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 Emission
s for different State
s.
- Author:
- Jens Keilwagen
Fields inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.SimpleState |
e, forward, name |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
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 subsequencesname
- the name of the stateforward
- a switch that decides whether to use the forward or the reverse complementary strand of a sequence
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 indicespartDer
- a list for the partial derivationsseq
- 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