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

Change the repository level.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/coord/test/Test_Set.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,282 @@
+# Copyright INRA (Institut National de la Recherche Agronomique)
+# http://www.inra.fr
+# http://urgi.versailles.inra.fr
+#
+# This software is governed by the CeCILL license under French law and
+# abiding by the rules of distribution of free software.  You can  use, 
+# modify and/ or redistribute the software under the terms of the CeCILL
+# license as circulated by CEA, CNRS and INRIA at the following URL
+# "http://www.cecill.info". 
+#
+# As a counterpart to the access to the source code and  rights to copy,
+# modify and redistribute granted by the license, users are provided only
+# with a limited warranty  and the software's author,  the holder of the
+# economic rights,  and the successive licensors  have only  limited
+# liability. 
+#
+# In this respect, the user's attention is drawn to the risks associated
+# with loading,  using,  modifying and/or developing or reproducing the
+# software by the user in light of its specific status of free software,
+# that may mean  that it is complicated to manipulate,  and  that  also
+# therefore means  that it is reserved for developers  and  experienced
+# professionals having in-depth computer knowledge. Users are therefore
+# encouraged to load and test the software's suitability as regards their
+# requirements in conditions enabling the security of their systems and/or 
+# data to be ensured and,  more generally, to use and operate it in the 
+# same conditions as regards security. 
+#
+# The fact that you are presently reading this means that you have had
+# knowledge of the CeCILL license and that you accept its terms.
+
+
+import unittest
+import os
+from commons.core.coord.Set import Set
+from commons.core.coord.Map import Map
+
+
+class Test_Set( unittest.TestCase ):
+    
+    def test__eq__sets_equals(self):
+        set1 = Set( 1, "set1", "seq1", 1, 2 )
+        set2 = Set( 1, "set1", "seq1", 1 ,2 )   
+        self.assertEquals( set1, set2 )
+        
+    def test__eq__sets_not_equals_ids(self):
+        set1 = Set( 1, "set1", "seq1", 1, 2 )
+        set2 = Set( 2, "set1", "seq1", 1 ,2 )   
+        self.assertNotEquals( set1, set2 )
+        
+    def test__eq__sets_not_equals_name(self):
+        set1 = Set( 1, "set1", "seq1", 1, 2 )
+        set2 = Set( 1, "set2", "seq1", 1 ,2 )   
+        self.assertNotEquals( set1, set2 )
+    
+    def test__eq__on_empty_set(self):
+        set1 = Set()
+        set2 = Set()
+        self.assertEquals( set1, set2 )
+        
+    def test_setFromTuple_equals_instances(self):
+        tuple = ( 1, "set1", "seq1", 1, 2 )
+        obsSet = Set()
+        obsSet.setFromTuple(tuple)
+        expSet = Set( 1, "set1", "seq1", 1, 2 )
+        self.assertEquals( expSet, obsSet )
+   
+    def test_setFromTuple_not_equals_instances(self):
+        tuple = ( 1, "set1", "seq1", 1, 2 )
+        obsSet = Set()
+        obsSet.setFromTuple(tuple)
+        expSet = Set( 2, "set1", "seq1", 1, 2 )
+        self.assertNotEquals( expSet, obsSet )
+        
+    def test_read_empty_line_file(self):
+        fileName = "dummyFile"
+        
+        os.system(" touch " + fileName)
+        
+        fileHandler = open(fileName, "r")
+        
+        obsSet = Set()
+        
+        obsRes = obsSet.read( fileHandler )
+        expRes = 0
+        
+        fileHandler.close()
+        os.remove(fileName)
+        
+        self.assertEquals( expRes, obsRes )
+
+    def test_read_one_line_file(self):
+        line = ( "1\tset1\tseq1\t1\t2" )
+        fileName = "dummyFile"
+        
+        fileHandler = open( fileName, "w" )
+        fileHandler.write( line )
+        fileHandler.close()
+        
+        fileHandler = open( fileName, "r" )
+        
+        tuple = line.split("\t")
+        expSet = Set()
+        expSet.setFromTuple(tuple)
+        
+        obsSet = Set()
+        
+        expRes = 1
+        obsRes = obsSet.read(fileHandler)
+        
+        fileHandler.close()
+        os.remove(fileName)
+        self.assertEquals( expRes, obsRes )
+        self.assertEquals( expSet, obsSet ) 
+        
+    def test_read_two_line_file(self):
+        line1 = ( "1\tset1\tseq1\t1\t2\n" )
+        line2 = ( "2\tset2\tseq2\t3\t4" )
+        fileName = "dummyFile"
+        
+        fileHandler = open( fileName, "w" )
+        fileHandler.write( line1 )
+        fileHandler.write( line2 )
+        fileHandler.close()
+        
+        tuple1 = line1.split("\t")
+        tuple2 = line2.split("\t")
+        
+        expSet1 = Set()
+        expSet2 = Set()
+        
+        expSet1.setFromTuple(tuple1)
+        expSet2.setFromTuple(tuple2)
+        
+        expSetList = [ expSet1, expSet2 ]
+        expResList = [ 1, 1 ]
+        
+        fileHandler = open( fileName, "r" )
+        
+        obsSet1 = Set()
+        obsSet2 = Set()
+
+        obsRes1 = obsSet1.read(fileHandler)
+        obsRes2 = obsSet2.read(fileHandler)
+        
+        obsSetList= [ obsSet1, obsSet2 ]
+        obsResList = [ obsRes1, obsRes2 ]
+        
+        fileHandler.close()
+        os.remove(fileName)
+        
+        self.assertEquals( expSetList, obsSetList )
+        self.assertEquals( expResList, obsResList )
+        
+    def test_merge_first_id_greater_than_second_id(self):
+        firstSet = Set( 2, "set1", "seq1", 10, 40 )
+        secondSet = Set( 1, "set2", "seq1", 20, 60 )
+        
+        firstSet.merge( secondSet )
+        
+        expSet = Set( 1, "set1", "seq1", 10, 60)
+        obsSet = firstSet
+        
+        self.assertEquals( expSet, obsSet)
+        
+    def test_merge_first_id_smaller_than_second_id(self):
+        firstSet = Set( 1, "set1", "seq1", 10, 40 )
+        secondSet = Set( 2, "set2", "seq1", 20, 60 )
+        
+        firstSet.merge( secondSet )
+        
+        expSet = Set( 1, "set1", "seq1", 10, 60)
+        obsSet = firstSet
+        
+        self.assertEquals( expSet, obsSet)
+
+    def test_merge_first_id_equals_second_id(self):
+        firstSet = Set( 1, "set1", "seq1", 10, 40 )
+        secondSet = Set( 1, "set2", "seq1", 20, 60 )
+        
+        firstSet.merge( secondSet )
+        
+        expSet = Set( 1, "set1", "seq1", 10, 60)
+        obsSet = firstSet
+        
+        self.assertEquals( expSet, obsSet)
+    
+    def test_merge_different_seqnames(self):
+        firstSet = Set( 2, "set1", "seq1", 10, 40 )
+        secondSet = Set( 1, "set1", "seq2", 20, 60 )
+        expSet = Set( 2, "set1", "seq1", 10, 40 )
+        firstSet.merge( secondSet )
+        obsSet = firstSet
+        self.assertEquals( expSet, obsSet )
+        
+    def test_diff_on_empty_sets(self):
+        firstSet = Set()
+        firstSet.seqname = "seq1"
+        secondSet = Set()
+        secondSet.seqname = "seq2"
+        
+        obsSet = firstSet.diff( secondSet )
+        expSet = Set()
+        
+        self.assertEquals( expSet, obsSet )
+    
+    def test_diff(self):
+        firstSet = Set( 2, "set1", "seq1", 10, 80 )
+        secondSet = Set( 1, "set2", "seq1", 20, 60 )
+        
+        expSet1 = Set( 2, "set1", "seq1", 10, 19 )
+        expSet2 = Set( 2, "set1", "seq1", 61, 80 )        
+        
+        obsSet2 = firstSet.diff( secondSet )
+        obsSet1 = firstSet
+                
+        self.assertEquals( expSet1, obsSet1 ) 
+        self.assertEquals( expSet2, obsSet2 )
+        
+    def test_diff_reverse(self):
+        firstSet = Set( 2, "set1", "seq1", 20, 60 )
+        secondSet = Set( 1, "set2", "seq1", 10, 80 )
+        
+        expSet1 = Set( 2, "set1", "seq1", 0, 0 )
+        expSet2 = Set( )        
+        
+        obsSet2 = firstSet.diff( secondSet )
+        obsSet1 = firstSet
+                
+        self.assertEquals( expSet1, obsSet1 ) 
+        self.assertEquals( expSet2, obsSet2 )
+        
+    def test_diff_list1_overlap_end_list2(self):
+        firstSet = Set( 2, "set1", "seq1", 20, 100 )
+        secondSet = Set( 1, "set2", "seq1", 10, 80 )
+        
+        expSet1 = Set( 2, "set1", "seq1", 81, 100 )  
+        expSet2 = Set( )             
+        
+        obsSet2 = firstSet.diff( secondSet )
+        obsSet1 = firstSet
+                
+        self.assertEquals( expSet1, obsSet1 ) 
+        self.assertEquals( expSet2, obsSet2 )
+        
+    def test_diff_with_empty_set1(self):
+        set2 = Set( 1, "set1", "seq1", 2, 45 )
+        set1 = Set( )
+        
+        expSet1 = Set( )
+        expSet2 = Set( )
+        
+        obsSet2 = set1.diff( set2 )
+        obsSet1 = set1
+        
+        self.assertEquals( expSet1, obsSet1 ) 
+        self.assertEquals( expSet2, obsSet2 )
+        
+    def test_diff_list2_overlap_end_list1(self):
+        firstSet = Set( 2, "set1", "seq1", 10, 70 )
+        secondSet = Set( 1, "set2", "seq1", 40, 100 )
+        
+        expSet1 = Set( 2, "set1", "seq1", 10, 39 )
+        expSet2 = Set( )        
+        
+        obsSet2 = firstSet.diff( secondSet )
+        obsSet1 = firstSet
+                
+        self.assertEquals( expSet1, obsSet1 ) 
+        self.assertEquals( expSet2, obsSet2 )
+        
+    def test_set2map(self):
+        set = Set( 1, "set", "seq", 1, 2 )
+        
+        expMap = Map( "set::1", "seq", 1, 2 )
+        obsMap = set.set2map()
+        
+        self.assertEquals( expMap, obsMap )
+    
+test_suite = unittest.TestSuite()
+test_suite.addTest( unittest.makeSuite( Test_Set ) )
+if __name__ == "__main__":
+    unittest.TextTestRunner(verbosity=2).run( test_suite )