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

Class LogDPAlgorithms

          object --+    
                   |    
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!

Instance Methods

[hide private]

__init__(self, markov_model, sequence)
Initialize to calculate forward and backward probabilities.

source code

Inherited from AbstractDPAlgorithms: backward_algorithm, forward_algorithm

Inherited from AbstractDPAlgorithms (private): _backward_recursion, _forward_recursion

Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __str__

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, markov_model, sequence)
(Constructor)

source code

Initialize to calculate forward 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: object.__init__: (inherited documentation)

Class LogDPAlgorithms

__init__(self, markov_model, sequence) (Constructor)

init(self, markov_model, sequence)
(Constructor)