bio-nexml 1.0.0 → 1.1.0

Sign up to get free protection for your applications and to get access to all the features.
@@ -0,0 +1,21 @@
1
+ module Bio
2
+ module NeXML
3
+ class TestParser < Test::Unit::TestCase
4
+
5
+ def setup
6
+ @doc = Parser.new( TEST_FILE, true )
7
+ end
8
+
9
+ def teardown
10
+ @doc.close if @doc
11
+ end
12
+
13
+ def test_parse
14
+ nexml = @doc.parse
15
+ assert_instance_of Bio::NeXML::Nexml, nexml, "Should return an object of Bio::NeXML::Nexml"
16
+ end
17
+
18
+ end #end class TestParser
19
+ end #end module NeXML
20
+
21
+ end #end module Bio
@@ -0,0 +1,118 @@
1
+ module Bio
2
+ module NeXML
3
+ class TestOtu < Test::Unit::TestCase
4
+ def setup
5
+ @otu = Bio::NeXML::Otu.new( 'taxon1', :label => 'A label for taxon1' )
6
+ end
7
+
8
+ def test_id
9
+ assert_equal( 'taxon1', @otu.id )
10
+ end
11
+
12
+ def test_label
13
+ assert_equal( 'A label for taxon1', @otu.label )
14
+ end
15
+
16
+ def test_id=
17
+ @otu.id = 'taxon2'
18
+ assert_equal( 'taxon2', @otu.id )
19
+ end
20
+
21
+ def test_label=
22
+ @otu.label = 'New label for taxon1'
23
+ assert_equal( 'New label for taxon1', @otu.label )
24
+ end
25
+ end
26
+
27
+ class TestOtus < Test::Unit::TestCase
28
+ def setup
29
+ @otu1 = Bio::NeXML::Otu.new( 'taxon1', :label => 'A label for taxon1' )
30
+ @otu2 = Bio::NeXML::Otu.new( 'taxon2', :label => 'A label for taxon2' )
31
+ @otu3 = Bio::NeXML::Otu.new( 'taxon3', :label => 'A label for taxon3' )
32
+ @otus = Bio::NeXML::Otus.new( 'taxa1', :label => 'A label for taxa1' )
33
+ @otus << @otu1 << @otu2
34
+ end
35
+
36
+ def test_id
37
+ assert_equal( 'taxa1', @otus.id )
38
+ end
39
+
40
+ def test_label
41
+ assert_equal( 'A label for taxa1', @otus.label )
42
+ end
43
+
44
+ def test_id=
45
+ @otus.id = 'taxa2'
46
+ assert_equal( 'taxa2', @otus.id )
47
+ end
48
+
49
+ def test_label=
50
+ @otus.label = 'New label for taxa1'
51
+ assert_equal( 'New label for taxa1', @otus.label )
52
+ end
53
+
54
+ def test_hash_notation
55
+ assert_equal( @otu1, @otus[ 'taxon1' ] )
56
+ end
57
+
58
+ def test_append_operator
59
+ assert !@otus.include?( @otu3 )
60
+ rvalue = @otus << @otu3
61
+
62
+ # it should append otu to self
63
+ assert @otus.include?( @otu3 )
64
+
65
+ # it should return self, so that appends can be chained
66
+ assert_instance_of Otus, rvalue
67
+ end
68
+
69
+ def test_delete
70
+ rvalue = @otus.delete( @otu2 )
71
+
72
+ # it should delete @otu2
73
+ assert !@otus.include?( @otu2 )
74
+
75
+ # it should return the deleted object
76
+ assert_equal @otu2, rvalue
77
+ end
78
+
79
+ def test_otus
80
+ [ @otu1, @otu2 ].each do |otu|
81
+ @otus.otus.include?( otu )
82
+ end
83
+ end
84
+
85
+ def test_otus=
86
+ assert !@otus.include?( @otu3 )
87
+ @otus.otus = [ @otu3 ]
88
+ assert @otus.include?( @otu3 )
89
+ end
90
+
91
+ def test_each
92
+ otus = [ @otu1, @otu2 ]
93
+ @otus.each do |otu|
94
+ assert otus.include?( otu )
95
+ end
96
+ end
97
+
98
+ def test_each_with_id
99
+ otus = [ @otu1, @otu2 ]
100
+ @otus.each_with_id do |id, otu|
101
+ assert otus.include?( otu )
102
+ assert otus.include?( @otus[ id ] )
103
+ end
104
+ end
105
+
106
+ def test_length
107
+ assert_equal 2, @otus.length
108
+ end
109
+
110
+ def test_include
111
+ # it should respond for an otu object
112
+ assert @otus.include?( @otu1 )
113
+
114
+ assert !@otus.include?( @otu3 )
115
+ end
116
+ end
117
+ end
118
+ end
@@ -0,0 +1,370 @@
1
+ class TestNode < Test::Unit::TestCase
2
+ def setup
3
+ @otu = Bio::NeXML::Otu.new( 'o1' )
4
+ @node = Bio::NeXML::Node.new( 'n1' )
5
+ @node.otu = @otu
6
+ end
7
+
8
+ def test_id
9
+ @node.id = 'foo'
10
+ assert_equal( 'foo', @node.id )
11
+ end
12
+
13
+ def test_label
14
+ @node.label = 'a node'
15
+ assert_equal( 'a node', @node.label )
16
+ end
17
+
18
+ def test_root?
19
+ assert( !@node.root? )
20
+ end
21
+
22
+ def test_root=
23
+ @node.root = true
24
+ assert( @node.root )
25
+ end
26
+
27
+ def test_otu
28
+ otu = Bio::NeXML::Otu.new( 'o2' )
29
+ @node.otu = otu
30
+
31
+ assert_equal( otu, @node.otu )
32
+ assert_equal( otu.nodes, [ @node ] )
33
+ end
34
+
35
+ end
36
+
37
+ class TestEdge < Test::Unit::TestCase
38
+ def setup
39
+ @n1 = Bio::NeXML::Node.new( 'n1' )
40
+ @n2 = Bio::NeXML::Node.new( 'n2' )
41
+ @edge = Bio::NeXML::Edge.new( 'e1', :source => @n1, :target => @n2 )
42
+ end
43
+
44
+ def test_id
45
+ @edge.id = 'e2'
46
+ assert_equal( 'e2', @edge.id )
47
+ end
48
+
49
+ def test_label
50
+ @edge.label = 'an edge'
51
+ assert_equal( 'an edge', @edge.label )
52
+ end
53
+
54
+ def test_source
55
+ n3 = Bio::NeXML::Node.new( 'n3' )
56
+ @edge.source = n3
57
+ assert_equal( n3, @edge.source )
58
+ end
59
+
60
+ def test_target
61
+ n3 = Bio::NeXML::Node.new( 'n3' )
62
+ @edge.target = n3
63
+ assert_equal( n3, @edge.target )
64
+ end
65
+
66
+ def test_length
67
+ @edge.length = 1
68
+ assert_equal( 1, @edge.length )
69
+ end
70
+ end
71
+
72
+ class TestRootEdge < TestEdge
73
+ def setup
74
+ @edge = Bio::NeXML::RootEdge.new( 're1', :target => @n1 )
75
+ end
76
+
77
+ def test_source
78
+ assert !@re.respond_to?( :source= )
79
+ end
80
+ end
81
+
82
+ class TestTree < Test::Unit::TestCase
83
+
84
+ def setup
85
+ @roots = %w|n1 n9|.map { |n| Bio::NeXML::Node.new( n, :root => true ) }
86
+ @nodes = %w|n2 n3 n4 n5 n6 n7 n8|.map { |n| Bio::NeXML::Node.new( n ) }
87
+ @nodes = @nodes + @roots
88
+
89
+ @edges = %w|e12 e13 e34 e37 e45 e46 e78 e79|.map do |e|
90
+ source = @nodes.find { |n| n.id == "n#{e[1,1]}" }
91
+ target = @nodes.find { |n| n.id == "n#{e[2,1]}" }
92
+ Bio::NeXML::Edge.new( e, :source => source, :target => target )
93
+ end
94
+
95
+ @re = Bio::NeXML::RootEdge.new( 're1', :target => @n1 )
96
+
97
+ @tree = Bio::NeXML::Tree.new( 'tree1', :nodes => @nodes, :edges => @edges, :rootedge => @re )
98
+ end
99
+
100
+ def test_id
101
+ assert_equal( 'tree1', @tree.id )
102
+ @tree.id = 'tree2'
103
+ assert_equal( 'tree2', @tree.id )
104
+ end
105
+
106
+ def test_label
107
+ assert_nil( @tree.label )
108
+ @tree.label = 'a tree'
109
+ assert_equal( 'a tree', @tree.label )
110
+ end
111
+
112
+ def test_rootedge
113
+ assert_equal( @re, @tree.rootedge )
114
+ re = Bio::NeXML::RootEdge.new( 're2', :target => @n9 )
115
+ @tree.rootedge = re
116
+ assert_equal( re, @tree.rootedge )
117
+ end
118
+
119
+ def test_roots
120
+ @roots.each do |r|
121
+ assert @tree.roots.include?( r )
122
+ end
123
+ end
124
+
125
+ def test_add_node
126
+ node = Bio::NeXML::Node.new( 'node' )
127
+ @tree.add_node( node )
128
+ assert @tree.include?( node )
129
+ assert_equal( @tree, node.tree )
130
+ end
131
+
132
+ def test_add_edge
133
+ node1 = Bio::NeXML::Node.new( 'node1' )
134
+ node2 = Bio::NeXML::Node.new( 'node2' )
135
+ edge = Bio::NeXML::Edge.new( 'edge', :source => node1, :target => node2 )
136
+ @tree << node1 << node2 << edge
137
+
138
+ assert @tree.include?( edge )
139
+ assert_equal( @tree, edge.tree )
140
+ end
141
+
142
+ def test_delete_node
143
+ n = @nodes[ 2 ]
144
+ @tree.delete_node( n )
145
+ assert !@tree.include?( n )
146
+ end
147
+
148
+ def test_delete_edge
149
+ @tree.delete_edge( @edges[ 1 ] )
150
+ assert !@tree.include?( @edges[ 1 ] )
151
+ end
152
+
153
+ def test_append_operator
154
+ n10 = Bio::NeXML::Node.new( 'n10' )
155
+ e9 = Bio::NeXML::Edge.new( 'e9', :source => @n9, :target => n10 )
156
+
157
+ @tree << n10
158
+ @tree << e9
159
+
160
+ @tree.include?( n10 )
161
+ @tree.include?( e9 )
162
+ end
163
+
164
+ def test_get_node_by_id
165
+ assert_equal( @nodes[ 0 ], @tree.get_node_by_id( 'n2' ) )
166
+ end
167
+
168
+ def test_get_edge_by_id
169
+ assert_equal( @edges[ 0 ], @tree.get_edge_by_id( 'e12' ) )
170
+ end
171
+
172
+ def test_hash_notation
173
+ assert_equal( @nodes[ 0 ], @tree[ 'n2' ] )
174
+ assert_equal( @edges[ 0 ], @tree[ 'e12' ] )
175
+ end
176
+
177
+ def test_has_node
178
+ assert @tree.has_node?( @nodes[ 0 ] )
179
+ assert !@tree.has_node?( Bio::NeXML::Node.new( 'foo' ) )
180
+ end
181
+
182
+ def test_has_edge
183
+ assert @tree.has_edge?( @edges[ 0 ] )
184
+ assert !@tree.has_edge?( Bio::NeXML::Edge.new( 'foo' ) )
185
+ end
186
+
187
+ def test_include
188
+ assert @tree.include?( @nodes[ 0 ] )
189
+ assert @tree.include?( @edges[ 0 ] )
190
+ end
191
+
192
+ def test_each_node
193
+ c = 0
194
+ @tree.each_node do |n|
195
+ assert @tree.include?( n )
196
+ c +=1
197
+ end
198
+ assert(@tree.number_of_nodes, c.to_s)
199
+ end
200
+
201
+ def test_each_node_with_id
202
+ c = 0
203
+ @tree.each_node_with_id do |i, n|
204
+ assert @tree.include?( n )
205
+ assert_equal( n.id, i )
206
+ c +=1
207
+ end
208
+ assert @tree.number_of_nodes, c.to_s
209
+ end
210
+
211
+ def test_each_edge
212
+ c = 0
213
+ @tree.each_edge do |e|
214
+ assert @tree.include?( e )
215
+ c +=1
216
+ end
217
+ assert @tree.number_of_edges, c.to_s
218
+ end
219
+
220
+ def test_each_edge_with_id
221
+ c = 0
222
+ @tree.each_edge_with_id do |i, e|
223
+ assert @tree.include?( e )
224
+ assert_equal( e.id, i )
225
+ c +=1
226
+ end
227
+ assert @tree.number_of_edges, c.to_s
228
+ end
229
+ end #end class TestTree
230
+
231
+ class TestTrees < Test::Unit::TestCase
232
+
233
+ def setup
234
+ @otus = Bio::NeXML::Otus.new( 'o1' )
235
+ @tree = Bio::NeXML::Tree.new( 't1' )
236
+ @network = Bio::NeXML::Network.new( 'n1' )
237
+ @trees = Bio::NeXML::Trees.new( 'trees1', :label => 'Tree container' )
238
+ @trees.add_tree( @tree )
239
+ @trees.add_network( @network )
240
+ end
241
+
242
+ def test_id
243
+ @trees.id = 'trees2'
244
+ assert_equal( 'trees2', @trees.id )
245
+ end
246
+
247
+ def test_label
248
+ @trees.label = 'Label changed'
249
+ assert_equal( 'Label changed', @trees.label )
250
+ end
251
+
252
+ def test_hash_notation
253
+ assert_equal( @trees[ 't1' ], @tree )
254
+ assert_equal( @trees[ 'n1' ], @network )
255
+ assert_nil( @trees[ 'foo' ] )
256
+ end
257
+
258
+ def test_append_operator
259
+ tree = Bio::NeXML::Tree.new( 't2' )
260
+ network = Bio::NeXML::Tree.new( 'n2' )
261
+
262
+ @trees << tree << network
263
+
264
+ assert( @trees.include?( tree ) )
265
+ assert( @trees.include?( network ) )
266
+
267
+ assert_equal( @trees, tree.trees )
268
+ assert_equal( @trees, network.trees )
269
+ end
270
+
271
+ def test_trees
272
+ assert_equal( [ @tree ], @trees.trees )
273
+ end
274
+
275
+ def test_network
276
+ assert_equal( [ @network ], @trees.networks )
277
+ end
278
+
279
+ def test_add_tree
280
+ tree = Bio::NeXML::Tree.new( 't2' )
281
+ @trees << tree
282
+ assert( @trees.include?( tree ) )
283
+ assert_equal( @trees, tree.trees )
284
+ end
285
+
286
+ def test_add_network
287
+ network = Bio::NeXML::Tree.new( 'n2' )
288
+ @trees << network
289
+ assert( @trees.include?( network ) )
290
+ assert_equal( @trees, network.trees )
291
+ end
292
+
293
+ def test_has_tree?
294
+ assert( @trees.has_tree?( @tree ) )
295
+ end
296
+
297
+ def test_has_network?
298
+ assert( @trees.has_network?( @network ) )
299
+ end
300
+
301
+ def test_include?
302
+ assert( @trees.include?( @tree ) )
303
+ assert( @trees.include?( @network ) )
304
+ assert( !@trees.include?( Bio::NeXML::Tree.new( 'foo' ) ) )
305
+ end
306
+
307
+ def test_number_of_trees
308
+ assert_equal( 1, @trees.number_of_trees )
309
+ end
310
+
311
+ def test_number_of_networks
312
+ assert_equal( 1, @trees.number_of_networks )
313
+ end
314
+
315
+ def test_count
316
+ assert_equal 2, @trees.count
317
+ end
318
+
319
+ def test_get_tree_by_id
320
+ assert_not_nil @trees.get_tree_by_id 't1'
321
+ assert_nil @trees.get_tree_by_id 'foo'
322
+ end
323
+
324
+ def test_get_network_by_id
325
+ assert_not_nil @trees.get_network_by_id 'n1'
326
+ assert_nil @trees.get_network_by_id 'foo'
327
+ end
328
+
329
+ def test_each_tree
330
+ c = 0
331
+ @trees.each_tree {|t| c+=1 }
332
+ assert_equal 1, c
333
+ end
334
+
335
+ def test_each_network
336
+ c = 0
337
+ @trees.each_network {|t| c+=1 }
338
+ assert_equal 1, c
339
+ end
340
+
341
+ def test_each
342
+ c = 0
343
+ @trees.each {|t| c+=1 }
344
+ assert_equal 2, c
345
+ end
346
+
347
+ end #end class TestTrees
348
+
349
+ #class TestTree < Test::Unit::TestCase
350
+
351
+ #def setup
352
+ #@tree = Bio::NeXML::Tree.new 'tree'
353
+ #end
354
+
355
+ #def teardown
356
+ #@tree = nil
357
+ #end
358
+
359
+ #def test_add_rootedge
360
+ #target = Bio::NeXML::Node.new 'node1'
361
+ #re = Bio::NeXML::RootEdge.new 're1', target, 2
362
+ #@tree.add_rootedge re
363
+ #assert @tree.rootedge
364
+ #end
365
+
366
+ #def test_target_cache
367
+ #assert_instance_of Array, @tree.target_cache
368
+ #end
369
+
370
+ #end