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):
