From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Fri, 3 Jul 2009 15:08:59 +0000 (+0000)
Subject: last cleanups
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=e446cc78c79404a09c5109e8f046567d9c9657ee;p=biopieces.git

last cleanups

git-svn-id: http://biopieces.googlecode.com/svn/trunk@553 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/code_ruby/Maasha/lib/seq.rb b/code_ruby/Maasha/lib/seq.rb
index f80d397..8146ab4 100644
--- a/code_ruby/Maasha/lib/seq.rb
+++ b/code_ruby/Maasha/lib/seq.rb
@@ -121,6 +121,12 @@ class Seq < String
 	class NA < Seq
 		# Class containing methods specific for DNA sequences.
 		class DNA < NA
+			# Method to initialize a new DNA sequence.
+			def initialize( seq = "" )
+				@seq      = seq
+				@seq_type = :DNA
+			end
+
 			# Method that complements DNA sequence including ambiguity codes.
 			def complement
 				@seq.tr!( 'AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'TCGAAYRWSKMDHBVNtcgaayrwskmdhbvn' )
@@ -129,6 +135,12 @@ class Seq < String
 
 		# Class containing methods specific for RNA sequences.
 		class RNA < NA
+			# Method to initialize a new RNA sequence.
+			def initialize( seq = "" )
+				@seq      = seq
+				@seq_type = :RNA
+			end
+
 			# Method that complements RNA sequence including ambiguity codes.
 			def complement
 				@seq.tr!( 'AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'UCGAAYRWSKMDHBVNucgaayrwskmdhbvn' )
diff --git a/code_ruby/Maasha/test/test_seq.rb b/code_ruby/Maasha/test/test_seq.rb
index 4297720..e6e28a2 100755
--- a/code_ruby/Maasha/test/test_seq.rb
+++ b/code_ruby/Maasha/test/test_seq.rb
@@ -263,5 +263,63 @@ class TestSeq < Test::Unit::TestCase
 		assert_equal( "SEQ", s.to_s )
 		assert_equal( :AA,  s.seq_type )
 	end
+
+	# Testing Seq::AA#mol_weight
+
+	def test_Seq_aa_mol_wight_bad_residue
+		s = Seq::AA.new( "7" )
+		assert_raise( RuntimeError ) { s.mol_weight }
+	end
+
+	def test_Seq_aa_mol_wight_return_correct
+		s = Seq::AA.new( "SEQ" )
+		assert_equal( 398.0, s.mol_weight )
+	end
+
+	# Testing Seq::NA::DNA#initialize
+
+ 	# test marked for deletion - too simple and not informative
+	def test_Seq_NA_DNA_inialize_with_0_args
+		s = Seq::NA::DNA.new
+		assert_equal( "", s.to_s )
+		assert_equal( :DNA, s.seq_type )
+	end
+
+ 	# test marked for deletion - too simple and not informative
+	def test_Seq_NA_DNA_inialize_with_1_args
+		s = Seq::NA::DNA.new( "ATCG" )
+		assert_equal( "ATCG", s.to_s )
+		assert_equal( :DNA, s.seq_type )
+	end
+
+	# Testing Seq::NA::DNA#complement
+
+	def test_Seq_NA_DNA_complement_correct
+		s = Seq::NA::DNA.new( "ATCG" )
+		assert_equal( "TAGC", s.complement.to_s )
+	end
+
+	# Testing Seq::NA::RNA#initialize
+
+ 	# test marked for deletion - too simple and not informative
+	def test_Seq_NA_RNA_inialize_with_0_args
+		s = Seq::NA::RNA.new
+		assert_equal( "", s.to_s )
+		assert_equal( :RNA, s.seq_type )
+	end
+
+ 	# test marked for deletion - too simple and not informative
+	def test_Seq_NA_RNA_inialize_with_1_args
+		s = Seq::NA::RNA.new( "AUCG" )
+		assert_equal( "AUCG", s.to_s )
+		assert_equal( :RNA, s.seq_type )
+	end
+
+	# Testing Seq::NA::RNA#complement
+
+	def test_Seq_NA_DNA_complement_correct
+		s = Seq::NA::RNA.new( "AUCG" )
+		assert_equal( "UAGC", s.complement.to_s )
+	end
 end