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Sourcecode: python-biopython version File versions

def Bio::HMM::MarkovModel::MarkovModelBuilder::__init__ (   self,
  state_alphabet,
  emission_alphabet 
)

Initialize a builder to create Markov Models.

Arguments:

o state_alphabet -- An alphabet containing all of the letters that
can appear in the states
       
o emission_alphabet -- An alphabet containing all of the letters for
states that can be emitted by the HMM.

Definition at line 24 of file MarkovModel.py.

00024                                                          :
        """Initialize a builder to create Markov Models.

        Arguments:

        o state_alphabet -- An alphabet containing all of the letters that
        can appear in the states
       
        o emission_alphabet -- An alphabet containing all of the letters for
        states that can be emitted by the HMM.
        """
        self._state_alphabet = state_alphabet
        self._emission_alphabet = emission_alphabet
        
        # the probabilities for transitions and emissions
        # by default we have no transitions and all possible emissions
        self.transition_prob = {}
        self.emission_prob = self._all_blank(state_alphabet,
                                             emission_alphabet)

        # the default pseudocounts for transition and emission counting
        self.transition_pseudo = {}
        self.emission_pseudo = self._all_pseudo(state_alphabet,
                                                emission_alphabet)

    def _all_blank(self, first_alphabet, second_alphabet):


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