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Sourcecode: python-biopython version File versions

def Bio::HMM::MarkovModel::MarkovModelBuilder::allow_transition (   self,
  from_state,
  to_state,
  probability = None,
  pseudocount = None 
)

Set a transition as being possible between the two states.

probability and pseudocount are optional arguments
specifying the probabilities and pseudo counts for the transition.
If these are not supplied, then the values are set to the
default values.

Raises:
KeyError -- if the two states already have an allowed transition.

Definition at line 167 of file MarkovModel.py.

                                            :
        """Set a transition as being possible between the two states.

        probability and pseudocount are optional arguments
        specifying the probabilities and pseudo counts for the transition.
        If these are not supplied, then the values are set to the
        default values.

        Raises:
        KeyError -- if the two states already have an allowed transition.
        """
        # check the sanity of adding these states
        for state in [from_state, to_state]:
            assert state in self._state_alphabet, \
                   "State %s was not found in the sequence alphabet" % state

        # ensure that the states are not already set
        if ((from_state, to_state) not in self.transition_prob.keys() and 
            (from_state, to_state) not in self.transition_pseudo.keys()):
            # set the initial probability
            if probability is None:
                probability = 0
            self.transition_prob[(from_state, to_state)] = probability

            # set the initial pseudocounts
            if pseudocount is None:
                pseudcount = DEFAULT_PSEUDO
            self.transition_pseudo[(from_state, to_state)] = pseudocount 
        else:
            raise KeyError("Transtion from %s to %s is already allowed."
                           % (from_state, to_state))

    def destroy_transition(self, from_state, to_state):


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