--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/test/Test_FindOverlaps_optim.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,149 @@
+import unittest
+import os
+from SMART.Java.Python.FindOverlapsOptim import FindOverlapsOptim
+from SMART.Java.Python.ncList.test.MockFindOverlapsWithSeveralIntervals import *
+
+class Test_FindOverlaps_optim(unittest.TestCase):
+
+    def setUp(self):
+        self._inputRefGff3FileName = 'sorted_Ref.gff3'
+        iMock = MockFindOverlapsWithServeralIntervals_case1()
+        iMock.write(self._inputRefGff3FileName)
+        self._inputQueryGff3FileName = 'sorted_Query.gff3'
+        self._writeQueryGff3File(self._inputQueryGff3FileName)
+        self._outputGff3FileName = 'overlaps.gff3'
+        self._iFOO = FindOverlaps_optim(self._inputRefGff3FileName, self._inputQueryGff3FileName)
+        self._iFOO.prepareIntermediateFiles_sorted()
+        self._iFOO.setOutputGff3FileName(self._outputGff3FileName)
+        
+    def tearDown(self):
+        os.remove(self._inputRefGff3FileName)
+        os.remove(self._inputQueryGff3FileName)
+        os.remove(self._outputGff3FileName)
+        self._iFOO.deletIntermediateFiles()
+    
+    def test_isOverlapping_true(self):
+        queryGff3Addr = 116
+        RefGff3Addr = 231
+        obs = self._iFOO.isOverlapping(queryGff3Addr, RefGff3Addr)
+        exp = 0
+        self.assertEquals(exp, obs)
+        
+    def test_isOverlapping_false_left(self):
+        queryGff3Addr = 116
+        RefGff3Addr = 58
+        obs = self._iFOO.isOverlapping(queryGff3Addr, RefGff3Addr)
+        exp = -1
+        self.assertEquals(exp, obs)
+    
+    def test_isOverlapping_false_right(self):
+        queryGff3Addr = 116
+        RefGff3Addr = 347
+        obs = self._iFOO.isOverlapping(queryGff3Addr, RefGff3Addr)
+        exp = 1
+        self.assertEquals(exp, obs) 
+           
+    def test_getHisFirstChild(self):
+        firstRefLAddr = 0
+        obsFirstChildLAddr = self._iFOO.getHisFirstChild(firstRefLAddr)
+        expFirstChildLAddr = 48
+        self.assertEquals(expFirstChildLAddr, obsFirstChildLAddr) 
+    
+    def test_isLastElement_true(self):
+        refLAddr = 96
+        obsBool = self._iFOO.isLastElement(refLAddr)
+        expBool = True
+        self.assertEquals(expBool, obsBool)
+    
+    def test_isLastElement_false(self):
+        refLAddr = 72
+        obsBool = self._iFOO.isLastElement(refLAddr)
+        expBool = False
+        self.assertEquals(expBool, obsBool)  
+        
+    def test_isLastElement_highestLevel_true(self):
+        refLAddr = 24
+        obsBool = self._iFOO.isLastElement(refLAddr)
+        expBool = True
+        self.assertEquals(expBool, obsBool)
+    
+    def test_isLastElement_highestLevel_false(self):
+        refLAddr = 0
+        obsBool = self._iFOO.isLastElement(refLAddr)
+        expBool = False
+        self.assertEquals(expBool, obsBool)           
+
+    def test_findOverlapIter(self):
+        queryGff3Addr = 175
+        firstRefLAddr = 0 
+        done = False
+        obsFirstOverlapLAddr = self._iFOO.findOverlapIter(queryGff3Addr, firstRefLAddr, done)
+        expFirstOverlapLAddr = 96, True
+        self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr)
+        
+    def test_not_findOverlapIter(self):
+        queryGff3Addr = 295
+        firstRefLAddr = 24 
+        done = False
+        obsFirstOverlapLAddr = self._iFOO.findOverlapIter(queryGff3Addr, firstRefLAddr, done)
+        expFirstOverlapLAddr = None, False
+        self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr)   
+        
+    def test_findOverlapIter_not_the_first_RefOverlap(self):
+        queryGff3Addr = 235
+        firstRefLAddr = 96 
+        done = True
+        obsFirstOverlapLAddr = self._iFOO.findOverlapIter(queryGff3Addr, firstRefLAddr, done)
+        expFirstOverlapLAddr = 24, False
+        self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr)  
+        
+    def test_changeToNewSubEndLAddr(self):
+        firstChildLAddr = 48
+        subEndLAddr = 48
+        expSubEndLAddr = 120
+        obsSubEndLAddr = self._iFOO.changeToNewSubEndLAddr(firstChildLAddr, subEndLAddr)
+        self.assertEquals(expSubEndLAddr, obsSubEndLAddr) 
+        
+    def test_defineSubEndLaddr(self):
+        parentLAddr = -1
+        expSubEndLAddr = 48
+        obsSubEndLAddr = self._iFOO.defineSubEndLaddr(parentLAddr)
+        self.assertEquals(expSubEndLAddr, obsSubEndLAddr)
+        
+    def test_getNextRefIntervalInCaseNotOverLap(self):
+        firstRefLAddr = 96
+        expRefLAddr = 24
+        obsRefLAddr = self._iFOO.getNext(firstRefLAddr)
+        self.assertEquals(expRefLAddr, obsRefLAddr)
+        
+
+    def test_not_findOverlapIter_between2RefIntervals(self):
+        inputQueryGff3FileName = 'query2.gff3'
+        self._writeQueryGff3File2(inputQueryGff3FileName)
+        self._iFOO.setQueryGff3FileName(inputQueryGff3FileName)
+        queryGff3Addr = 0
+        firstRefLAddr = 0
+        done = False
+        obsFirstOverlapLAddr = self._iFOO.findOverlapIter(queryGff3Addr, firstRefLAddr, done)
+        expFirstOverlapLAddr = 24, False
+        self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr) 
+        os.remove(inputQueryGff3FileName) 
+
+    def _writeQueryGff3File2(self, fileName):
+        f = open(fileName, 'w')
+        f.write("chr1\tquery\ttest1\t1100\t1150\t126\t+\t.\tID=test1.1;Name=test1.1\n")
+        f.write("chr1\tquery\ttest2\t1250\t1300\t781\t+\t.\tID=test1.2;Name=test1.2\n")
+        f.close()  
+        
+    def _writeQueryGff3File(self, fileName):
+        f = open(fileName, 'w')
+        f.write("chr1\tquery\ttest1.1\t25\t150\t126\t+\t.\tID=test1.1;Name=test1.1\n")
+        f.write("chr1\tquery\ttest1.2\t70\t850\t781\t+\t.\tID=test1.2;Name=test1.2\n")
+        f.write("chr1\tquery\ttest1.3\t550\t850\t201\t+\t.\tID=test1.3;Name=test1.3\n")
+        f.write("chr1\tquery\ttest1.4\t925\t1025\t101\t+\t.\tID=test1.4;Name=test1.4\n")
+        f.write("chr1\tquery\ttest1.5\t1201\t1210\t10\t+\t.\tID=test1.5;Name=test1.5\n")
+        f.write("chr1\tquery\ttest1.6\t1500\t1600\t101\t+\t.\tID=test1.6;Name=test1.6\n")
+        f.close()
+        
+if __name__ == "__main__":
+    unittest.main()
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