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

Class SimpleDifferentiableState

java.lang.Object

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

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

All Implemented Interfaces:

DifferentiableState, State, TrainableState

public class SimpleDifferentiableState
extends SimpleState
implements DifferentiableState

This class implements a State based on Emission that allows to reuse Emissions for different States.

Author:

Jens Keilwagen

Field Summary

Fields inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.SimpleState

e, forward, name

Constructor Summary

Constructors

Constructor and Description
SimpleDifferentiableState(DifferentiableEmission e, String name, boolean forward) This is the constructor of a SimpleState.

Method Summary

Methods

Modifier and Type	Method and Description
double	getLogScoreAndPartialDerivation(int startPos, int endPos, IntList indices, DoubleList partDer, Sequence seq) This method allows to compute the logarithm of the score and the gradient for the given subsequences.

Methods inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.SimpleState

addToStatistic, getGraphvizNodeOptions, getLogScoreFor, getName, isSilent, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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

getGraphvizNodeOptions, getLogScoreFor, isSilent, toString

Constructor Detail

SimpleDifferentiableState

public SimpleDifferentiableState(DifferentiableEmission e,
                         String name,
                         boolean forward)

This is the constructor of a SimpleState.

Parameters:

e - the emission that is internally used for scoring subsequences

name - the name of the state

forward - a switch that decides whether to use the forward or the reverse complementary strand of a sequence

Method Detail

getLogScoreAndPartialDerivation

public double getLogScoreAndPartialDerivation(int startPos,
                                     int endPos,
                                     IntList indices,
                                     DoubleList partDer,
                                     Sequence seq)
                                       throws WrongLengthException,
                                              OperationNotSupportedException

Description copied from interface: DifferentiableState

This method allows to compute the logarithm of the score and the gradient for the given subsequences.

Specified by:

getLogScoreAndPartialDerivation in interface DifferentiableState

Parameters:

startPos - the start position (inclusive)

endPos - the end position (inclusive)

indices - a list for the parameter indices

partDer - a list for the partial derivations

seq - the Sequence(s)

Returns:

the logarithm of the score

Throws:

WrongLengthException - if the length can not be modeled

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