de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.positionprior

Class UniformPositionPrior

java.lang.Object

de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.positionprior.PositionPrior

de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.positionprior.UniformPositionPrior

All Implemented Interfaces:

Storable, Cloneable

public class UniformPositionPrior
extends PositionPrior

This prior implements a uniform distribution for the start position.

Author:

Jens Keilwagen

Field Summary

Fields inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.positionprior.PositionPrior

motifLength

Constructor Summary

Constructors

Constructor and Description
UniformPositionPrior() This empty constructor creates an instance with motif length -1.
UniformPositionPrior(StringBuffer xml) The standard constructor for the interface Storable.

Method Summary

Modifier and Type	Method and Description
protected void	extractAdditionalInformation(StringBuffer xml) This method extracts additional information from a StringBuffer.
protected StringBuffer	getAdditionalInformation() This method returns a StringBuffer containing additional information for the XML representation.
String	getInstanceName() Returns the instance name.
int	getLength() Returns the length that is supported by this prior.
double	getLogPriorForPositions(int seqLength, int... starts) The logarithmic value of the prior for specified start positions of the part motifs.

Methods inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.positionprior.PositionPrior

clone, setMotifLength, toXML

Methods inherited from class java.lang.Object

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

Constructor Detail

UniformPositionPrior

public UniformPositionPrior()

This empty constructor creates an instance with motif length -1.

UniformPositionPrior

public UniformPositionPrior(StringBuffer xml)
                     throws NonParsableException

The standard constructor for the interface Storable. Creates a new UniformPositionPrior out of its XML representation.

Parameters:

xml - the XML representation as StringBuffer

Throws:

NonParsableException - if the StringBuffer can not be parsed

Method Detail

getLogPriorForPositions

public double getLogPriorForPositions(int seqLength,
                                      int... starts)
                               throws IllegalArgumentException

Description copied from class: PositionPrior

The logarithmic value of the prior for specified start positions of the part motifs.

Specified by:

getLogPriorForPositions in class PositionPrior

Parameters:

seqLength - the length of the sequence

starts - the start positions of the part motifs

Returns:

the value of the prior for given start positions

Throws:

IllegalArgumentException - if something went wrong, e.g. the motif length is not set.

getLength

public final int getLength()

Description copied from class: PositionPrior

Returns the length that is supported by this prior. If all lengths greater than the minimal length are supported, this method returns 0.

Specified by:

getLength in class PositionPrior

Returns:

the length that is supported or 0 for all lengths

getInstanceName

public String getInstanceName()

Description copied from class: PositionPrior

Returns the instance name.

Specified by:

getInstanceName in class PositionPrior

Returns:

the instance name

getAdditionalInformation

protected StringBuffer getAdditionalInformation()

Description copied from class: PositionPrior

This method returns a StringBuffer containing additional information for the XML representation.

Specified by:

getAdditionalInformation in class PositionPrior

Returns:

a StringBuffer containing additional information for the XML representation

extractAdditionalInformation

protected void extractAdditionalInformation(StringBuffer xml)

Description copied from class: PositionPrior

This method extracts additional information from a StringBuffer.

Specified by:

extractAdditionalInformation in class PositionPrior

Parameters:

xml - the StringBuffer containing the additional information of the XML representation