def makeMotifProbsDefn(self):
"""Makes the first part of a parameter controller definition for this
model, the calculation of motif probabilities"""
return substitution_calculation.PartitionDefn(
name="mprobs",
default=None,
dimensions=('locus', 'edge'),
dimension=('motif', tuple(self.getInputAlphabet())))
def makeMotifWordProbDefns(self):
monomer_probs = substitution_calculation.PartitionDefn(
name="psmprobs",
default=None,
dimensions=('locus', 'position', 'edge'),
dimension=('motif', tuple(self.getInputAlphabet())))
monomer_probs3 = monomer_probs.acrossDimension(
'position', [str(i) for i in range(self.word_length)])
monomer_probs3 = substitution_calculation.CalcDefn(
lambda *x: numpy.array(x), name='mprobs')(*monomer_probs3)
word_probs = substitution_calculation.CalcDefn(
self.calcWordProbs, name="wprobs")(monomer_probs3)
mprobs_matrix = substitution_calculation.CalcDefn(
self.calcWordWeightMatrix, name="mprobs_matrix")(monomer_probs3)
return (monomer_probs, word_probs, mprobs_matrix)