def __init__(self, default=None, name=None, dimensions=None,
dimension=None, size=None, **kw):
PartitionDefn.__init__(self, default, name, dimensions,
dimension, size, **kw)
(dim_name, dim_cats) = self.internal_dimension
self.internal_dimensions = (dim_name, dim_name+"2")
self.array_template = DictArrayTemplate(dim_cats, dim_cats)
def __init__(self,
default=None,
name=None,
dimensions=None,
dimension=None,
size=None,
**kw):
PartitionDefn.__init__(self, default, name, dimensions, dimension,
size, **kw)
(dim_name, dim_cats) = self.internal_dimension
self.internal_dimensions = (dim_name, dim_name + "2")
self.array_template = DictArrayTemplate(dim_cats, dim_cats)
def makeForwardTreeDefn(subst_model,
tree,
bin_names,
with_indel_params=True,
kn=True):
"""Pairwise Fwd"""
indel = makeIndelModelDefn(with_indel_params, kn)
subst = subst_model.makeFundamentalParamControllerDefns(bin_names)
leaf = NonParamDefn('leaf', dimensions=('edge', ))
if len(bin_names) > 1:
switch = ProbabilityParamDefn('bin_switch', dimensions=['locus'])
bprobs = PartitionDefn([1.0 / len(bin_names) for bin in bin_names],
name="bprobs",
dimensions=['locus'],
dimension=('bin', bin_names))
edge_args = [switch, bprobs]
edge_defn_constructor = EdgeSumAndAlignDefnWithBins
else:
edge_args = []
edge_defn_constructor = EdgeSumAndAlignDefn
mprobs = subst['word_probs']
bin_data = CalcDefn(BinData)(mprobs, indel, subst['Qd'])
bin_data = bin_data.acrossDimension('bin', bin_names)
edge_args.extend(bin_data)
(top, scores) = _recursive_defns(tree, subst, leaf, edge_defn_constructor,
edge_args)
defn = FwdDefn(top)
#defn = SumDefn(*scores)
return AnnotateFloatDefn(defn, top)
def checkValueIsValid(self, value, is_constant):
if value.shape != (self.size,self.size):
raise ValueError("Wrong array shape %s for %s, expected (%s,%s)" %
(value.shape, self.name, self.size, self.size))
for part in value:
PartitionDefn.checkValueIsValid(self, part, is_constant)
def checkValueIsValid(self, value, is_constant):
if value.shape != (self.size, self.size):
raise ValueError("Wrong array shape %s for %s, expected (%s,%s)" %
(value.shape, self.name, self.size, self.size))
for part in value:
PartitionDefn.checkValueIsValid(self, part, is_constant)
