--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/structure/test/Test_Transcript.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,351 @@
+import unittest
+from SMART.Java.Python.structure.Interval import Interval
+from SMART.Java.Python.structure.Transcript import Transcript
+
+class Test_Transcript(unittest.TestCase):
+  
+    def test_getSize(self):
+        transcript1 = Transcript()
+        transcript1.setDirection("+")
+        transcript1.setStart(2000)
+        transcript1.setEnd(3000)
+        transcript1.setChromosome("arm_X")
+    
+        self.assertEqual(transcript1.getSize(), 1001)
+      
+        transcript2 = Transcript()
+        transcript2.copy(transcript1)
+        self.assertEqual(transcript1.getSize(), 1001)
+    
+        transcript3 = Transcript()
+        transcript3.setDirection("+")
+        transcript3.setChromosome("arm_X")
+    
+        exon1 = Interval()
+        exon1.setDirection("+")
+        exon1.setChromosome("arm_X")
+        exon1.setStart(100)
+        exon1.setEnd(200)
+        transcript3.addExon(exon1)
+    
+        exon2 = Interval()
+        exon2.setDirection("+")
+        exon2.setChromosome("arm_X")
+        exon2.setStart(300)
+        exon2.setEnd(400)
+        transcript3.addExon(exon2)
+    
+        self.assertEqual(transcript3.getSize(), 203)
+
+
+    def test_overlapWithExons(self):
+        exon1_1 = Interval()
+        exon1_1.setChromosome("chr1")
+        exon1_1.setStart(100)
+        exon1_1.setEnd(200)
+        exon1_1.setDirection("+")
+
+        exon1_2 = Interval()
+        exon1_2.setChromosome("chr1")
+        exon1_2.setStart(500)
+        exon1_2.setEnd(600)
+        exon1_2.setDirection("+")
+
+        transcript1 = Transcript()
+        transcript1.setChromosome("chr1")
+        transcript1.setStart(100)
+        transcript1.setEnd(600)
+        transcript1.setDirection("+")
+        transcript1.addExon(exon1_1)
+        transcript1.addExon(exon1_2)
+
+        exon2_1 = Interval()
+        exon2_1.copy(exon1_1)
+
+        transcript2 = Transcript()
+        transcript2.setChromosome("chr1")
+        transcript2.setStart(100)
+        transcript2.setEnd(200)
+        transcript2.setDirection("+")
+        transcript2.addExon(exon2_1)
+    
+        self.assertTrue(transcript1.overlapWithExon(transcript2))
+
+        transcript2.reverse()
+        try:
+            self.assertFalse(transcript1.overlapWithExon(transcript2))
+        except Exception:
+            pass
+      
+        transcript2.reverse()
+        transcript2.setChromosome("chr2")
+        self.assertFalse(transcript1.overlapWithExon(transcript2))
+
+        exon3_1 = Interval()
+        exon3_1.copy(exon1_1)
+        exon3_1.setEnd(400)
+        exon3_1.setStart(300)
+
+        transcript3 = Transcript()
+        transcript3.setChromosome("chr1")
+        transcript3.setStart(300)
+        transcript3.setEnd(400)
+        transcript3.setDirection("+")
+        transcript3.addExon(exon3_1)
+        self.assertFalse(transcript1.overlapWithExon(transcript3))
+
+
+    def test_merge(self):
+        exon1_1 = Interval()
+        exon1_1.setChromosome("chr1")
+        exon1_1.setStart(100)
+        exon1_1.setEnd(200)
+        exon1_1.setDirection("+")
+
+        exon1_2 = Interval()
+        exon1_2.setChromosome("chr1")
+        exon1_2.setStart(500)
+        exon1_2.setEnd(600)
+        exon1_2.setDirection("+")
+
+        transcript1 = Transcript()
+        transcript1.setChromosome("chr1")
+        transcript1.setEnd(600)
+        transcript1.setStart(100)
+        transcript1.setDirection("+")
+        transcript1.addExon(exon1_1)
+        transcript1.addExon(exon1_2)
+
+        exon2_1 = Interval()
+        exon2_1.copy(exon1_1)
+
+        transcript2 = Transcript()
+        transcript2.setChromosome("chr1")
+        transcript2.setEnd(200)
+        transcript2.setStart(100)
+        transcript2.setDirection("+")
+        transcript2.addExon(exon2_1)
+    
+        transcript1.merge(transcript2)
+        transcript1.sortExonsIncreasing()
+        exons = transcript1.getExons()
+        self.assertEqual(len(exons), 2)
+        exon1, exon2 = exons
+        self.assertEqual(exon1.getStart(), 100)
+        self.assertEqual(exon1.getEnd(),   200)
+        self.assertEqual(exon2.getStart(), 500)
+        self.assertEqual(exon2.getEnd(),   600)
+
+        transcript2.setChromosome("chr2")
+        try:
+            transcript1.merge(transcript2)
+            self.fail()
+        except Exception:
+            pass
+      
+        exon3_1 = Interval()
+        exon3_1.copy(exon1_1)
+        exon3_1.setEnd(650)
+        exon3_1.setStart(550)
+
+        transcript3 = Transcript()
+        transcript3.setChromosome("chr1")
+        transcript3.setEnd(650)
+        transcript3.setStart(550)
+        transcript3.setDirection("+")
+        transcript3.addExon(exon3_1)
+
+        transcript1.merge(transcript3)
+        self.assertEqual(transcript1.getStart(), 100)
+        self.assertEqual(transcript1.getEnd(),   650)
+        exons = transcript1.getExons()
+        self.assertEqual(len(exons), 2)
+        exon1, exon2 = exons
+        self.assertEqual(exon1.getStart(), 100)
+        self.assertEqual(exon1.getEnd(),   200)
+        self.assertEqual(exon2.getStart(), 500)
+        self.assertEqual(exon2.getEnd(),   650)
+
+        exon4_1 = Interval()
+        exon4_1.copy(exon1_1)
+        exon4_1.setEnd(400)
+        exon4_1.setStart(300)
+
+        transcript4 = Transcript()
+        transcript4.setChromosome("chr1")
+        transcript4.setStart(300)
+        transcript4.setEnd(400)
+        transcript4.setDirection("+")
+        transcript4.addExon(exon4_1)
+
+        transcript1.merge(transcript4)
+        self.assertEqual(transcript1.getStart(), 100)
+        self.assertEqual(transcript1.getEnd(),   650)
+        transcript1.sortExonsIncreasing()
+        exons = transcript1.getExons()
+        self.assertEqual(len(exons), 3)
+        exon1, exon2, exon3 = exons
+        self.assertEqual(exon1.getStart(), 100)
+        self.assertEqual(exon1.getEnd(),   200)
+        self.assertEqual(exon2.getStart(), 300)
+        self.assertEqual(exon2.getEnd(),   400)
+        self.assertEqual(exon3.getStart(), 500)
+        self.assertEqual(exon3.getEnd(),   650)
+
+
+    def test_extendStart(self):
+        transcript1 = Transcript()
+        transcript1.setStart(2000)
+        transcript1.setEnd(3000)
+        transcript1.setDirection("+")
+        transcript1.setChromosome("arm_X")
+      
+        transcript2 = Transcript()
+        transcript2.copy(transcript1)
+        transcript2.setDirection("-")
+    
+        transcript1.extendStart(1000)
+        transcript2.extendStart(1000)
+
+    
+        self.assertEqual(transcript1.getDirection(),  1)
+        self.assertEqual(transcript1.getStart(),      1000)
+        self.assertEqual(transcript1.getEnd(),        3000)
+        self.assertEqual(transcript1.getChromosome(), "arm_X")
+    
+        self.assertEqual(transcript2.getDirection(),  -1)
+        self.assertEqual(transcript2.getStart(),      2000)
+        self.assertEqual(transcript2.getEnd(),        4000)
+        self.assertEqual(transcript2.getChromosome(), "arm_X")
+
+
+    def test_restrictStart(self):
+        exon1_1 = Interval()
+        exon1_1.setChromosome("chr1")
+        exon1_1.setStart(100)
+        exon1_1.setEnd(200)
+        exon1_1.setDirection("+")
+
+        exon1_2 = Interval()
+        exon1_2.setChromosome("chr1")
+        exon1_2.setStart(300)
+        exon1_2.setEnd(500)
+        exon1_2.setDirection("+")
+
+        transcript1 = Transcript()
+        transcript1.setChromosome("chr1")
+        transcript1.setStart(100)
+        transcript1.setEnd(500)
+        transcript1.setDirection("+")
+        transcript1.addExon(exon1_1)
+        transcript1.addExon(exon1_2)
+
+        transcript1.restrictStart(301)
+        exons = transcript1.getExons()
+        self.assertEqual(len(exons), 2)
+        exon1, exon2 = exons
+        self.assertEqual(exon1.getStart(), 100)
+        self.assertEqual(exon1.getEnd(),   200)
+        self.assertEqual(exon2.getStart(), 300)
+        self.assertEqual(exon2.getEnd(),   400)
+
+
+    def test__include(self):
+        iTranscript1 = Transcript()
+        iTranscript1.setName("transcript1")
+        iTranscript1.setChromosome("chr1")
+        iTranscript1.setStart(100)
+        iTranscript1.setEnd(200)
+        iTranscript1.setDirection("+")
+        
+        iTranscript2 = Transcript()
+        iTranscript2.copy(iTranscript1)
+        iTranscript2.setName("transcript2")
+        self.assertTrue(iTranscript1.include(iTranscript2))
+        self.assertTrue(iTranscript2.include(iTranscript1))
+
+        iTranscript2.setChromosome("chr2")
+        self.assertFalse(iTranscript1.include(iTranscript2))
+        self.assertFalse(iTranscript2.include(iTranscript1))
+
+        iTranscript2.setChromosome("chr1")
+        exon = Interval()
+        exon.setChromosome("chr1")
+        exon.setDirection("+")
+        exon.setStart(300)
+        exon.setEnd(400)
+        iTranscript1.addExon(exon)
+        self.assertTrue(iTranscript1.include(iTranscript2))
+        self.assertFalse(iTranscript2.include(iTranscript1))
+        
+        exon = Interval()
+        exon.setChromosome("chr1")
+        exon.setDirection("+")
+        exon.setStart(500)
+        exon.setEnd(600)
+        iTranscript2.addExon(exon)
+        self.assertFalse(iTranscript1.include(iTranscript2))
+        self.assertFalse(iTranscript2.include(iTranscript1))
+        
+
+    def test__getDifference(self):
+        iTranscript1 = Transcript()
+        iTranscript1.setName("transcript1")
+        iTranscript1.setChromosome("chr1")
+        iTranscript1.setStart(100)
+        iTranscript1.setEnd(400)
+        iTranscript1.setDirection("+")
+        
+        iTranscript2 = Transcript()
+        iTranscript2.setName("transcript1")
+        iTranscript2.setChromosome("chr1")
+        iTranscript2.setStart(200)
+        iTranscript2.setEnd(400)
+        iTranscript2.setDirection("+")
+
+        newTranscript = iTranscript1.getDifference(iTranscript2)
+        self.assertTrue(newTranscript.getStart(), 100)
+        self.assertTrue(newTranscript.getEnd(),   199)
+        exons = newTranscript.getExons()
+        self.assertTrue(len(exons), 1)
+        exon1 = exons[0]
+        self.assertTrue(exon1.getStart(), 100)
+        self.assertTrue(exon1.getEnd(),   199)
+
+        iTranscript2 = Transcript()
+        iTranscript2.setName("transcript1")
+        iTranscript2.setChromosome("chr1")
+        iTranscript2.setStart(100)
+        iTranscript2.setEnd(200)
+        iTranscript2.setDirection("+")
+
+        newTranscript = iTranscript1.getDifference(iTranscript2)
+        self.assertTrue(newTranscript.getStart(), 201)
+        self.assertTrue(newTranscript.getEnd(),   400)
+        exons = newTranscript.getExons()
+        self.assertTrue(len(exons), 1)
+        exon1 = exons[0]
+        self.assertTrue(exon1.getStart(), 201)
+        self.assertTrue(exon1.getEnd(),   400)
+
+        iTranscript2 = Transcript()
+        iTranscript2.setName("transcript1")
+        iTranscript2.setChromosome("chr1")
+        iTranscript2.setStart(200)
+        iTranscript2.setEnd(300)
+        iTranscript2.setDirection("+")
+
+        newTranscript = iTranscript1.getDifference(iTranscript2)
+        self.assertTrue(newTranscript.getStart(), 100)
+        self.assertTrue(newTranscript.getEnd(),   400)
+        exons = newTranscript.getExons()
+        self.assertTrue(len(exons), 2)
+        exon1, exon2 = exons
+        self.assertTrue(exon1.getStart(), 100)
+        self.assertTrue(exon1.getEnd(),   199)
+        self.assertTrue(exon2.getStart(), 301)
+        self.assertTrue(exon2.getEnd(),   400)
+
+
+if __name__ == '__main__':
+    unittest.main()