Mercurial > repos > yufei-luo > s_mart

comparison commons/core/coord/test/Test_Set.py @ 6:769e306b7933

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author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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5:ea3082881bf8 6:769e306b7933
1 # Copyright INRA (Institut National de la Recherche Agronomique)
2 # http://www.inra.fr
3 # http://urgi.versailles.inra.fr
4 #
5 # This software is governed by the CeCILL license under French law and
6 # abiding by the rules of distribution of free software. You can use,
7 # modify and/ or redistribute the software under the terms of the CeCILL
8 # license as circulated by CEA, CNRS and INRIA at the following URL
9 # "http://www.cecill.info".
10 #
11 # As a counterpart to the access to the source code and rights to copy,
12 # modify and redistribute granted by the license, users are provided only
13 # with a limited warranty and the software's author, the holder of the
14 # economic rights, and the successive licensors have only limited
15 # liability.
16 #
17 # In this respect, the user's attention is drawn to the risks associated
18 # with loading, using, modifying and/or developing or reproducing the
19 # software by the user in light of its specific status of free software,
20 # that may mean that it is complicated to manipulate, and that also
21 # therefore means that it is reserved for developers and experienced
22 # professionals having in-depth computer knowledge. Users are therefore
23 # encouraged to load and test the software's suitability as regards their
24 # requirements in conditions enabling the security of their systems and/or
25 # data to be ensured and, more generally, to use and operate it in the
26 # same conditions as regards security.
27 #
28 # The fact that you are presently reading this means that you have had
29 # knowledge of the CeCILL license and that you accept its terms.
30
31
32 import unittest
33 import os
34 from commons.core.coord.Set import Set
35 from commons.core.coord.Map import Map
36
37
38 class Test_Set( unittest.TestCase ):
39
40 def test__eq__sets_equals(self):
41 set1 = Set( 1, "set1", "seq1", 1, 2 )
42 set2 = Set( 1, "set1", "seq1", 1 ,2 )
43 self.assertEquals( set1, set2 )
44
45 def test__eq__sets_not_equals_ids(self):
46 set1 = Set( 1, "set1", "seq1", 1, 2 )
47 set2 = Set( 2, "set1", "seq1", 1 ,2 )
48 self.assertNotEquals( set1, set2 )
49
50 def test__eq__sets_not_equals_name(self):
51 set1 = Set( 1, "set1", "seq1", 1, 2 )
52 set2 = Set( 1, "set2", "seq1", 1 ,2 )
53 self.assertNotEquals( set1, set2 )
54
55 def test__eq__on_empty_set(self):
56 set1 = Set()
57 set2 = Set()
58 self.assertEquals( set1, set2 )
59
60 def test_setFromTuple_equals_instances(self):
61 tuple = ( 1, "set1", "seq1", 1, 2 )
62 obsSet = Set()
63 obsSet.setFromTuple(tuple)
64 expSet = Set( 1, "set1", "seq1", 1, 2 )
65 self.assertEquals( expSet, obsSet )
66
67 def test_setFromTuple_not_equals_instances(self):
68 tuple = ( 1, "set1", "seq1", 1, 2 )
69 obsSet = Set()
70 obsSet.setFromTuple(tuple)
71 expSet = Set( 2, "set1", "seq1", 1, 2 )
72 self.assertNotEquals( expSet, obsSet )
73
74 def test_read_empty_line_file(self):
75 fileName = "dummyFile"
76
77 os.system(" touch " + fileName)
78
79 fileHandler = open(fileName, "r")
80
81 obsSet = Set()
82
83 obsRes = obsSet.read( fileHandler )
84 expRes = 0
85
86 fileHandler.close()
87 os.remove(fileName)
88
89 self.assertEquals( expRes, obsRes )
90
91 def test_read_one_line_file(self):
92 line = ( "1\tset1\tseq1\t1\t2" )
93 fileName = "dummyFile"
94
95 fileHandler = open( fileName, "w" )
96 fileHandler.write( line )
97 fileHandler.close()
98
99 fileHandler = open( fileName, "r" )
100
101 tuple = line.split("\t")
102 expSet = Set()
103 expSet.setFromTuple(tuple)
104
105 obsSet = Set()
106
107 expRes = 1
108 obsRes = obsSet.read(fileHandler)
109
110 fileHandler.close()
111 os.remove(fileName)
112 self.assertEquals( expRes, obsRes )
113 self.assertEquals( expSet, obsSet )
114
115 def test_read_two_line_file(self):
116 line1 = ( "1\tset1\tseq1\t1\t2\n" )
117 line2 = ( "2\tset2\tseq2\t3\t4" )
118 fileName = "dummyFile"
119
120 fileHandler = open( fileName, "w" )
121 fileHandler.write( line1 )
122 fileHandler.write( line2 )
123 fileHandler.close()
124
125 tuple1 = line1.split("\t")
126 tuple2 = line2.split("\t")
127
128 expSet1 = Set()
129 expSet2 = Set()
130
131 expSet1.setFromTuple(tuple1)
132 expSet2.setFromTuple(tuple2)
133
134 expSetList = [ expSet1, expSet2 ]
135 expResList = [ 1, 1 ]
136
137 fileHandler = open( fileName, "r" )
138
139 obsSet1 = Set()
140 obsSet2 = Set()
141
142 obsRes1 = obsSet1.read(fileHandler)
143 obsRes2 = obsSet2.read(fileHandler)
144
145 obsSetList= [ obsSet1, obsSet2 ]
146 obsResList = [ obsRes1, obsRes2 ]
147
148 fileHandler.close()
149 os.remove(fileName)
150
151 self.assertEquals( expSetList, obsSetList )
152 self.assertEquals( expResList, obsResList )
153
154 def test_merge_first_id_greater_than_second_id(self):
155 firstSet = Set( 2, "set1", "seq1", 10, 40 )
156 secondSet = Set( 1, "set2", "seq1", 20, 60 )
157
158 firstSet.merge( secondSet )
159
160 expSet = Set( 1, "set1", "seq1", 10, 60)
161 obsSet = firstSet
162
163 self.assertEquals( expSet, obsSet)
164
165 def test_merge_first_id_smaller_than_second_id(self):
166 firstSet = Set( 1, "set1", "seq1", 10, 40 )
167 secondSet = Set( 2, "set2", "seq1", 20, 60 )
168
169 firstSet.merge( secondSet )
170
171 expSet = Set( 1, "set1", "seq1", 10, 60)
172 obsSet = firstSet
173
174 self.assertEquals( expSet, obsSet)
175
176 def test_merge_first_id_equals_second_id(self):
177 firstSet = Set( 1, "set1", "seq1", 10, 40 )
178 secondSet = Set( 1, "set2", "seq1", 20, 60 )
179
180 firstSet.merge( secondSet )
181
182 expSet = Set( 1, "set1", "seq1", 10, 60)
183 obsSet = firstSet
184
185 self.assertEquals( expSet, obsSet)
186
187 def test_merge_different_seqnames(self):
188 firstSet = Set( 2, "set1", "seq1", 10, 40 )
189 secondSet = Set( 1, "set1", "seq2", 20, 60 )
190 expSet = Set( 2, "set1", "seq1", 10, 40 )
191 firstSet.merge( secondSet )
192 obsSet = firstSet
193 self.assertEquals( expSet, obsSet )
194
195 def test_diff_on_empty_sets(self):
196 firstSet = Set()
197 firstSet.seqname = "seq1"
198 secondSet = Set()
199 secondSet.seqname = "seq2"
200
201 obsSet = firstSet.diff( secondSet )
202 expSet = Set()
203
204 self.assertEquals( expSet, obsSet )
205
206 def test_diff(self):
207 firstSet = Set( 2, "set1", "seq1", 10, 80 )
208 secondSet = Set( 1, "set2", "seq1", 20, 60 )
209
210 expSet1 = Set( 2, "set1", "seq1", 10, 19 )
211 expSet2 = Set( 2, "set1", "seq1", 61, 80 )
212
213 obsSet2 = firstSet.diff( secondSet )
214 obsSet1 = firstSet
215
216 self.assertEquals( expSet1, obsSet1 )
217 self.assertEquals( expSet2, obsSet2 )
218
219 def test_diff_reverse(self):
220 firstSet = Set( 2, "set1", "seq1", 20, 60 )
221 secondSet = Set( 1, "set2", "seq1", 10, 80 )
222
223 expSet1 = Set( 2, "set1", "seq1", 0, 0 )
224 expSet2 = Set( )
225
226 obsSet2 = firstSet.diff( secondSet )
227 obsSet1 = firstSet
228
229 self.assertEquals( expSet1, obsSet1 )
230 self.assertEquals( expSet2, obsSet2 )
231
232 def test_diff_list1_overlap_end_list2(self):
233 firstSet = Set( 2, "set1", "seq1", 20, 100 )
234 secondSet = Set( 1, "set2", "seq1", 10, 80 )
235
236 expSet1 = Set( 2, "set1", "seq1", 81, 100 )
237 expSet2 = Set( )
238
239 obsSet2 = firstSet.diff( secondSet )
240 obsSet1 = firstSet
241
242 self.assertEquals( expSet1, obsSet1 )
243 self.assertEquals( expSet2, obsSet2 )
244
245 def test_diff_with_empty_set1(self):
246 set2 = Set( 1, "set1", "seq1", 2, 45 )
247 set1 = Set( )
248
249 expSet1 = Set( )
250 expSet2 = Set( )
251
252 obsSet2 = set1.diff( set2 )
253 obsSet1 = set1
254
255 self.assertEquals( expSet1, obsSet1 )
256 self.assertEquals( expSet2, obsSet2 )
257
258 def test_diff_list2_overlap_end_list1(self):
259 firstSet = Set( 2, "set1", "seq1", 10, 70 )
260 secondSet = Set( 1, "set2", "seq1", 40, 100 )
261
262 expSet1 = Set( 2, "set1", "seq1", 10, 39 )
263 expSet2 = Set( )
264
265 obsSet2 = firstSet.diff( secondSet )
266 obsSet1 = firstSet
267
268 self.assertEquals( expSet1, obsSet1 )
269 self.assertEquals( expSet2, obsSet2 )
270
271 def test_set2map(self):
272 set = Set( 1, "set", "seq", 1, 2 )
273
274 expMap = Map( "set::1", "seq", 1, 2 )
275 obsMap = set.set2map()
276
277 self.assertEquals( expMap, obsMap )
278
279 test_suite = unittest.TestSuite()
280 test_suite.addTest( unittest.makeSuite( Test_Set ) )
281 if __name__ == "__main__":
282 unittest.TextTestRunner(verbosity=2).run( test_suite )