CloneSet353

Bio/HMM/DynamicProgramming.py

Bio/HMM/DynamicProgramming.py

            # now loop over the letters in the state path
            for main_state in state_letters: 
                 # calculate the forward value using the appropriate
                 # method to prevent underflow errors
                 forward_value = self._forward_recursion(main_state,i,forward_var) 


                 if forward_value is not None: 
                      forward_var[(main_state,i)] =  forward_value 

          # -- termination step - calculate the probability of the sequence
                 

            # now loop over the letters in the state path
            for main_state in state_letters: 
                 # calculate the backward value using the appropriate
                 # method to prevent underflow errors
                 backward_value = self._backward_recursion(main_state,i,backward_var) 


                 if backward_value is not None: 
                      backward_var[(main_state,i)] =  backward_value 

          # skip the termination step to avoid recalculations -- you should
          # get sequence probabilities using the forward algorithm
                 

  # now loop over the letters in the state path
  for main_state in state_letters:
  
    # calculate the forward value using the appropriate
    # calculate the backward value using the appropriate
    # method to prevent underflow errors
     [[#variable77a84160]]= self. [[#variable77a840a0]](main_state,i, [[#variable78b5bfa0]]) 
    if [[#variable77a84160]]is not None:
    
       [[#variable78b5bfa0]][(main_state,i)] = [[#variable77a84160]]
      # -- termination step - calculate the probability of the sequence
      # skip the termination step to avoid recalculations -- you should
      # get sequence probabilities using the forward algorithm
    
 

forward_value 

backward_value 

_forward_recursion 

_backward_recursion 

forward_var 

backward_var