def setUp(self):
super(TestProfileHMMSegment, self).setUp()
self.hmm = build_hmm()
self.segment = ProfileHMMSegment(self.hmm, 1, 2)
self.string = self.config.getContent('test2.hhm')
def testConstructor(self):
self.segment.convert_scores(ScoreUnits.Probability)
self.assertEqual(self.hmm.segment(1, 1).layers.length, 1)
self.assertEqual(self.segment.layers.length, 2)
self.assertEqual(
self.segment.start.transitions[States.Match].probability, 1)
self.assertEqual(
self.segment.layers[1][States.Match].emission[ProteinAlphabet.CYS],
0.5)
self.assertRaises(IndexError, self.hmm.segment, 1, 3)
self.hmm.convert_scores(ScoreUnits.LogScales)
segment = ProfileHMMSegment(self.hmm, 1, 2)
self.assertEqual(segment.source_start, 1)