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Sourcecode: python-biopython version File versions

def Bio::HMM::MarkovModel::MarkovModelBuilder::set_transition_pseudocount (   self,
  from_state,
  to_state,
  count 
)

Set the default pseudocount for a transition.

To avoid computational problems, it is helpful to be able to
set a 'default' pseudocount to start with for estimating
transition and emission probabilities (see p62 in Durbin et al
for more discussion on this. By default, all transitions have
a pseudocount of 1.

Raises:
KeyError if the transition is not allowed.

Definition at line 225 of file MarkovModel.py.

00225                                                                      :
        """Set the default pseudocount for a transition.

        To avoid computational problems, it is helpful to be able to
        set a 'default' pseudocount to start with for estimating
        transition and emission probabilities (see p62 in Durbin et al
        for more discussion on this. By default, all transitions have
        a pseudocount of 1.

        Raises:
        KeyError if the transition is not allowed.
        """
        if self.transition_pseudo.has_key((from_state, to_state)):
            self.transition_pseudo[(from_state, to_state)] = count
        else:
            raise KeyError("Transition from %s to %s is not allowed."
                           % (from_state, to_state))

    # --- functions to deal with emissions from the sequence

    def set_emission_score(self, seq_state, emission_state, probability):


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