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

Class GaussianLikePositionPrior

java.lang.Object

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

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

All Implemented Interfaces:

Storable, Cloneable

public class GaussianLikePositionPrior
extends PositionPrior

This class implements a gaussian like discrete truncated prior.

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
GaussianLikePositionPrior(int length, double max, double sigma) This constructor creates an instance with given sequence length, maximal value and sigma for the Gaussian.
GaussianLikePositionPrior(StringBuffer rep) 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) Returns only the important part and leaving the logarithm of the normalization constant out.
void	setMotifLength(int motifLength) Sets the length of the current motif.

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

clone, toXML

Methods inherited from class java.lang.Object

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

Constructor Detail

GaussianLikePositionPrior

public GaussianLikePositionPrior(int length,
                                 double max,
                                 double sigma)

This constructor creates an instance with given sequence length, maximal value and sigma for the Gaussian.

Parameters:

length - the sequence length

max - the maximal position

sigma - the standard deviation (sigma) of the Gaussian

GaussianLikePositionPrior

public GaussianLikePositionPrior(StringBuffer rep)
                          throws NonParsableException

The standard constructor for the interface Storable. Creates a new GaussianLikePositionPrior out of a StringBuffer.

Parameters:

rep - the StringBuffer

Throws:

NonParsableException - if the StringBuffer can not be parsed

Method Detail

setMotifLength

public void setMotifLength(int motifLength)

Description copied from class: PositionPrior

Sets the length of the current motif.

Overrides:

setMotifLength in class PositionPrior

Parameters:

motifLength - the motif length

getLogPriorForPositions

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

Returns only the important part and leaving the logarithm of the normalization constant out.

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 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)
                                     throws NonParsableException

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

Throws:

NonParsableException - if the StringBuffer is not parsable