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

Class SimpleState

java.lang.Object

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

All Implemented Interfaces:

State, TrainableState

Direct Known Subclasses:

SimpleDifferentiableState, SimpleSamplingState

public class SimpleState
extends Object
implements TrainableState

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

Author:

Jens Keilwagen

Field Summary

Fields

Modifier and Type	Field and Description
protected Emission	e The emission that is internally used for scoring subsequences.
protected boolean	forward A switch that decides whether to use the forward or the reverse complementary strand of a sequence.
protected String	name The name of the state.

Constructor Summary

Constructors

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

Method Summary

Methods

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).
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.
String	getName() Returns the name of the state.
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.

Methods inherited from class java.lang.Object

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

Field Detail

e

protected Emission e

The emission that is internally used for scoring subsequences.

name

protected String name

The name of the state.

forward

protected boolean forward

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

Constructor Detail

SimpleState

public SimpleState(Emission 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

getGraphvizNodeOptions

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

Description copied from interface: State

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

Specified by:

getGraphvizNodeOptions in interface 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

getLogScoreFor

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

Description copied from interface: State

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.

Specified by:

getLogScoreFor in interface State

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

addToStatistic

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

Description copied from interface: TrainableState

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

Specified by:

addToStatistic in interface TrainableState

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

isSilent

public boolean isSilent()

Description copied from interface: State

This method returns whether a state is silent or not.

Specified by:

isSilent in interface State

Returns:

true if the state is silent, otherwise false

See Also:

SilentEmission

toString

public String toString(NumberFormat nf)

Description copied from interface: State

This method returns a String representation of the instance.

Specified by:

toString in interface State

Parameters:

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

Returns:

a String representation of the instance

getName

public String getName()

Returns the name of the state.

Returns:

the name