CloneSet273

Bio/HMM/MarkovModel.py

Bio/HMM/MarkovModel.py

    def set_emission_score(self,seq_state,emission_state,probability):   
        """Set the probability of a emission from a particular state.

        Raises:
        KeyError if the emission from the given state is not allowed.
        """ 
        if self.emission_prob.has_key((seq_state,emission_state)): 
            self.emission_prob[(seq_state,emission_state)] =  probability 
        else: 
             raise KeyError("Emission of %s from %s is not allowed."%(emission_state,seq_state)) 
        

    def set_emission_pseudocount(self,seq_state,emission_state,count):   
        """Set the default pseudocount for an emission.

        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 emissions have
        a pseudocount of 1.

        Raises:
        KeyError if the emission from the given state is not allowed.
        """ 
        if self.emission_pseudo.has_key((seq_state,emission_state)): 
            self.emission_pseudo[(seq_state,emission_state)] =  count 
        else: 
             raise KeyError("Emission of %s from %s is not allowed."%(emission_state,seq_state)) 
        

def [[#variable76bb04c0]](self,seq_state,emission_state, [[#variable76bb0080]]):
   [[#variable76bb0420]]
  if self. [[#variable76bb0480]].has_key((seq_state,emission_state)):
  
    self. [[#variable76bb0480]][(seq_state,emission_state)] = [[#variable76bb0080]]
  else:
  
    raise KeyError("Emission of %s from %s is not allowed."%(emission_state,seq_state)) 
  
 

set_emission_pseudocount 

set_emission_score 

count 

probability 

"""Set the default pseudocount for an emission.

        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 emissions have
        a pseudocount of 1.

        Raises:
        KeyError if the emission from the given state is not allowed.
        """ 

"""Set the probability of a emission from a particular state.

        Raises:
        KeyError if the emission from the given state is not allowed.
        """ 

emission_pseudo 

emission_prob