--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/manipulate/extend_linearcode/test_linearcode_extend.py	Wed Mar 23 14:35:56 2016 -0400
@@ -0,0 +1,146 @@
+__license__ = "MIT"
+
+import unittest
+import lc_extend as lc
+
+
+class SimpleUnitTest(unittest.TestCase):
+    def setUp(self):
+        import os
+
+        os.environ["http_proxy"] = ""  # work around for IOError: [Errno url error] invalid proxy for http:
+        self.examplelc = """(Ma3(Ma3(Ma6)Ma6)Mb4GNb4GN)
+(Ma2Ma3(Ma3(Ma6)Ma6)Mb4GNb4GN)
+(GN??Ma3(GN??Ma6)Mb4GNb4(Fa6)GN)
+(GN??(GN??)Ma3(GN??Ma6)Mb4GNb4GN)
+(Ma2Ma3(Ma3(Ma6)Ma6)Mb4GNb4GN,M)
+(A??GN??Ma3(GN??Ma6)Mb4GNb4(Fa6)GN)
+(GNb4(GN??Ma3)(GN??Ma6)Mb4GNb4(Fa6)GN)
+(GNb4(A??GN??Ma3)(GN??Ma6)Mb4GNb4GN)
+(NN??A??GN??Ma3(Ma6)Mb4GNb4(Fa6)GN)
+(Ma2Ma3(Ma3(Ma6)Ma6)Mb4GNb4GN,M,M)
+(A??GN??Ma3(A??GN??Ma6)Mb4GNb4(Fa6)GN)
+(GNb4(A??GN??Ma3)(GN??Ma6)Mb4GNb4(Fa6)GN)
+(GNb4(A??GN??Ma3)(A??GN??Ma6)Mb4GNb4GN)
+(Ma2Ma2Ma3(Ma2Ma3(Ma2Ma6)Ma6)Mb4GNb4GN)
+(NN??A??GN??Ma3(A??GN??Ma6)Mb4GNb4GN)
+(GNb4(A??(Fa3)GN??Ma3)(GN??Ma6)Mb4GNb4(Fa6)GN)
+(GNb4(A??GN??Ma3)(A??GN??Ma6)Mb4GNb4(Fa6)GN)
+(A??GN??(A??GN??)Ma3(A??GN??Ma6)Mb4GNb4GN)
+(NN??A??GN??Ma3(A??GN??Ma6)Mb4GNb4(Fa6)GN)
+(GNb4(A??(Fa3)GN??Ma3)(A??GN??Ma6)Mb4GNb4(Fa6)GN)
+(A??GN??(A??GN??)Ma3(A??GN??Ma6)Mb4GNb4(Fa6)GN)
+(NN??A??GN??Ma3(A??GN??Ma6)Mb4GNb4(Fa6)GN,F)
+(NN??A??GN??Ma3(A??GN??Ma6)Mb4GNb4(Fa6)GN,F)
+(NN??A??GN??Ma3(NN??A??GN??Ma6)Mb4GNb4GN)
+(GNb4(NN??A??GN??Ma3)(A??GN??Ma6)Mb4GNb4(Fa6)GN)
+(NN??A??GN??(A??GN??)Ma3(A??GN??Ma6)Mb4GNb4GN)
+(NN??A??GN??Ma3(NN??A??GN??Ma6)Mb4GNb4(Fa6)GN)
+(NN??A??GN??(A??GN??)Ma3(A??GN??Ma6)Mb4GNb4(Fa6)GN)
+(GNb4(A??(Fa3)GN??(A??GN??)Ma3)(A??GN??Ma6)Mb4GNb4(Fa6)GN)
+(NN??A??(Fa3)GN??Ma3(NN??A??GN??Ma6)Mb4GNb4(Fa6)GN)
+(NN??A??GN??(A??GN??)Ma3(A??GN??Ma6)Mb4GNb4(Fa6)GN,F)
+(GNb4(A??(Fa3)GN??(A??(Fa3)GN??)Ma3)(A??GN??Ma6)Mb4GNb4(Fa6)GN)
+(NN??A??GN??(A??GN??)Ma3(A??GN??Ma6)Mb4GNb4(Fa6)GN,F,F)
+(NN??A??GN??(NN??A??GN??)Ma3(A??GN??Ma6)Mb4GNb4(Fa6)GN)
+(GNb4(NN??A??GN??(A??GN??)Ma3)(A??GN??Ma6)Mb4GNb4(Fa6)GN,F)
+(NN??A??GN??(A??GN??)Ma3(A??GN??(A??GN??)Ma6)Mb4GNb4(Fa6)GN)
+(NN??A??GN??(NN??A??GN??)Ma3(A??GN??Ma6)Mb4GNb4(Fa6)GN,F)
+(GNb4(NN??A??GN??(A??GN??)Ma3)(A??GN??Ma6)Mb4GNb4(Fa6)GN,F,F)
+(NN??A??GN??(A??GN??)Ma3(A??GN??(A??GN??)Ma6)Mb4GNb4(Fa6)GN,F)
+(NN??A??GN??(NN??A??GN??)Ma3(NN??A??GN??Ma6)Mb4GNb4(Fa6)GN)
+(NN??A??GN??(NN??A??GN??)Ma3(A??GN??(A??GN??)Ma6)Mb4GNb4(Fa6)GN)
+(NN??A??GN??Ma3(NN??A??GN??(NN??A??(Fa3)GN??)Ma6)Mb4GNb4(Fa6)GN)
+(GNb4(NN??A??GN??Ma3)(NN??A??GN??(NN??A??GN??)Ma6)Mb4GNb4(Fa6)GN)
+(NN??A??GN??(NN??A??GN??)Ma3(A??GN??(A??GN??)Ma6)Mb4GNb4(Fa6)GN,F)
+(NN??A??GN??(NN??A??GN??)Ma3(A??GN??(A??GN??)Ma6)Mb4GNb4(Fa6)GN,F,F)
+(A??GN??(A??GN??)Ma3(A??GN??(A??GN??)Ma6)Mb4GNb4(Fa6)GN,NN,NN,A??GN)
+(NN??A??GN??(NN??A??GN??)Ma3(NN??A??GN??(A??GN??)Ma6)Mb4GNb4(Fa6)GN,F)
+(A??GN??(A??GN??)Ma3(A??GN??(A??GN??)Ma6)Mb4GNb4(Fa6)GN,F,NN,NN,A??GN)
+(NN??A??(Fa3)GN??(NN??A??GN??)Ma3(NN??A??GN??(NN??A??GN??)Ma6)Mb4GNb4(Fa6)GN)
+(A??GN??(A??GN??)Ma3(A??GN??(A??GN??)Ma6)Mb4GNb4(Fa6)GN,NN,NN,NN,F,A??GN)
+(A??GN??(A??GN??)Ma3(A??GN??(A??GN??)Ma6)Mb4GNb4(Fa6)GN,NN,NN,NN,NN,A??GN,F)
+(A??GN??(A??GN??)Ma3(A??GN??(A??GN??)Ma6)Mb4GNb4(Fa6)GN,NN,NN,NN,NN,A??GN,A??GN,F)
+"""
+        pass
+
+    def tearDown(self):
+        pass
+
+
+    def test_simple_lc(self):
+        import StringIO
+
+        lcinput = ["(Ma3(Ma3(Ma6)Ma6)Mb4GNb4GN)"]
+        lchandle = StringIO.StringIO('\n'.join(lcinput))
+        m = lc.read_linearcode(lchandle, "logging.log")
+        self.assertIsNotNone(m)
+        self.assertEqual(1, len(m))
+
+    def test_commad_lc_extend(self):
+        import StringIO
+
+        lcinput = ["(Ma2Ma3(Ma3(Ma6)Ma6)Mb4GNb4GN,M)"]
+        lchandle = StringIO.StringIO('\n'.join(lcinput))
+        m = lc.read_linearcode(lchandle, "logging.log", True)
+        self.assertIsNotNone(m)
+        self.assertEqual(3, len(m))
+        self.assertEqual(['M??Ma2Ma3(Ma3(Ma6)Ma6)Mb4GNb4GN', 'Ma2Ma3(M??Ma3(Ma6)Ma6)Mb4GNb4GN', 'Ma2Ma3(Ma3(M??Ma6)Ma6)Mb4GNb4GN'],m)
+
+    def test_commad_lc_append(self):
+        import StringIO
+
+        lcinput = ["(Ma2Ma3(Ma3(Ma6)Ma6)Mb4GNb4GN,M)"]
+        lchandle = StringIO.StringIO('\n'.join(lcinput))
+        m = lc.read_linearcode(lchandle, "logging.log")
+        self.assertIsNotNone(m)
+        self.assertEqual(1, len(m))
+        self.assertEqual("((M??)X??)(Ma2Ma3(Ma3)(Ma6)Ma6)Mb4GNb4GN", m[0])
+
+    def test_empty_stream(self):
+        """
+        should raise IOError
+        """
+        with self.assertRaises(IOError):
+            m = lc.read_linearcode([], "logging.log")
+        with self.assertRaises(IOError):
+            m = lc.read_linearcode("", "logging.log")
+        with self.assertRaises(IOError):
+            m = lc.read_linearcode([], "logging.log")
+
+    def test_empty_logger(self):
+        """
+        should work as usual as logger is defined by default
+        """
+        import StringIO
+
+        lcinput = ["(Ma3(Ma3(Ma6)Ma6)Mb4GNb4GN)"]
+        lchandle = StringIO.StringIO('\n'.join(lcinput))
+        m = lc.read_linearcode(lchandle)
+        self.assertIsNotNone(m)
+
+    def test_many_lc_extend(self):
+        import StringIO
+
+        lchandle = StringIO.StringIO(''.join(self.examplelc))
+        m = lc.read_linearcode(lchandle, extend=True)
+        self.assertIsNotNone(m)
+        self.assertEqual(150, len(m))
+
+    def test_many_lc_append(self):
+        import StringIO
+
+        lchandle = StringIO.StringIO(''.join(self.examplelc))
+        m = lc.read_linearcode(lchandle)
+        self.assertIsNotNone(m)
+        self.assertEqual(52, len(m))  # that is equal to number of examples
+
+
+def run_tests():
+    unittest.main()
+
+
+if __name__ == '__main__':
+    run_tests()
+
+