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Bio::HMM::DynamicProgramming::AbstractDPAlgorithms Class Reference

Inheritance diagram for Bio::HMM::DynamicProgramming::AbstractDPAlgorithms:

Bio::HMM::DynamicProgramming::LogDPAlgorithms Bio::HMM::DynamicProgramming::ScaledDPAlgorithms

List of all members.


Detailed Description

An abstract class to calculate forward and backward probabiliies.

This class should not be instantiated directly, but should be used
through a derived class which implements proper scaling of variables.

This class is just meant to encapsulate the basic foward and backward
algorithms, and allow derived classes to deal with the problems of
multiplying probabilities.

Derived class of this must implement:

o _forward_recursion -- Calculate the forward values in the recursion
using some kind of technique for preventing underflow errors.

o _backward_recursion -- Calculate the backward values in the recursion
step using some technique to prevent underflow errors.

Definition at line 7 of file DynamicProgramming.py.


Public Member Functions

def __init__
def backward_algorithm
def forward_algorithm

Private Member Functions

def _backward_recursion
def _foward_recursion

Private Attributes

 _mm
 _seq

The documentation for this class was generated from the following file:

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