def test_uncertainties(self):
"""Alignment.uncertainties should match hand-calculated values"""
aln = Alignment(['abc', 'axc'])
obs = aln.uncertainties()
self.assertFloatEqual(obs, [0, 1, 0])
#check what happens with only one input sequence
aln = Alignment(['abc'])
obs = aln.uncertainties()
self.assertFloatEqual(obs, [0, 0, 0])
#check that we can screen out bad items OK
aln = Alignment(['abc', 'def', 'ghi', 'jkl', 'GHI'])
obs = aln.uncertainties('abcdefghijklmnop')
self.assertFloatEqual(obs, [2.0] * 3)
