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src/c/o/cogent-1.5.3/cogent/evolve/substitution_model.py   cogent(Download)
from cogent.core import moltype
from cogent.evolve import parameter_controller, predicate, motif_prob_model
from cogent.evolve.substitution_calculation import (
    SubstitutionParameterDefn as ParamDefn, 
    RateDefn, LengthDefn, ProductDefn, CallDefn, CalcDefn,
    def _makeBinParamDefn(self, edge_par_name, bin_par_name, bprob_defn):
        # if no ordered param defined, behaves as old, everything indexed by and edge
        if edge_par_name not in self.partitioned_params:
            return ParamDefn(dimensions=['bin'], name=bin_par_name)
 
    def makeRateParams(self, bprobs):
        params = []
        for param_name in self.parameter_order:
            if bprobs is None or param_name not in self.partitioned_params:
                defn = ParamDefn(param_name)
            else:
                e_defn = ParamDefn(param_name, dimensions=['edge', 'locus'])

src/p/y/pycogent-HEAD/cogent/evolve/substitution_model.py   pycogent(Download)
from cogent.core import moltype
from cogent.evolve import parameter_controller, predicate, motif_prob_model
from cogent.evolve.substitution_calculation import (
    SubstitutionParameterDefn as ParamDefn, 
    RateDefn, LengthDefn, ProductDefn, CallDefn, CalcDefn,
    def _makeBinParamDefn(self, edge_par_name, bin_par_name, bprob_defn):
        # if no ordered param defined, behaves as old, everything indexed by and edge
        if edge_par_name not in self.partitioned_params:
            return ParamDefn(dimensions=['bin'], name=bin_par_name)
 
    def makeRateParams(self, bprobs):
        params = []
        for param_name in self.parameter_order:
            if bprobs is None or param_name not in self.partitioned_params:
                defn = ParamDefn(param_name)
            else:
                e_defn = ParamDefn(param_name, dimensions=['edge', 'locus'])