg"
+    @entry.type = "dna"
+    @entry.qual = "IIII"
+    assert_nothing_raised { @entry << Seq.new("test", "atcg", "dna", "IIII") }
+  end
+
+  test "#<< without qual returns correctly" do
+    @entry.seq  = "atcg"
+    @entry <<  Seq.new("test", "ATCG")
+    assert_equal("atcgATCG", @entry.seq)
+  end
+
+  test "#<< with qual returns correctly" do
+    @entry.seq  = "atcg"
+    @entry.type = "dna"
+    @entry.qual = "HHHH"
+    @entry <<  Seq.new("test", "ATCG", "dna", "IIII")
+    assert_equal("atcgATCG", @entry.seq)
+    assert_equal("HHHHIIII", @entry.qual)
+  end
+
   test "#subseq with start < 0 raises" do
     @entry.seq = "ATCG"
     assert_raise(SeqError) { @entry.subseq(-1, 1) }