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

Class PositionPrior

java.lang.Object

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

All Implemented Interfaces:

Storable, Cloneable

Direct Known Subclasses:

GaussianLikePositionPrior, UniformPositionPrior

public abstract class PositionPrior
extends Object
implements Storable, Cloneable

This is the main class for any position prior that can be used in a motif discovery.

Author:

Jens Keilwagen

Field Summary

Fields

Modifier and Type	Field and Description
protected int	motifLength The length of the motif.

Constructor Summary

Constructors

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

Method Summary

Methods

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

Methods inherited from class java.lang.Object

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

Field Detail

motifLength

protected int motifLength

The length of the motif.

Constructor Detail

PositionPrior

protected PositionPrior()

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

PositionPrior

protected PositionPrior(StringBuffer rep)
                 throws NonParsableException

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

Parameters:

rep - the StringBuffer containing the model

Throws:

NonParsableException - if the StringBuffer can not be parsed

Method Detail

clone

public PositionPrior clone()
                    throws CloneNotSupportedException

Overrides:

clone in class Object

Throws:

CloneNotSupportedException

getLogPriorForPositions

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

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

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 abstract int getLength()

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

Returns:

the length that is supported or 0 for all lengths

getInstanceName

public abstract String getInstanceName()

Returns the instance name.

Returns:

the instance name

setMotifLength

public void setMotifLength(int motifLength)
                    throws IllegalArgumentException

Sets the length of the current motif.

Parameters:

motifLength - the motif length

Throws:

IllegalArgumentException - if the length is not positive or to big

toXML

public StringBuffer toXML()

Description copied from interface: Storable

This method returns an XML representation as StringBuffer of an instance of the implementing class.

Specified by:

toXML in interface Storable

Returns:

the XML representation

getAdditionalInformation

protected abstract StringBuffer getAdditionalInformation()

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

Returns:

a StringBuffer containing additional information for the XML representation

extractAdditionalInformation

protected abstract void extractAdditionalInformation(StringBuffer xml)
                                              throws NonParsableException

This method extracts additional information from a StringBuffer.

Parameters:

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

Throws:

NonParsableException - if the StringBuffer is not parsable