def test_init(self):
"""PC: init functions as expected """
# instantiate the class
pc = PerformanceCalculator(self._gold_standard_data)
# Check one of the values
self.assertEqual(\
pc._gold_standard['12206666'][PointMutation(95,'D','N')],2)
def test_normalized_mutations_blank_gs(self):
"""PC: Normalized Mutations functions with no gold standard mutations
"""
# Functions with an empty gold standard dict
pc = PerformanceCalculator(self._blank_mutation_data)
perf = pc.calculate_normalized_mutations(\
self._gold_standard_data)
self.assertEqual(perf.TruePositive,0)
self.assertEqual(perf.FalsePositive,6)
self.assertEqual(perf.FalseNegative,0)
self.assertEqual(perf.TrueNegative,None)
def test_document_retrieval_blank_gs(self):
"""PC: Document Retrieval functions with no gold standard mutations
"""
# Functions with an empty gold standard dict
pc = PerformanceCalculator(self._blank_mutation_data)
perf = pc.calculate_document_retrieval(\
self._gold_standard_data)
self.assertEqual(perf.TruePositive,0)
self.assertEqual(perf.FalsePositive,3)
self.assertEqual(perf.FalseNegative,0)
self.assertEqual(perf.TrueNegative,1)
def test_normalized_mutations_invalid_input(self):
"""PC: Normalized Mutations handles invalid input correctly
"""
# Handles gold-standard and extractor output which does
# not completely overlap correctly -- this is explictly
# not allowed because it is not clear how it should be
# handled
pc = PerformanceCalculator({'1':{},'2':{}})
self.assertRaises(PerformanceCalculatorError,\
pc.calculate_normalized_mutations,{'1':{},'3':{}})
self.assertRaises(PerformanceCalculatorError,\
pc.calculate_normalized_mutations,{'1':{}})
self.assertRaises(PerformanceCalculatorError,\
pc.calculate_normalized_mutations,{'1':{},'2':{},'3':{}})
def setUp(self):
""" Set up variables for the tests"""
self._gold_standard_data = gold_standard_data
self._blank_mutation_data =\
{'3476160':{},'14500716':{},'12206666':{},'11327835':{}}
self._pc = PerformanceCalculator(self._gold_standard_data)
