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

Interface State

All Known Subinterfaces:

DifferentiableState, SamplingState, TrainableState

All Known Implementing Classes:

SimpleDifferentiableState, SimpleSamplingState, SimpleState

public interface State

This interface declares the methods of any state used in a hidden Markov model.

Author:

Jan Grau, Jens Keilwagen, Michael Scharfe

See Also:

AbstractHMM

Method Summary

Modifier and Type	Method and Description
String	getGraphvizNodeOptions(double weight, double maxWeight, NumberFormat nf) This method returns a String representation of the node options that can be used in Graphviz to create the node for this state.
double	getLogScoreFor(int startPos, int endPos, Sequence seq) This method returns the logarithm of the score for a given sequence with given start and end position.
boolean	isSilent() This method returns whether a state is silent or not.
String	toString(NumberFormat nf) This method returns a String representation of the instance.

Method Detail

getLogScoreFor

double getLogScoreFor(int startPos,
                      int endPos,
                      Sequence seq)
               throws WrongLengthException,
                      OperationNotSupportedException

This method returns the logarithm of the score for a given sequence with given start and end position. The method provides the basics for quantifying emission probability/density.

Parameters:

startPos - the start position within the sequence(s)

endPos - the end position within the sequence(s)

seq - the sequence(s)

Returns:

the logarithm of score for the given sequence(s)

Throws:

WrongLengthException - if the length can not be modeled

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

getGraphvizNodeOptions

String getGraphvizNodeOptions(double weight,
                              double maxWeight,
                              NumberFormat nf)

This method returns a String representation of the node options that can be used in Graphviz to create the node for this state.

Parameters:

weight - for state

maxWeight - the maximal weight for the state

nf - the NumberFormat for the output, can be null

Returns:

String representation of the state

isSilent

boolean isSilent()

This method returns whether a state is silent or not.

Returns:

true if the state is silent, otherwise false

See Also:

SilentEmission

toString

String toString(NumberFormat nf)

This method returns a String representation of the instance.

Parameters:

nf - the NumberFormat for the String representation of parameters or probabilities

Returns:

a String representation of the instance