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src/c/o/cogent-1.5.3/cogent/evolve/likelihood_calculation.py   cogent(Download)
from cogent.evolve.likelihood_tree import LikelihoodTreeEdge
from cogent.evolve.simulate import argpick
from cogent.maths.markov import SiteClassTransitionMatrix
 
__author__ = "Peter Maxwell"
 
        self.bprobs = [p/pprobs[self.alloc[i]] for (i,p) in enumerate(bprobs)]
        self.transition_matrix = SiteClassTransitionMatrix(switch, pprobs)
 
    def getWeightedSumLhs(self, lhs):

src/c/o/cogent-1.5.3/cogent/align/dp_calculation.py   cogent(Download)
#!/usr/bin/env/python
 
from cogent.maths.markov import SiteClassTransitionMatrix
from cogent.recalculation.definition import PositiveParamDefn, \
    ProbabilityParamDefn, CalculationDefn, CalcDefn, NonParamDefn, \
    else:
        assert bprobs
        R = SiteClassTransitionMatrix(switch, bprobs)
        TM = R.nestTransitionMatricies(tms)
    assert min(TM.Matrix.flat) >=0, bin_data

src/p/y/pycogent-HEAD/cogent/evolve/likelihood_calculation.py   pycogent(Download)
from cogent.evolve.likelihood_tree import LikelihoodTreeEdge
from cogent.evolve.simulate import argpick
from cogent.maths.markov import SiteClassTransitionMatrix
 
__author__ = "Peter Maxwell"
 
        self.bprobs = [p/pprobs[self.alloc[i]] for (i,p) in enumerate(bprobs)]
        self.transition_matrix = SiteClassTransitionMatrix(switch, pprobs)
 
    def getWeightedSumLhs(self, lhs):

src/p/y/pycogent-HEAD/cogent/align/dp_calculation.py   pycogent(Download)
#!/usr/bin/env/python
 
from cogent.maths.markov import SiteClassTransitionMatrix
from cogent.recalculation.definition import PositiveParamDefn, \
    ProbabilityParamDefn, CalculationDefn, CalcDefn, NonParamDefn, \
    else:
        assert bprobs
        R = SiteClassTransitionMatrix(switch, bprobs)
        TM = R.nestTransitionMatricies(tms)
    assert min(TM.Matrix.flat) >=0, bin_data