Added exception and unittest for dist_mat_to_vec of analysis/psa.py (Part of #597)

package/MDAnalysis/analysis/psa.py

@@ -573,6 +573,10 @@ def dist_mat_to_vec(N, i, j):
     :Returns:
       int, index (of the matrix element) in the corresponding distance vector
     """
+    try:
+        validate_dist_mat_to_vec_inputs(N, i, j)
+    except Exception as E:
+        raise E
     if i > N or j > N:
         err_str = "Matrix indices are out of range; i and j must be less than"  \
                 + " N = {0:d}".format(N)
@@ -591,6 +595,30 @@ def dist_mat_to_vec(N, i, j):
         raise ValueError(err_str)
 
 
+def validate_dist_mat_to_vec_inputs(N, i, j):
+    """
+    Validate the inputs of the function dist_mat_to_vec else raise an exception
+    :param N: int
+    :param i: int
+    :param j: int
+    :return: null
+    """
+
+    # Validating if the inputs are integer
+    try:
+        NValue = int(N)
+        iValue = int(i)
+        jValue = int(j)
+    except ValueError:
+        raise ValueError
+
+    # Check if the inputs are not out of bounds
+    if N-1 > i > 0 and N >= 2 and i < j < N:
+        pass
+    else:
+        raise ValueError
+
+
 class Path(object):
     """Pre-process a :class:`MDAnalysis.Universe` object: (1) fit the
     trajectory to a reference structure, (2) convert fitted time series to a

testsuite/MDAnalysisTests/analysis/test_psa.py

@@ -26,7 +26,7 @@
 
 from numpy.testing import (TestCase, dec, assert_array_less,
                            assert_array_almost_equal, assert_,
-                           assert_almost_equal)
+                           assert_almost_equal, assert_equal)
 import numpy as np
 
 from MDAnalysisTests.datafiles import PSF, DCD, DCD2
@@ -93,6 +93,15 @@ def test_dendrogram_produced(self):
         err_msg = "Dendrogram dictionary object was not produced"
         assert_(type(self.plot_data[1]) is dict, err_msg)
 
+    def test_dist_mat_to_vec_i_less_j(self):
+        """Test the index of corresponding distance vector is correct if i < j"""
+        err_msg = "dist_mat_to_vec function returning wrong values"
+        assert_equal(PSA.dist_mat_to_vec(5, 3, 4), 9, err_msg)
+
+    def test_dist_mat_to_vec_i_greater_j(self):
+        """Test the index of corresponding distance vector is correct if i > j"""
+        err_msg = "dist_mat_to_vec function returning wrong values"
+        assert_equal(PSA.dist_mat_to_vec(5, 4, 3), 9, err_msg)
 
 class TestPSAExceptions(TestCase):
     '''Tests for exceptions that should be raised
@@ -108,13 +117,45 @@ def test_get_path_metric_func_bad_key(self):
             self.fail('KeyError should be caught')
 
     def test_get_coord_axes_bad_dims(self):
-        '''Test that ValueError is raised when
+        """Test that ValueError is raised when
         numpy array with incorrect dimensions
-        is fed to get_coord_axes().'''
+        is fed to get_coord_axes()."""
 
         with self.assertRaises(ValueError):
             PSA.get_coord_axes(np.zeros((5,5,5,5)))
 
+    def test_dist_mat_to_vec_func_out_of_bounds(self):
+        """Test that ValueError is raised when i or j or both are
+        out of bounds of N"""
+
+        # Check if i is out of bounds of N
+        with self.assertRaises(ValueError):
+            PSA.dist_mat_to_vec(5, 6, 4)
+
+        # Check if j is out of bounds of N
+        with self.assertRaises(ValueError):
+            PSA.dist_mat_to_vec(5, 4, 6)
+
+        # Check if both i and j are out of bounds of N
+        with self.assertRaises(ValueError):
+            PSA.dist_mat_to_vec(5, 6, 7)
+
+    def test_dist_mat_to_vec_func_i_equals_j(self):
+        """Test that ValueError is raised when i == j"""
+
+        with self.assertRaises(ValueError):
+            PSA.dist_mat_to_vec(5, 4, 4)
+
+    def test_dist_mat_to_vec_func_bad_integers(self):
+        """Test that ValueError is raised when i or j are
+        not Integers"""
+
+        with self.assertRaises(ValueError):
+            PSA.dist_mat_to_vec(5, '6', '7')
+
+        with self.assertRaises(ValueError):
+            PSA.dist_mat_to_vec(5, float(6), 7)
+
 class _BaseHausdorffDistance(TestCase):
     '''Base Class setup and unit tests
     for various Hausdorff distance