Package Bio :: Package HMM :: Module DynamicProgramming :: Class LogDPAlgorithms
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Class LogDPAlgorithms

AbstractDPAlgorithms --+
                       |
                      LogDPAlgorithms


Implement forward and backward algorithms using a log approach.

This uses the approach of calculating the sum of log probabilities using a lookup table for common values.

XXX This is not implemented yet!
Method Summary
  __init__(self, markov_model, sequence)
Initialize to calculate foward and backward probabilities.
    Inherited from AbstractDPAlgorithms
  backward_algorithm(self)
Calculate sequence probability using the backward algorithm.
  forward_algorithm(self)
Calculate sequence probability using the forward algorithm.
  _backward_recursion(self, cur_state, sequence_pos, forward_vars)
Calculate the backward recursion value.
  _foward_recursion(self, cur_state, sequence_pos, forward_vars)
Calculate the forward recursion value.

Method Details

__init__(self, markov_model, sequence)
(Constructor)

Initialize to calculate foward and backward probabilities.

Arguments:

o markov_model -- The current Markov model we are working with.

o sequence -- A training sequence containing a set of emissions.
Overrides:
Bio.HMM.DynamicProgramming.AbstractDPAlgorithms.__init__ (inherited documentation)

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