def makeQdDefn(self, word_probs, mprobs_matrix, rate_params):
"""Diagonalized Q, ie: rate matrix prepared for exponentiation"""
Q = CalcDefn(self.calcQ, name='Q')(word_probs, mprobs_matrix, *rate_params)
expm = NonParamDefn('expm')
exp = ExpDefn(expm)
Qd = CallDefn(exp, Q, name='Qd')
return Qd
def makeQdDefn(self, word_probs, mprobs_matrix, rate_params):
expm = NonParamDefn('expm')
exp = ExpDefn(expm)
calcExMat = CalcDefn(lambda: self.calcExchangeabilityMatrix,
name='calculate_exchangeability_matrix')()
Qd = CalcDefn(CalcQd, name='Qd')(exp, calcExMat, word_probs,
mprobs_matrix, *rate_params)
return Qd
def makeAlignmentDefn(self, model):
align = NonParamDefn('alignment', ('locus', ))
# The name of this matters, it's used in likelihood_function.py
# to retrieve the correct (adapted) alignment.
return AlignmentAdaptDefn(model, align)