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src/c/o/cogent-1.5.3/cogent/evolve/solved_models.py   cogent(Download)
    def makeContinuousPsubDefn(self, word_probs, mprobs_matrix, distance, rate_params):
        # Only one set of mprobs will be used
        assert word_probs is mprobs_matrix
        # Order of bases is assumed later, so check it really is Y,Y,R,R:
        alphabet = self.getAlphabet()

src/p/y/pycogent-HEAD/cogent/evolve/solved_models.py   pycogent(Download)
    def makeContinuousPsubDefn(self, word_probs, mprobs_matrix, distance, rate_params):
        # Only one set of mprobs will be used
        assert word_probs is mprobs_matrix
        # Order of bases is assumed later, so check it really is Y,Y,R,R:
        alphabet = self.getAlphabet()

src/p/y/pycogent-HEAD/tests/test_evolve/test_substitution_model.py   pycogent(Download)
    def test_excludeinggaps(self):
        """testing excluding gaps from model"""
        model = substitution_model.Nucleotide(model_gaps=False)
        assert len(model.getAlphabet()) == 4
 
    def test_includinggaps(self):
        """testing excluding gaps from model"""
        model = substitution_model.Nucleotide(model_gaps=True)
        assert len(model.getAlphabet()) == 5

src/c/o/cogent-1.5.3/tests/test_evolve/test_substitution_model.py   cogent(Download)
    def test_excludeinggaps(self):
        """testing excluding gaps from model"""
        model = substitution_model.Nucleotide(model_gaps=False)
        assert len(model.getAlphabet()) == 4
 
    def test_includinggaps(self):
        """testing excluding gaps from model"""
        model = substitution_model.Nucleotide(model_gaps=True)
        assert len(model.getAlphabet()) == 5