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 5eddd7e0b245a223ca38df8db9435156a722f54a..95b25a92fb2f2a1e764a373d5d9d5a4fbe4ae404 100755 (executable)
--- 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!