r27385 - /trunk/test_suite/unit_tests/_data_store/test_seq_align.py -- January 30, 2015 - 11:45

Author: bugman
Date: Fri Jan 30 11:45:54 2015
New Revision: 27385

URL: http://svn.gna.org/viewcvs/relax?rev=27385&view=rev
Log:
Added the Test_seq_align.test_find_alignment and 
Test_seq_align.test_find_missing_alignment unit tests.

These are in the _data_store.test_seq_align unit test module.  They check the 
functionality of the
currently unimplemented Sequence_alignment.find_alignment() method which will 
be used to return
pre-existing alignments.


Modified:
    trunk/test_suite/unit_tests/_data_store/test_seq_align.py

Modified: trunk/test_suite/unit_tests/_data_store/test_seq_align.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_data_store/test_seq_align.py?rev=27385&r1=27384&r2=27385&view=diff
==============================================================================
--- trunk/test_suite/unit_tests/_data_store/test_seq_align.py   (original)
+++ trunk/test_suite/unit_tests/_data_store/test_seq_align.py   Fri Jan 30 
11:45:54 2015
@@ -36,8 +36,8 @@
         self.seq_align = Sequence_alignments()
 
 
-    def test_alignment_addition(self):
-        """Test the creation of a new sequence alignment object."""
+    def return_align_data(self):
+        """Return a data set for alignment testing."""
 
         # The data.
         object_ids = ['frame_order', 'ensemble', 'ensemble', 'ensemble', 
'ensemble', 'ensemble', 'ensemble', 'ensemble']
@@ -92,6 +92,16 @@
         end_gap_open_penalty = 0.0
         end_gap_extend_penalty = 0.0
 
+        # Return the data.
+        return object_ids, models, molecules, sequences, strings, gaps, 
msa_algorithm, pairwise_algorithm, matrix, gap_open_penalty, 
gap_extend_penalty, end_gap_open_penalty, end_gap_extend_penalty
+
+
+    def test_alignment_addition(self):
+        """Test the creation of a new sequence alignment object."""
+
+        # The data.
+        object_ids, models, molecules, sequences, strings, gaps, 
msa_algorithm, pairwise_algorithm, matrix, gap_open_penalty, 
gap_extend_penalty, end_gap_open_penalty, end_gap_extend_penalty = 
self.return_align_data()
+
         # Add the alignment.
         self.seq_align.add(object_ids=object_ids, models=models, 
molecules=molecules, sequences=sequences, strings=strings, gaps=gaps, 
msa_algorithm=msa_algorithm, pairwise_algorithm=pairwise_algorithm, 
matrix=matrix, gap_open_penalty=gap_open_penalty, 
gap_extend_penalty=gap_extend_penalty, 
end_gap_open_penalty=end_gap_open_penalty, 
end_gap_extend_penalty=end_gap_extend_penalty)
 
@@ -120,3 +130,45 @@
             self.assertEqual(self.seq_align[0].gap_extend_penalty, 
gap_extend_penalty)
             self.assertEqual(self.seq_align[0].end_gap_open_penalty, 
end_gap_open_penalty)
             self.assertEqual(self.seq_align[0].end_gap_extend_penalty, 
end_gap_extend_penalty)
+
+
+    def test_find_alignment(self):
+        """Test the retrieval of pre-existing alignment."""
+
+        # Execute the body of the test_alignment_addition() unit test to set 
up the object.
+        self.test_alignment_addition()
+
+        # The identifying data.
+        object_ids, models, molecules, sequences, strings, gaps, 
msa_algorithm, pairwise_algorithm, matrix, gap_open_penalty, 
gap_extend_penalty, end_gap_open_penalty, end_gap_extend_penalty = 
self.return_align_data()
+
+        # Retrieve the alignment.
+        align = self.seq_align.find_alignment(object_ids=object_ids, 
models=models, molecules=molecules, sequences=sequences, 
msa_algorithm=msa_algorithm, pairwise_algorithm=pairwise_algorithm, 
matrix=matrix, gap_open_penalty=gap_open_penalty, 
gap_extend_penalty=gap_extend_penalty, 
end_gap_open_penalty=end_gap_open_penalty, 
end_gap_extend_penalty=end_gap_extend_penalty)
+
+        # Check that something was returned.
+        self.assertNotEqual(align, None)
+
+        # Check some of the data.
+        for i in range(8):
+            print("Checking \"%s\"" % ids[i])
+            self.assertEqual(self.seq_align[0].object_ids[i], object_ids[i])
+            self.assertEqual(self.seq_align[0].models[i], models[i])
+            self.assertEqual(self.seq_align[0].molecules[i], molecules[i])
+
+
+    def test_find_missing_alignment(self):
+        """Test the retrieval of non-existent alignment."""
+
+        # Execute the body of the test_alignment_addition() unit test to set 
up the object.
+        self.test_alignment_addition()
+
+        # The identifying data.
+        object_ids, models, molecules, sequences, strings, gaps, 
msa_algorithm, pairwise_algorithm, matrix, gap_open_penalty, 
gap_extend_penalty, end_gap_open_penalty, end_gap_extend_penalty = 
self.return_align_data()
+
+        # Change a gap penalty.
+        gap_open_penalty = 0.5
+
+        # Retrieve the alignment.
+        align = self.seq_align.find_alignment(object_ids=object_ids, 
models=models, molecules=molecules, sequences=sequences, 
msa_algorithm=msa_algorithm, pairwise_algorithm=pairwise_algorithm, 
matrix=matrix, gap_open_penalty=gap_open_penalty, 
gap_extend_penalty=gap_extend_penalty, 
end_gap_open_penalty=end_gap_open_penalty, 
end_gap_extend_penalty=end_gap_extend_penalty)
+
+        # Check that nothing was returned.
+        self.assertEqual(align, None)