def get_predefined_predicates(self):
codon_preds = _CodonPredicates(self.get_alphabet().get_genetic_code())
preds = _TimeReversibleNucleotide.get_predefined_predicates(self)
preds.update(
{
"indel": predicate.parse("???/---"),
"silent": predicate.UserPredicate(codon_preds.silent),
"replacement": predicate.UserPredicate(codon_preds.replacement),
"omega": predicate.UserPredicate(codon_preds.replacement),
}
)
return preds
def adapt_predicate(self, pred, label=None):
if isinstance(pred, str):
pred = predicate.parse(pred)
elif isinstance(pred, Callable):
pred = predicate.UserPredicate(pred)
pred_func = pred.make_model_predicate(self)
label = label or repr(pred)
mask = predicate2matrix(self.get_alphabet(),
pred_func,
mask=self._instantaneous_mask)
return (label, mask)