From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 30 Jun 2009 18:39:51 +0000 (+0000)
Subject: added unit testing for ruby
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=74b77379918ed11c827f5caba6e9e012a1cc106a;p=biopieces.git

added unit testing for ruby

git-svn-id: http://biopieces.googlecode.com/svn/trunk@547 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/code_ruby/Maasha/test/test_seq.rb b/code_ruby/Maasha/test/test_seq.rb
index 5eddd7e..95b25a9 100755
--- a/code_ruby/Maasha/test/test_seq.rb
+++ b/code_ruby/Maasha/test/test_seq.rb
@@ -4,106 +4,165 @@ require 'Maasha/lib/seq'
 require 'test/unit'
 
 class TestSeq < Test::Unit::TestCase 
-	def test_Seq_new
-		my_seq1 = Seq.new
-		assert_equal( nil, my_seq1.seq ) 
-		assert_equal( nil, my_seq1.seq_type ) 
-
-		my_seq2 = Seq.new( "ATCG" )
-		assert_equal( "ATCG", my_seq2.seq ) 
-		assert_equal( nil,    my_seq2.seq_type )
-
-		my_seq3 = Seq.new( "ATCG", "DNA" )
-		assert_equal( "ATCG", my_seq3.seq ) 
-		assert_equal( "DNA", my_seq3.seq_type ) 
+	def test_Seq_initialize_with_0_args
+		my_seq = Seq.new
+		assert_equal( nil, my_seq.seq ) 
+		assert_equal( nil, my_seq.seq_type ) 
+	end
+
+	def test_Seq_initialize_with_1_args
+		my_seq = Seq.new( "ATCG" )
+		assert_equal( "ATCG", my_seq.seq ) 
+		assert_equal( nil,    my_seq.seq_type )
+	end
+
+	def test_Seq_initialize_with_2_args
+		my_seq = Seq.new( "ATCG", "DNA" )
+		assert_equal( "ATCG", my_seq.seq ) 
+		assert_equal( "DNA", my_seq.seq_type ) 
 	end 
 
-	def test_seq_type_guess
+	def test_seq_type_guess_DNA
 		my_seq = Seq.new
 
 		my_seq.seq   = "ATCG"
 		assert_equal( "DNA", my_seq.seq_type_guess )
 		assert_equal( nil, my_seq.seq_type )
 
-		my_seq.seq   = "AUCG"
-		assert_equal( "RNA", my_seq.seq_type_guess )
+		my_seq.seq   = "atcg"
+		assert_equal( "DNA", my_seq.seq_type_guess )
 		assert_equal( nil, my_seq.seq_type )
+	end
 
-		my_seq.seq   = "SEQ"
-		assert_equal( "AA", my_seq.seq_type_guess )
-		assert_equal( nil, my_seq.seq_type )
+	def test_seq_type_guess_RNA
+		my_seq = Seq.new
 
-		my_seq.seq   = "atcg"
-		assert_equal( "DNA", my_seq.seq_type_guess )
+		my_seq.seq   = "AUCG"
+		assert_equal( "RNA", my_seq.seq_type_guess )
 		assert_equal( nil, my_seq.seq_type )
 
 		my_seq.seq   = "aucg"
 		assert_equal( "RNA", my_seq.seq_type_guess )
 		assert_equal( nil, my_seq.seq_type )
+	end
+
+	def test_seq_type_guess_AA
+		my_seq = Seq.new
+
+		my_seq.seq   = "SEQ"
+		assert_equal( "AA", my_seq.seq_type_guess )
+		assert_equal( nil, my_seq.seq_type )
 
 		my_seq.seq   = "seq"
 		assert_equal( "AA", my_seq.seq_type_guess )
 		assert_equal( nil, my_seq.seq_type )
 	end
 
-	def test_seq_type_guess!
+	def test_seq_type_guess_DNA!
 		my_seq = Seq.new
 
 		my_seq.seq   = "ATCG"
 		assert_equal( "DNA", my_seq.seq_type_guess! )
 		assert_equal( "DNA", my_seq.seq_type )
 
-		my_seq.seq   = "AUCG"
-		assert_equal( "RNA", my_seq.seq_type_guess! )
-		assert_equal( "RNA", my_seq.seq_type )
-
-		my_seq.seq   = "SEQ"
-		assert_equal( "AA", my_seq.seq_type_guess! )
-		assert_equal( "AA", my_seq.seq_type )
-
 		my_seq.seq   = "atcg"
 		assert_equal( "DNA", my_seq.seq_type_guess! )
 		assert_equal( "DNA", my_seq.seq_type )
+	end
+
+	def test_seq_type_guess_RNA!
+		my_seq = Seq.new
+
+		my_seq.seq   = "AUCG"
+		assert_equal( "RNA", my_seq.seq_type_guess! )
+		assert_equal( "RNA", my_seq.seq_type )
 
 		my_seq.seq   = "aucg"
 		assert_equal( "RNA", my_seq.seq_type_guess! )
 		assert_equal( "RNA", my_seq.seq_type )
+	end
+
+	def test_seq_type_guess_AA!
+		my_seq = Seq.new
+
+		my_seq.seq   = "SEQ"
+		assert_equal( "AA", my_seq.seq_type_guess! )
+		assert_equal( "AA", my_seq.seq_type )
 
 		my_seq.seq   = "seq"
 		assert_equal( "AA", my_seq.seq_type_guess! )
 		assert_equal( "AA", my_seq.seq_type )
 	end
 
-	def test_seq_alph
+	def test_seq_alph_DNA
 		my_seq = Seq.new
 
 		assert_equal( %w{ A T C G }, my_seq.seq_alph( "DNA" ) )
 		assert_equal( %w{ A T C G }, my_seq.seq_alph( "dna" ) )
+	end
+
+	def test_seq_alph_RNA
+		my_seq = Seq.new
 
 		assert_equal( %w{ A U C G }, my_seq.seq_alph( "RNA" ) )
 		assert_equal( %w{ A U C G }, my_seq.seq_alph( "rna" ) )
+	end
+
+	def test_seq_alph_AA
+		my_seq = Seq.new
 
 		assert_equal( %w{ F L S Y C W P H Q R I M T N K V A D E G }, my_seq.seq_alph( "AA" ) )
 		assert_equal( %w{ F L S Y C W P H Q R I M T N K V A D E G }, my_seq.seq_alph( "aa" ) )
+	end
+
+	def test_seq_alph_invalid
+		my_seq = Seq.new
 
 		assert_raise( RuntimeError ) { my_seq.seq_alph( "protein" )}
 	end
 
-	def test_wrap
-		my_seq = Seq.new( "ACTGACTAGCATCGACTACGACTGACACGACGACGACGACCGAACGATCGATCGCAGACGACGCAGCATGACGACGTACGACTACGACT" )
+	def test_wrap_arg_is_a_number
+		my_seq = Seq.new
 
 		assert_raise( RuntimeError ) { my_seq.wrap( "FOO" ) }
+	end
+
+	def test_wrap_arg_is_a_positive_number
+		my_seq = Seq.new
+
 		assert_raise( RuntimeError ) { my_seq.wrap( 0 ) }
 		assert_raise( RuntimeError ) { my_seq.wrap( -10 ) }
+	end
+
+	def test_wrap_with_0_args
+		my_seq = Seq.new( "ACTGACTAGCATCGACTACGACTGACACGACGACGACGACCGAACGATCGATCGCAGACGACGCAGCATGACGACGTACGACTACGACT" )
 
 		assert_equal( "ACTGACTAGCATCGACTACGACTGACACGACGACGACGACCGAACGATCGATCGCAGACGACGCAGCATGACGACGTACG\nACTACGACT", my_seq.wrap )
+	end
+
+	def test_wrap_with_1_args
+		my_seq = Seq.new( "ACTGACTAGCATCGACTACGACTGACACGACGACGACGACCGAACGATCGATCGCAGACGACGCAGCATGACGACGTACGACTACGACT" )
+
 		assert_equal( "ACTGACTAGCATCGACTACGACTGACACGACGACGACGAC\nCGAACGATCGATCGCAGACGACGCAGCATGACGACGTACG\nACTACGACT", my_seq.wrap( 40 ) )
+	end
+
+	def test_wrap_with_2_args
+		my_seq = Seq.new( "ACTGACTAGCATCGACTACGACTGACACGACGACGACGACCGAACGATCGATCGCAGACGACGCAGCATGACGACGTACGACTACGACT" )
+
 		assert_equal( "ACTGACTAGCATCGACTACGACTGACACGACGACGACGAC\rCGAACGATCGATCGCAGACGACGCAGCATGACGACGTACG\rACTACGACT", my_seq.wrap( 40, "\r" ) )
 
 		assert_equal( "ACTGACTAGCATCGACTACGACTGACACGACGACGACGACCGAACGATCGATCGCAGACGACGCAGCATGACGACGTACGACTACGACT", my_seq.seq )
 	end
 
-	def test_wrap!
+	def test_wrap_dont_change_instance_var
+		my_seq = Seq.new( "ACTGACTAGCATCGACTACGACTGACACGACGACGACGACCGAACGATCGATCGCAGACGACGCAGCATGACGACGTACGACTACGACT" )
+
+		my_seq.wrap
+
+		assert_equal( "ACTGACTAGCATCGACTACGACTGACACGACGACGACGACCGAACGATCGATCGCAGACGACGCAGCATGACGACGTACGACTACGACT", my_seq.seq )
+	end
+
+	def test_wrap_with_0_args!
 		my_seq = Seq.new( "ACTGACTAGCATCGACTACGACTGACACGACGACGACGACCGAACGATCGATCGCAGACGACGCAGCATGACGACGTACGACTACGACT" )
 
 		my_seq.wrap!