Bio.HMM.DynamicProgramming.LogDPAlgorithms

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

[show private | hide private]

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

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)

Generated by Epydoc 2.1 on Wed Jan 31 09:57:59 2007