--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/coord/test/Test_Path.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,146 @@
+# 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
+from commons.core.coord.Path import Path
+from commons.core.coord.Align import Align
+from commons.core.coord.Set import Set
+
+
+class Test_Path( unittest.TestCase ):
+    
+    def setUp( self ):
+        self._path = Path()
+        
+    def test_setFromTuple( self ):
+        line = "1\tchr1\t1\t10\tTE2\t11\t17\t1e-20\t30\t90.2"
+        self._path.setFromTuple( line.split("\t") )
+        self.assertEqual( self._path.id, 1 )
+        self.assertEqual( self._path.range_query.seqname, "chr1" )
+        self.assertEqual( self._path.range_query.start, 1 )
+        self.assertEqual( self._path.range_query.end, 10 )
+        self.assertEqual( self._path.range_subject.seqname, "TE2" )
+        self.assertEqual( self._path.range_subject.start, 11 )
+        self.assertEqual( self._path.range_subject.end, 17 )
+        self.assertEqual( self._path.e_value, float("1e-20") )
+        self.assertEqual( self._path.score, float("30") )
+        self.assertEqual( self._path.identity, float("90.2") )
+        
+    def test___eq__( self ):
+        self._path.setFromString( "1\tchr1\t1\t6\tTE2\t11\t16\t1e-20\t30\t90.2\n" )
+        o = Path()
+        o.setFromString( "1\tchr1\t1\t6\tTE2\t11\t16\t1e-20\t30\t90.2\n" )
+        self.assertEqual( self._path,  o )
+        o.setFromString( "2\tchr1\t1\t6\tTE2\t11\t16\t1e-20\t30\t90.2\n" )
+        self.assertNotEqual( self._path,  o )
+        o.setFromString( "1\tchr1\t1\t6\tTE2\t11\t16\t1e-20\t3000000\t90.2\n" )
+        self.assertNotEqual( self._path,  o )
+        
+    def test_canMerge( self ):
+        tuple = ("1", "chr1","1", "10","TE2","11","17","1e-20","30","90.2")
+        self._path.setFromTuple(tuple)
+        tuple = ("2", "chr1","2", "9","TE2","10","13","1e-20","30","90.2")
+        o = Path()
+        o.setFromTuple(tuple)
+        self.assertTrue(self._path.canMerge(o))
+        
+    def test_canMerge_on_same_id ( self ): 
+        tuple = ("1", "chr1","1", "10","TE2","11","17","1e-20","30","90.2")
+        self._path.setFromTuple(tuple)
+        tuple = ("1", "chr1","2", "9","TE2","10","13","1e-20","30","90.2")
+        o = Path()
+        o.setFromTuple(tuple)
+        self.assertFalse(self._path.canMerge(o))
+        
+    def test_canMerge_on_same_chr( self ):     
+        tuple = ("1", "chr1","1", "10","TE2","11","17","1e-20","30","90.2")
+        self._path.setFromTuple(tuple)
+        tuple = ("2", "chr2","2", "9","TE2","10","13","1e-20","30","90.2")
+        o = Path()
+        o.setFromTuple(tuple)
+        self.assertFalse(self._path.canMerge(o))
+        
+    def test_canMerge_on_diff_subj( self ):      
+        tuple = ("1", "chr1","1", "10","TE2","11","17","1e-20","30","90.2")
+        self._path.setFromTuple(tuple)
+        tuple = ("2", "chr1","2", "9","TE3","10","13","1e-20","30","90.2")
+        o = Path()
+        o.setFromTuple(tuple)
+        self.assertFalse(self._path.canMerge(o)) 
+        
+    def test_canMerge_on_queries_that_do_not_overlap( self ):
+        tuple = ("1", "chr1","5", "11","TE2","11","17","1e-20","30","90.2")
+        self._path.setFromTuple(tuple)
+        tuple = ("2", "chr1","1", "4","TE2","10","13","1e-20","30","90.2")
+        o = Path()
+        o.setFromTuple(tuple)
+        self.assertFalse(self._path.canMerge(o)) 
+        
+    def test_canMerge_on_subjects_that_do_not_overlap( self ):    
+        tuple = ("1", "chr1","1", "10","TE2","11","17","1e-20","30","90.2")
+        self._path.setFromTuple(tuple)
+        tuple = ("2", "chr1","2", "9","TE2","1","10","1e-20","30","90.2")
+        o = Path()
+        o.setFromTuple(tuple)
+        self.assertFalse(self._path.canMerge(o))
+        
+    def test_getSubjectAsSetOfQuery( self ):
+        tuple = ("1","chr1","1","10","TE2","11","17","1e-20","30","90.2")
+        self._path.setFromTuple(tuple)
+        exp = Set(1,"TE2","chr1",1,10)
+        obs = self._path.getSubjectAsSetOfQuery()
+        self.assertEqual( exp, obs )
+        
+    def test_getSubjectAsSetOfQuery_on_neg_strand( self ):
+        tuple = ("1","chr1","10","1","TE2","11","17","1e-20","30","90.2")
+        self._path.setFromTuple(tuple)
+        exp = Set(1,"TE2","chr1",10,1)
+        obs = self._path.getSubjectAsSetOfQuery()
+        self.assertEqual( exp, obs )
+        
+    def test_toString( self ):
+        self._path.setFromString( "1\tchr1\t1\t10\tTE3\t11\t17\t1e-20\t30\t85.2\n" )
+        exp = "1\tchr1\t1\t10\tTE3\t11\t17\t%g\t30\t%f" % ( 1e-20, 85.2 )
+        obs = self._path.toString()
+        self.assertEqual( obs, exp )
+        
+    def test_getAlignInstance( self ):
+        self._path.setFromTuple( ( "2", "chr3", "250", "151", "seq5", "1", "100", "1e-32", "147", "87.9" ) )
+        expAlign = Align()
+        expAlign.setFromTuple( ( "chr3", "151", "250", "seq5", "100", "1", "1e-32", "147", "87.9" ) )
+        obsAlign = self._path.getAlignInstance()
+        self.assertEqual( expAlign, obsAlign )
+        
+        
+test_suite = unittest.TestSuite()
+test_suite.addTest( unittest.makeSuite( Test_Path ) )
+if __name__ == "__main__":
+    unittest.TextTestRunner(verbosity=2).run( test_suite )