def evaluate(ancestry, lengths=None):
if lengths is None:
(wls_err, init_lengths) = wls_eval(ancestry)
else:
init_lengths = lengths
tree = ancestry2tree(ancestry, init_lengths, names)
lf = self.lf_factory(tree)
lf.setAlignment(subalign)
if lengths is not None:
lf.setParamRule('length', is_constant=True)
lf.optimise(show_progress=False, **self.opt_args)
err = -1.0 * lf.getLogLikelihood()
tree = lf.getAnnotatedTree()
return (err, tree)
def evaluate(ancestry, lengths=None):
if lengths is None:
(wls_err, init_lengths) = wls_eval(ancestry)
else:
init_lengths = lengths
tree = ancestry2tree(ancestry, init_lengths, names)
lf = self.lf_factory(tree)
lf.setAlignment(subalign)
if lengths is not None:
lf.setParamRule('length', is_constant=True)
lf.optimise(show_progress=False, **self.opt_args)
err = -1.0 * lf.getLogLikelihood()
tree = lf.getAnnotatedTree()
return (err, tree)
def result2output(self, err, ancestry, lengths, names):
return (err, ancestry2tree(ancestry, lengths, names))
def result2output(self, err, ancestry, lengths, names):
return (err, ancestry2tree(ancestry, lengths, names))
