bio 1.4.2 → 1.4.3

data/test/unit/bio/data/test_na.rb

@@ -42,7 +42,7 @@ module Bio
     end
 
     def test_to_re
-      re = /[tcy][agr][atw][gcw][tgk][acm][tgcyskb][atgrwkd][agcmrsv][atgcyrwskmbdhvn]atgc/
+      re = /[tcy][agr][atw][gcs][tgk][acm][tgcyskb][atgrwkd][agcmrsv][atgcyrwskmbdhvn]atgc/
       str = 'yrwskmbdvnatgc'
       str0 = str.clone
       assert_equal(re, @obj.to_re(str))

data/test/unit/bio/db/embl/test_embl.rb

@@ -124,13 +124,8 @@ module Bio
     end
 
     def test_os
-#      assert_equal('', @obj.os)
-      assert_raises(RuntimeError) { @obj.os }
-    end
-
-    def test_os_valid
-      @obj.instance_eval { @data['OS'] = "Haplochromis sp. 'muzu rukwa'" }
-      assert_equal("Haplochromis sp. 'muzu rukwa'", @obj.os)
+      assert_equal("Haplochromis sp. 'muzu, rukwa'", @obj.os[0]['os'])
+      assert_nil(@obj.os[0]['name'])
     end
 
     # Bio::EMBLDB::COMMON#oc

data/test/unit/bio/db/embl/test_embl_rel89.rb

@@ -129,13 +129,8 @@ module Bio
     end
 
     def test_os
-#      assert_equal('', @obj.os)
-      assert_raises(RuntimeError) { @obj.os }
-    end
-
-    def test_os_valid
-      @obj.instance_eval { @data['OS'] = "Haplochromis sp. 'muzu rukwa'" }
-      assert_equal("Haplochromis sp. 'muzu rukwa'", @obj.os)
+      assert_equal("Haplochromis sp. 'muzu, rukwa'", @obj.os[0]['os'])
+      assert_nil(@obj.os[0]['name'])
     end
 
     # Bio::EMBLDB::COMMON#oc

data/test/unit/bio/db/fasta/test_defline.rb

@@ -12,7 +12,7 @@ load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
 
 # libraries needed for the tests
 require 'test/unit'
-require 'bio/db/fasta/defline.rb'
+require 'bio/db/fasta/defline'
 
 module Bio
   class TestBioFastaDefline < Test::Unit::TestCase

data/test/unit/bio/db/genbank/test_genpept.rb

@@ -12,7 +12,7 @@ load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
 
 # libraries needed for the tests
 require 'test/unit'
-require 'bio/db/genbank/genpept.rb'
+require 'bio/db/genbank/genpept'
 
 #The coverage of this class is 100%
 #It tests only the methods descripbed in the soruce class.(It dosen't test the inherited methods from NCBIDB)

data/test/unit/bio/db/kegg/test_drug.rb

@@ -12,7 +12,7 @@ load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
 
 # libraries needed for the tests
 require 'test/unit'
-require 'bio/db/kegg/drug.rb'
+require 'bio/db/kegg/drug'
 
 module Bio
   class TestBioKeggDRUG < Test::Unit::TestCase

data/test/unit/bio/db/kegg/test_genome.rb

@@ -12,7 +12,7 @@ load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
 
 # libraries needed for the tests
 require 'test/unit'
-require 'bio/db/kegg/genome.rb'
+require 'bio/db/kegg/genome'
 
 module Bio
   class TestBioKEGGGENOME_T00005 < Test::Unit::TestCase

data/test/unit/bio/db/kegg/test_glycan.rb

@@ -12,7 +12,7 @@ load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
 
 # libraries needed for the tests
 require 'test/unit'
-require 'bio/db/kegg/glycan.rb'
+require 'bio/db/kegg/glycan'
 
 module Bio
 

data/test/unit/bio/db/kegg/test_kgml.rb

@@ -0,0 +1,1022 @@
+#
+# test/unit/bio/db/kegg/test_kgml.rb - Unit test for Bio::KEGG::KGML
+#
+#              Copyright (C) 2012 Naohisa Goto <ng@bioruby.org>
+# License::    The Ruby License
+
+# loading helper routine for testing bioruby
+require 'pathname'
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+
+# libraries needed for the tests
+require 'test/unit'
+require 'bio/db/kegg/kgml'
+
+module Bio; module TestKeggKGML
+
+  filename = File.join(BioRubyTestDataPath, 'KEGG', 'test.kgml')
+  KGMLTestXMLstr = File.read(filename).freeze
+
+  class TestKGMLPathway < Test::Unit::TestCase
+    def setup
+      xmlstr = KGMLTestXMLstr
+      @obj = Bio::KEGG::KGML.new(xmlstr)
+    end
+
+    def test_name
+      assert_equal 'path:xxx09876', @obj.name
+    end
+
+    def test_org
+      assert_equal 'xxx', @obj.org
+    end
+
+    def test_number
+      assert_equal '09876', @obj.number
+    end
+
+    def test_title
+      assert_equal 'This is test title', @obj.title
+    end
+
+    def test_image
+      assert_equal 'http://example.com/pathway/ec/09876.png', @obj.image
+    end
+
+    def test_link
+      assert_equal 'http://example.com/show_pathway?xxx09876', @obj.link
+    end
+
+    def test_entries__size
+      assert_equal 3, @obj.entries.size
+    end
+
+    def test_relations__size
+      assert_equal 1, @obj.relations.size
+    end
+
+    def test_reactions__size
+      assert_equal 1, @obj.reactions.size
+    end
+
+    def test_entries=()
+      a = [ nil, nil, nil ]
+      b = [ nil, nil, nil, nil ]
+      assert_equal a, (@obj.entries = a)
+      assert_equal a, @obj.entries
+      assert_equal b, (@obj.entries = b)
+      assert_equal b, @obj.entries
+    end
+
+    def test_relations=()
+      a = [ nil, nil, nil ]
+      b = [ nil, nil, nil, nil ]
+      assert_equal a, (@obj.relations = a)
+      assert_equal a, @obj.relations
+      assert_equal b, (@obj.relations = b)
+      assert_equal b, @obj.relations
+    end
+
+    def test_reactions=()
+      a = [ nil, nil, nil ]
+      b = [ nil, nil, nil, nil ]
+      assert_equal a, (@obj.reactions = a)
+      assert_equal a, @obj.reactions
+      assert_equal b, (@obj.reactions = b)
+      assert_equal b, @obj.reactions
+    end
+  end #class TestKGMLPathway
+
+  class TestKGMLEntrySetter < Test::Unit::TestCase
+    def setup
+      @obj = Bio::KEGG::KGML::Entry.new
+    end
+
+    def test_id=()
+      assert_nil @obj.id
+      assert_equal 1234, (@obj.id = 1234)
+      assert_equal 1234, @obj.id
+      assert_equal 4567, (@obj.id = 4567)
+      assert_equal 4567, @obj.id
+    end
+
+    def test_name=()
+      assert_nil @obj.name
+      assert_equal 'cpd:C99999', (@obj.name = 'cpd:C99999')
+      assert_equal 'cpd:C99999', @obj.name
+      assert_equal 'cpd:C98765', (@obj.name = 'cpd:C98765')
+      assert_equal 'cpd:C98765', @obj.name
+    end
+
+    def test_type=()
+      assert_equal 'compound', (@obj.type = 'compound')
+      assert_equal 'compound', @obj.type
+      assert_equal 'enzyme', (@obj.type = 'enzyme')
+      assert_equal 'enzyme', @obj.type
+    end
+
+    def test_link=()
+      str1 = 'http://example.com/dbget-bin/www_bget?C99999'.freeze
+      str2 = 'http://example.com/dbget-bin/www_bget?C98765'.freeze
+      assert_equal str1, (@obj.link = str1)
+      assert_equal str1, @obj.link
+      assert_equal str2, (@obj.link = str2)
+      assert_equal str2, @obj.link
+    end
+
+    def test_reaction=()
+      assert_equal "rn:R99999", (@obj.reaction = 'rn:R99999')
+      assert_equal "rn:R99999", @obj.reaction
+      assert_equal "rn:R98765", (@obj.reaction = 'rn:R98765')
+      assert_equal "rn:R98765", @obj.reaction
+    end
+
+    def test_graphics=()
+      a = [ nil, nil ]
+      b = [ nil, nil, nil ]
+      assert_equal a, (@obj.graphics = a)
+      assert_equal a, @obj.graphics
+      assert_equal b, (@obj.graphics = b)
+      assert_equal b, @obj.graphics
+    end
+
+    def test_components=()
+      a = [ nil, nil ]
+      b = [ nil, nil, nil ]
+      assert_equal a, (@obj.components = a)
+      assert_equal a, @obj.components
+      assert_equal b, (@obj.components = b)
+      assert_equal b, @obj.components
+    end
+  end #class TestKGMLEntrySetter
+
+  # for deprecated methods/attributes
+  class TestKGMLEntrySetterDeprecated < Test::Unit::TestCase
+    def setup
+      @obj = Bio::KEGG::KGML::Entry.new
+    end
+
+    def test_entry_id=()
+      assert_nil @obj.entry_id
+      assert_equal 1234, (@obj.entry_id = 1234)
+      assert_equal 1234, @obj.entry_id
+      assert_equal 4567, (@obj.entry_id = 4567)
+      assert_equal 4567, @obj.entry_id
+
+      assert_equal 4567, @obj.id
+      @obj.id = 7890
+      assert_equal 7890, @obj.entry_id
+    end
+
+    def test_category=()
+      assert_nil @obj.category
+      assert_equal 'compound', (@obj.category = 'compound')
+      assert_equal 'compound', @obj.category
+      assert_equal 'enzyme', (@obj.category = 'enzyme')
+      assert_equal 'enzyme', @obj.category
+
+      assert_equal 'enzyme', @obj.type
+      @obj.type = 'gene'
+      assert_equal 'gene', @obj.category
+    end
+
+    def test_pathway=()
+      assert_nil @obj.pathway
+      assert_equal 'deprecated', (@obj.pathway = 'deprecated')
+      assert_equal 'deprecated', @obj.pathway
+      assert_equal "don't use", (@obj.pathway = "don't use")
+      assert_equal "don't use", @obj.pathway
+    end
+
+    def test_label=()
+      assert_nil @obj.label
+      assert_equal 'deprecated', (@obj.label = 'deprecated')
+      assert_equal 'deprecated', @obj.label
+
+      assert_equal "don't use", (@obj.label = "don't use")
+      assert_equal "don't use", @obj.label
+
+      assert_equal "don't use", @obj.graphics[-1].name
+      @obj.graphics[-1].name = 'test'
+      assert_equal 'test', @obj.label
+    end
+
+    def test_shape=()
+      assert_nil @obj.shape
+      assert_equal 'deprecated', (@obj.shape = 'deprecated')
+      assert_equal 'deprecated', @obj.shape
+
+      assert_equal "don't use", (@obj.shape = "don't use")
+      assert_equal "don't use", @obj.shape
+
+      assert_equal "don't use", @obj.graphics[-1].type
+      @obj.graphics[-1].type = 'test'
+      assert_equal 'test', @obj.shape
+    end
+
+    def test_x=()
+      assert_equal 123, (@obj.x = 123)
+      assert_equal 123, @obj.x
+
+      assert_equal 456, (@obj.x = 456)
+      assert_equal 456, @obj.x
+
+      assert_equal 456, @obj.graphics[-1].x
+      @obj.graphics[-1].x = 789
+      assert_equal 789, @obj.x
+    end
+
+    def test_y=()
+      assert_equal 123, (@obj.y = 123)
+      assert_equal 123, @obj.y
+
+      assert_equal 456, (@obj.y = 456)
+      assert_equal 456, @obj.y
+
+      assert_equal 456, @obj.graphics[-1].y
+      @obj.graphics[-1].y = 789
+      assert_equal 789, @obj.y
+    end
+
+    def test_width=()
+      assert_equal 123, (@obj.width = 123)
+      assert_equal 123, @obj.width
+
+      assert_equal 456, (@obj.width = 456)
+      assert_equal 456, @obj.width
+
+      assert_equal 456, @obj.graphics[-1].width
+      @obj.graphics[-1].width = 789
+      assert_equal 789, @obj.width
+    end
+
+    def test_height=()
+      assert_equal 123, (@obj.height = 123)
+      assert_equal 123, @obj.height
+
+      assert_equal 456, (@obj.height = 456)
+      assert_equal 456, @obj.height
+
+      assert_equal 456, @obj.graphics[-1].height
+      @obj.graphics[-1].height = 789
+      assert_equal 789, @obj.height
+    end
+
+    def test_fgcolor=()
+      assert_equal "#E0E0E0", (@obj.fgcolor = "#E0E0E0")
+      assert_equal "#E0E0E0", @obj.fgcolor
+
+      assert_equal "#FFFFFF", (@obj.fgcolor = "#FFFFFF")
+      assert_equal "#FFFFFF", @obj.fgcolor
+
+      assert_equal "#FFFFFF", @obj.graphics[-1].fgcolor
+      @obj.graphics[-1].fgcolor = "#99CCFF"
+      assert_equal "#99CCFF", @obj.fgcolor
+    end
+
+    def test_bgcolor=()
+      assert_equal "#E0E0E0", (@obj.bgcolor = "#E0E0E0")
+      assert_equal "#E0E0E0", @obj.bgcolor
+
+      assert_equal "#FFFFFF", (@obj.bgcolor = "#FFFFFF")
+      assert_equal "#FFFFFF", @obj.bgcolor
+
+      assert_equal "#FFFFFF", @obj.graphics[-1].bgcolor
+      @obj.graphics[-1].bgcolor = "#99CCFF"
+      assert_equal "#99CCFF", @obj.bgcolor
+    end
+  end #class TestKGMLEntrySetterDeprecated
+
+  class TestKGMLEntry1234 < Test::Unit::TestCase
+    def setup
+      xmlstr = KGMLTestXMLstr
+      @obj = Bio::KEGG::KGML.new(xmlstr).entries[0]
+    end
+
+    def test_id
+      assert_equal 1234, @obj.id
+    end
+
+    def test_name
+      assert_equal 'cpd:C99999', @obj.name
+    end
+
+    def test_type
+      assert_equal 'compound', @obj.type
+    end
+
+    def test_link
+      assert_equal 'http://example.com/dbget-bin/www_bget?C99999', @obj.link
+    end
+
+    def test_reaction
+      assert_equal nil, @obj.reaction
+    end
+
+    def test_graphics__size
+      assert_equal 1, @obj.graphics.size
+    end
+
+    def test_components
+      assert_equal nil, @obj.components
+    end
+  end #class TestKGMLEntry1234
+
+  class TestKGMLEntry1 < Test::Unit::TestCase
+    def setup
+      xmlstr = KGMLTestXMLstr
+      @obj = Bio::KEGG::KGML.new(xmlstr).entries[1]
+    end
+
+    def test_id
+      assert_equal 1, @obj.id
+    end
+
+    def test_name
+      assert_equal 'ec:1.1.1.1', @obj.name
+    end
+
+    def test_type
+      assert_equal 'enzyme', @obj.type
+    end
+
+    def test_link
+      assert_equal 'http://example.com/dbget-bin/www_bget?1.1.1.1', @obj.link
+    end
+
+    def test_reaction
+      assert_equal 'rn:R99999', @obj.reaction
+    end
+
+    def test_graphics__size
+      assert_equal 2, @obj.graphics.size
+    end
+
+    def test_components
+      assert_equal nil, @obj.components
+    end
+  end #class TestKGMLEntry1
+
+  # for deprecated methods/attributes
+  class TestKGMLEntry1Deprecated < Test::Unit::TestCase
+    def setup
+      xmlstr = KGMLTestXMLstr
+      @obj = Bio::KEGG::KGML.new(xmlstr).entries[1]
+    end
+
+    def test_entry_id
+      assert_equal 1, @obj.entry_id
+    end
+
+    def test_category
+      assert_equal 'enzyme', @obj.category
+    end
+
+    def test_label=()
+      assert_equal '1.1.1.1', @obj.label
+      assert_equal '1.2.3.4', (@obj.label = '1.2.3.4')
+      assert_equal '1.2.3.4', @obj.label
+      assert_equal '1.2.3.4', @obj.graphics[-1].name
+      assert_equal '9.8.7.6', (@obj.graphics[-1].name = '9.8.7.6')
+      assert_equal '9.8.7.6', @obj.label
+      # check if it doesn't modify graphics[0]
+      assert_equal '1.1.1.1', @obj.graphics[0].name
+    end
+
+    def test_shape=()
+      assert_equal 'line', @obj.shape
+      assert_equal 'circle', (@obj.shape = 'circle')
+      assert_equal 'circle', @obj.shape
+      assert_equal 'circle', @obj.graphics[-1].type
+      assert_equal 'rectangle', (@obj.graphics[-1].type = 'rectangle')
+      assert_equal 'rectangle', @obj.shape
+      # check if it doesn't modify graphics[0]
+      assert_equal 'line', @obj.graphics[0].type
+    end
+
+    def test_x=()
+      assert_equal 0, @obj.x
+
+      assert_equal 123, (@obj.x = 123)
+      assert_equal 123, @obj.x
+
+      assert_equal 456, (@obj.x = 456)
+      assert_equal 456, @obj.x
+
+      assert_equal 456, @obj.graphics[-1].x
+      @obj.graphics[-1].x = 789
+      assert_equal 789, @obj.x
+
+      # check if it doesn't modify graphics[0]
+      assert_equal 0, @obj.graphics[0].x
+    end
+
+    def test_y=()
+      assert_equal 0, @obj.y
+
+      assert_equal 123, (@obj.y = 123)
+      assert_equal 123, @obj.y
+
+      assert_equal 456, (@obj.y = 456)
+      assert_equal 456, @obj.y
+
+      assert_equal 456, @obj.graphics[-1].y
+      @obj.graphics[-1].y = 789
+      assert_equal 789, @obj.y
+
+      # check if it doesn't modify graphics[0]
+      assert_equal 0, @obj.graphics[0].y
+    end
+
+    def test_width=()
+      assert_equal 0, @obj.width
+
+      assert_equal 123, (@obj.width = 123)
+      assert_equal 123, @obj.width
+
+      assert_equal 456, (@obj.width = 456)
+      assert_equal 456, @obj.width
+
+      assert_equal 456, @obj.graphics[-1].width
+      @obj.graphics[-1].width = 789
+      assert_equal 789, @obj.width
+
+      # check if it doesn't modify graphics[0]
+      assert_equal 0, @obj.graphics[0].width
+    end
+
+    def test_height=()
+      assert_equal 0, @obj.height
+
+      assert_equal 123, (@obj.height = 123)
+      assert_equal 123, @obj.height
+
+      assert_equal 456, (@obj.height = 456)
+      assert_equal 456, @obj.height
+
+      assert_equal 456, @obj.graphics[-1].height
+      @obj.graphics[-1].height = 789
+      assert_equal 789, @obj.height
+
+      # check if it doesn't modify graphics[0]
+      assert_equal 0, @obj.graphics[0].height
+    end
+
+    def test_fgcolor=()
+      assert_equal '#FF99CC', @obj.fgcolor
+
+      assert_equal "#E0E0E0", (@obj.fgcolor = "#E0E0E0")
+      assert_equal "#E0E0E0", @obj.fgcolor
+
+      assert_equal "#E0E0E0", @obj.graphics[-1].fgcolor
+      @obj.graphics[-1].fgcolor = "#C0C0C0"
+      assert_equal "#C0C0C0", @obj.fgcolor
+
+      # check if it doesn't modify graphics[0]
+      assert_equal "#99CCFF", @obj.graphics[0].fgcolor
+    end
+
+    def test_bgcolor=()
+      assert_equal "#CC99FF", @obj.bgcolor
+
+      assert_equal "#E0E0E0", (@obj.bgcolor = "#E0E0E0")
+      assert_equal "#E0E0E0", @obj.bgcolor
+
+      assert_equal "#E0E0E0", @obj.graphics[-1].bgcolor
+      @obj.graphics[-1].bgcolor = "#C0C0C0"
+      assert_equal "#C0C0C0", @obj.bgcolor
+
+      # check if it doesn't modify graphics[0]
+      assert_equal "#FFFFFF", @obj.graphics[0].bgcolor
+    end
+  end #class TestKGMLEntry1Deprecated
+
+  class TestKGMLEntry567 < Test::Unit::TestCase
+    def setup
+      xmlstr = KGMLTestXMLstr
+      @obj = Bio::KEGG::KGML.new(xmlstr).entries[2]
+    end
+
+    def test_id
+      assert_equal 567, @obj.id
+    end
+
+    def test_name
+      assert_equal 'undefined', @obj.name
+    end
+
+    def test_type
+      assert_equal 'group', @obj.type
+    end
+
+    def test_link
+      assert_equal nil, @obj.link
+    end
+
+    def test_reaction
+      assert_equal nil, @obj.reaction
+    end
+
+    def test_graphics__size
+      assert_equal 1, @obj.graphics.size
+    end
+
+    def test_components
+      assert_equal [ 34, 56, 78, 90 ], @obj.components
+    end
+  end #class TestKGMLEntry567
+
+  class TestKGMLGraphicsSetter < Test::Unit::TestCase
+    def setup
+      @obj = Bio::KEGG::KGML::Graphics.new
+    end
+
+    def test_name=()
+      assert_equal '1.1.1.1', (@obj.name = '1.1.1.1')
+      assert_equal '1.1.1.1', @obj.name
+      assert_equal 'C99999', (@obj.name = 'C99999')
+      assert_equal 'C99999', @obj.name
+    end
+
+    def test_type=()
+      assert_equal 'line', (@obj.type = 'line')
+      assert_equal 'line', @obj.type
+      assert_equal 'circle', (@obj.type = 'circle')
+      assert_equal 'circle', @obj.type
+    end
+
+    def test_x=()
+      assert_equal 123, (@obj.x = 123)
+      assert_equal 123, @obj.x
+      assert_equal 456, (@obj.x = 456)
+      assert_equal 456, @obj.x
+    end
+
+    def test_y=()
+      assert_equal 123, (@obj.y = 123)
+      assert_equal 123, @obj.y
+      assert_equal 456, (@obj.y = 456)
+      assert_equal 456, @obj.y
+    end
+
+    def test_width=()
+      assert_equal 123, (@obj.width = 123)
+      assert_equal 123, @obj.width
+      assert_equal 456, (@obj.width = 456)
+      assert_equal 456, @obj.width
+    end
+
+    def test_height=()
+      assert_equal 123, (@obj.height = 123)
+      assert_equal 123, @obj.height
+      assert_equal 456, (@obj.height = 456)
+      assert_equal 456, @obj.height
+    end
+
+    def test_fgcolor=()
+      assert_equal "#E0E0E0", (@obj.fgcolor = "#E0E0E0")
+      assert_equal "#E0E0E0", @obj.fgcolor
+      assert_equal "#FFFFFF", (@obj.fgcolor = "#FFFFFF")
+      assert_equal "#FFFFFF", @obj.fgcolor
+    end
+
+    def test_bgcolor=()
+      assert_equal "#E0E0E0", (@obj.bgcolor = "#E0E0E0")
+      assert_equal "#E0E0E0", @obj.bgcolor
+      assert_equal "#FFFFFF", (@obj.bgcolor = "#FFFFFF")
+      assert_equal "#FFFFFF", @obj.bgcolor
+    end
+
+    def test_coords=()
+      a = [[1, 2], [3, 4]]
+      b = [[5, 6], [7, 8], [9, 10]]
+      assert_equal a, (@obj.coords = a)
+      assert_equal a, @obj.coords
+      assert_equal b, (@obj.coords = b)
+      assert_equal b, @obj.coords
+    end
+  end #class TestKGMLGraphicsSetter
+
+  class TestKGMLGraphics1234 < Test::Unit::TestCase
+    def setup
+      xmlstr = KGMLTestXMLstr
+      @obj = Bio::KEGG::KGML.new(xmlstr).entries[0].graphics[0]
+    end
+
+    def test_name
+      assert_equal 'C99999', @obj.name
+    end
+
+    def test_type
+      assert_equal 'circle', @obj.type
+    end
+
+    def test_fgcolor
+      assert_equal "#E0E0E0", @obj.fgcolor
+    end
+
+    def test_bgcolor
+      assert_equal "#D0E0F0", @obj.bgcolor
+    end
+
+    def test_x
+      assert_equal 1314, @obj.x
+    end
+
+    def test_y
+      assert_equal 1008, @obj.y
+    end
+
+    def test_width
+      assert_equal 14, @obj.width
+    end
+
+    def test_height
+      assert_equal 28, @obj.height
+    end
+
+    def test_coords
+      assert_equal nil, @obj.coords
+    end
+  end #class TestKGMLGraphics1234
+
+  class TestKGMLGraphics1_0 < Test::Unit::TestCase
+    def setup
+      xmlstr = KGMLTestXMLstr
+      @obj = Bio::KEGG::KGML.new(xmlstr).entries[1].graphics[0]
+    end
+
+    def test_name
+      assert_equal '1.1.1.1', @obj.name
+    end
+
+    def test_type
+      assert_equal 'line', @obj.type
+    end
+
+    def test_fgcolor
+      assert_equal "#99CCFF", @obj.fgcolor
+    end
+
+    def test_bgcolor
+      assert_equal "#FFFFFF", @obj.bgcolor
+    end
+
+    def test_x
+      assert_equal 0, @obj.x
+    end
+
+    def test_y
+      assert_equal 0, @obj.y
+    end
+
+    def test_width
+      assert_equal 0, @obj.width
+    end
+
+    def test_height
+      assert_equal 0, @obj.height
+    end
+
+    def test_coords
+      assert_equal [[314,159], [265,358], [979,323]], @obj.coords
+    end
+  end #class TestKGMLGraphics1_0
+
+  class TestKGMLRelationSetter < Test::Unit::TestCase
+    def setup
+      @obj = Bio::KEGG::KGML::Relation.new
+    end
+
+    def test_entry1=()
+      assert_nil @obj.entry1
+      assert_equal 123, (@obj.entry1 = 123)
+      assert_equal 123, @obj.entry1
+      assert_equal 456, (@obj.entry1 = 456)
+      assert_equal 456, @obj.entry1
+    end
+
+    def test_entry2=()
+      assert_nil @obj.entry2
+      assert_equal 123, (@obj.entry2 = 123)
+      assert_equal 123, @obj.entry2
+      assert_equal 456, (@obj.entry2 = 456)
+      assert_equal 456, @obj.entry2
+    end
+
+    def test_type=()
+      assert_nil @obj.type
+      assert_equal "ECrel", (@obj.type = "ECrel")
+      assert_equal "ECrel", @obj.type
+      assert_equal "maplink", (@obj.type = "maplink")
+      assert_equal "maplink", @obj.type
+    end
+
+    def test_name=()
+      assert_nil @obj.name
+      assert_equal "hidden compound", (@obj.name = "hidden compound")
+      assert_equal "hidden compound", @obj.name
+      assert_equal "indirect effect", (@obj.name = "indirect effect")
+      assert_equal "indirect effect", @obj.name
+    end
+
+    def test_value=()
+      assert_nil @obj.value
+      assert_equal "123", (@obj.value = "123")
+      assert_equal "123", @obj.value
+      assert_equal "-->", (@obj.value = "-->")
+      assert_equal "-->", @obj.value
+    end
+  end #class TestKGMLRelationSetter
+
+  # for deprecated methods/attributes
+  class TestKGMLRelationDeprecated < Test::Unit::TestCase
+    def setup
+      @obj = Bio::KEGG::KGML::Relation.new
+    end
+
+    def test_node1=()
+      assert_nil @obj.node1
+      assert_equal 123, (@obj.node1 = 123)
+      assert_equal 123, @obj.node1
+      assert_equal 456, (@obj.node1 = 456)
+      assert_equal 456, @obj.node1
+
+      assert_equal 456, @obj.entry1
+      @obj.entry1 = 789
+      assert_equal 789, @obj.node1
+    end
+
+    def test_node2=()
+      assert_nil @obj.node2
+      assert_equal 123, (@obj.node2 = 123)
+      assert_equal 123, @obj.node2
+      assert_equal 456, (@obj.node2 = 456)
+      assert_equal 456, @obj.node2
+
+      assert_equal 456, @obj.entry2
+      @obj.entry2 = 789
+      assert_equal 789, @obj.node2
+    end
+
+    def test_rel=()
+      assert_nil @obj.rel
+      assert_equal "ECrel", (@obj.rel = "ECrel")
+      assert_equal "ECrel", @obj.rel
+      assert_equal "maplink", (@obj.rel = "maplink")
+      assert_equal "maplink", @obj.rel
+
+      assert_equal "maplink", @obj.type
+      @obj.type = "PCrel"
+      assert_equal "PCrel", @obj.rel
+    end
+
+    def test_edge
+      @obj.value = "123"
+      assert_equal 123, @obj.edge
+    end
+  end #class TestKGMLRelationDeprecated
+
+  class TestKGMLRelation < Test::Unit::TestCase
+    def setup
+      xmlstr = KGMLTestXMLstr
+      @obj = Bio::KEGG::KGML.new(xmlstr).relations[0]
+    end
+
+    def test_entry1
+      assert_equal 109, @obj.entry1
+    end
+
+    def test_entry2
+      assert_equal 87, @obj.entry2
+    end
+
+    def test_type
+      assert_equal "ECrel", @obj.type
+    end
+
+    def test_name
+      assert_equal "compound", @obj.name
+    end
+
+    def test_value
+      assert_equal "100", @obj.value
+    end
+  end #class TestKGMLRelation
+
+  class TestKGMLReactionSetter < Test::Unit::TestCase
+    def setup
+      @obj = Bio::KEGG::KGML::Reaction.new
+    end
+
+    def test_id=()
+      assert_nil @obj.id
+      assert_equal 1234, (@obj.id = 1234)
+      assert_equal 1234, @obj.id
+      assert_equal 4567, (@obj.id = 4567)
+      assert_equal 4567, @obj.id
+    end
+
+    def test_name=()
+      assert_nil @obj.name
+      assert_equal 'rn:R99999 rn:R99998',
+      (@obj.name = 'rn:R99999 rn:R99998')
+      assert_equal 'rn:R99999 rn:R99998', @obj.name
+      assert_equal 'rn:R98765 rn:R98764',
+      (@obj.name = 'rn:R98765 rn:R98764')
+      assert_equal 'rn:R98765 rn:R98764', @obj.name
+    end
+
+    def test_type=()
+      assert_nil @obj.type
+      assert_equal 'reversible', (@obj.type = 'reversible')
+      assert_equal 'reversible', @obj.type
+      assert_equal 'irreversible', (@obj.type = 'irreversible')
+      assert_equal 'irreversible', @obj.type
+    end
+
+    def test_substraces=()
+      assert_nil @obj.substrates
+      a = [ nil, nil ]
+      b = [ nil, nil, nil ]
+      assert_equal a, (@obj.substrates = a)
+      assert_equal a, @obj.substrates
+      assert_equal b, (@obj.substrates = b)
+      assert_equal b, @obj.substrates
+    end
+
+    def test_products=()
+      assert_nil @obj.products
+      a = [ nil, nil ]
+      b = [ nil, nil, nil ]
+      assert_equal a, (@obj.products = a)
+      assert_equal a, @obj.products
+      assert_equal b, (@obj.products = b)
+      assert_equal b, @obj.products
+    end
+
+    # TODO: add tests for alt
+  end #class TestKGMLReactionSetter
+
+  class TestKGMLReactionSetterDeprecated < Test::Unit::TestCase
+    def setup
+      @obj = Bio::KEGG::KGML::Reaction.new
+    end
+
+    def test_entry_id=()
+      assert_nil @obj.entry_id
+      assert_equal "rn:R99999 rn:R99998",
+      (@obj.entry_id = "rn:R99999 rn:R99998")
+      assert_equal "rn:R99999 rn:R99998", @obj.entry_id
+      assert_equal "rn:R99990 rn:R99991",
+      (@obj.entry_id = "rn:R99990 rn:R99991")
+      assert_equal "rn:R99990 rn:R99991", @obj.entry_id
+
+      assert_equal "rn:R99990 rn:R99991", @obj.name
+      @obj.name = "rn:R98765 rn:R98766"
+      assert_equal "rn:R98765 rn:R98766", @obj.entry_id
+    end
+
+    def test_direction=()
+      assert_nil @obj.direction
+      assert_equal 'reversible', (@obj.direction = 'reversible')
+      assert_equal 'reversible', @obj.direction
+      assert_equal 'irreversible', (@obj.direction = 'irreversible')
+      assert_equal 'irreversible', @obj.direction
+
+      assert_equal 'irreversible', @obj.type
+      @obj.type = 'this is test'
+      assert_equal 'this is test', @obj.direction
+    end
+  end #class TestKGMLReactionSetterDreprecated
+
+  class TestKGMLReaction < Test::Unit::TestCase
+    def setup
+      xmlstr = KGMLTestXMLstr
+      @obj = Bio::KEGG::KGML.new(xmlstr).reactions[0]
+    end
+
+    def test_id
+      assert_equal 3, @obj.id
+    end
+
+    def test_name
+      assert_equal "rn:R99999 rn:R99998", @obj.name
+    end
+
+    def test_type
+      assert_equal "reversible", @obj.type
+    end
+
+    def test_substrates
+      assert_equal [ "cpd:C99990", "cpd:C99991" ],
+      @obj.substrates.collect { |x| x.name }
+
+      assert_equal [ 3330, 3331 ],
+      @obj.substrates.collect { |x| x.id }
+    end
+
+    def test_products
+      assert_equal [ "cpd:C99902", "cpd:C99903" ],
+      @obj.products.collect { |x| x.name }
+
+      assert_equal [ 3332, 3333 ],
+      @obj.products.collect { |x| x.id }
+    end
+  end #class TestKGMLReaction
+
+  class TestKGMLSubstrate < Test::Unit::TestCase
+    def setup
+      xmlstr = KGMLTestXMLstr
+      @obj0 = Bio::KEGG::KGML.new(xmlstr).reactions[0].substrates[0]
+      @obj1 = Bio::KEGG::KGML.new(xmlstr).reactions[0].substrates[1]
+    end
+
+    def test_id
+      assert_equal 3330, @obj0.id
+      assert_equal 3331, @obj1.id
+    end
+
+    def test_name
+      assert_equal 'cpd:C99990', @obj0.name
+      assert_equal 'cpd:C99991', @obj1.name
+    end
+  end #class TestKGMLSubstrate
+
+  class TestKGMLProduct < Test::Unit::TestCase
+    def setup
+      xmlstr = KGMLTestXMLstr
+      @obj0 = Bio::KEGG::KGML.new(xmlstr).reactions[0].products[0]
+      @obj1 = Bio::KEGG::KGML.new(xmlstr).reactions[0].products[1]
+    end
+
+    def test_id
+      assert_equal 3332, @obj0.id
+      assert_equal 3333, @obj1.id
+    end
+
+    def test_name
+      assert_equal 'cpd:C99902', @obj0.name
+      assert_equal 'cpd:C99903', @obj1.name
+    end
+  end #class TestKGMLProduct
+
+  module TestKGMLSubstrateProductSetterMethods
+    def test_initialize_0
+      assert_nil @obj.id
+      assert_nil @obj.name
+    end
+
+    def test_initialize_1
+      obj = Bio::KEGG::KGML::SubstrateProduct.new(123)
+      assert_equal 123, obj.id
+      assert_nil obj.name
+    end
+
+    def test_initialize_2
+      obj = Bio::KEGG::KGML::SubstrateProduct.new(123, 'test')
+      assert_equal 123, obj.id
+      assert_equal 'test', obj.name
+    end
+
+    def test_id=()
+      assert_nil @obj.id
+      assert_equal 123, (@obj.id = 123)
+      assert_equal 123, @obj.id
+      assert_equal 456, (@obj.id = 456)
+      assert_equal 456, @obj.id
+    end
+
+    def test_name=()
+      assert_nil @obj.name
+      assert_equal "cpd:C99990", (@obj.name = "cpd:C99990")
+      assert_equal "cpd:C99990", @obj.name
+      assert_equal "cpd:C99902", (@obj.name = "cpd:C99902")
+      assert_equal "cpd:C99902", @obj.name
+    end
+  end #module TestKGMLSubstrateProductSetterMethods
+
+  class TestKGMLSubstrateProductSetter < Test::Unit::TestCase
+    include TestKGMLSubstrateProductSetterMethods
+    def setup
+      @obj = Bio::KEGG::KGML::SubstrateProduct.new
+    end
+  end # class TestKGMLSubstrateProductSetter
+
+  class TestKGMLSubstrateSetter < Test::Unit::TestCase
+    include TestKGMLSubstrateProductSetterMethods
+    def setup
+      @obj = Bio::KEGG::KGML::Substrate.new
+    end
+  end # class TestKGMLSubstrateSetter
+
+  class TestKGMLProductSetter < Test::Unit::TestCase
+    include TestKGMLSubstrateProductSetterMethods
+    def setup
+      @obj = Bio::KEGG::KGML::Product.new
+    end
+  end # class TestKGMLProductSetter
+
+end; end #module TestKeggKGML; #module Bio
+