de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states

Interface TrainableState

All Superinterfaces:

State

All Known Subinterfaces:

SamplingState

All Known Implementing Classes:

SimpleDifferentiableState, SimpleSamplingState, SimpleState

public interface TrainableState
extends State

This class implements method that allows to fill a statistic, which is used to estimate the parameters of a state during, for instance, the Baum-Welch training. All other methods that allow, for instance, to reset the statistic, to estimate the parameters from the statistic, ... are not defined in this interface to allow parameter sharing between states, and, hence, have to be defined on their own.

Author:

Jens Keilwagen

Method Summary

Modifier and Type	Method and Description
void	addToStatistic(int startPos, int endPos, double weight, Sequence seq) This method allows to add a certain weight to the sufficient statistic of the parameters that are used for scoring the specific subsequence(s).

Methods inherited from interface de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.State

getGraphvizNodeOptions, getLogScoreFor, isSilent, toString

Method Detail

addToStatistic

void addToStatistic(int startPos,
                    int endPos,
                    double weight,
                    Sequence seq)
             throws OperationNotSupportedException

This method allows to add a certain weight to the sufficient statistic of the parameters that are used for scoring the specific subsequence(s).

Parameters:

startPos - the start position

endPos - the end position

weight - the weight which will be added to the sufficient statistic

seq - the Sequence(s)

Throws:

OperationNotSupportedException - if the reverse complement of the sequence can not be computed