de.jstacs.motifDiscovery

Interface MutableMotifDiscoverer

All Superinterfaces:

Cloneable, MotifDiscoverer, Storable

All Known Implementing Classes:

ExtendedZOOPSDiffSM, IndependentProductDiffSM, MappingDiffSM, MixtureDiffSM, VariableLengthMixtureDiffSM

public interface MutableMotifDiscoverer
extends MotifDiscoverer

This is the interface that any tool for de-novo motif discovery should implement that allows any modify-operations like shift, shrink and expand. These operations are possible if the motif is mutable.

Author:

Jan Grau, Jens Keilwagen

See Also:

Mutable

Nested Class Summary

Nested classes/interfaces inherited from interface de.jstacs.motifDiscovery.MotifDiscoverer

MotifDiscoverer.KindOfProfile

Method Summary

Methods

Modifier and Type	Method and Description
void	adjustHiddenParameters(int index, DataSet[] data, double[][] weights) Adjusts all hidden parameters including duration and mixture parameters according to the current values of the remaining parameters.
void	initializeMotif(int motifIndex, DataSet data, double[] weights) This method allows to initialize the model of a motif manually using a weighted data set.
void	initializeMotifRandomly(int motif) This method initializes the motif with index motif randomly using for instance DifferentiableSequenceScore.initializeFunctionRandomly(boolean).
boolean	modifyMotif(int motifIndex, int offsetLeft, int offsetRight) Manually modifies the motif model with index motifIndex.

Methods inherited from interface de.jstacs.motifDiscovery.MotifDiscoverer

clone, getGlobalIndexOfMotifInComponent, getIndexOfMaximalComponentFor, getMotifLength, getNumberOfComponents, getNumberOfMotifs, getNumberOfMotifsInComponent, getProfileOfScoresFor, getStrandProbabilitiesFor

Methods inherited from interface de.jstacs.Storable

toXML

Method Detail

modifyMotif

boolean modifyMotif(int motifIndex,
                  int offsetLeft,
                  int offsetRight)
                    throws Exception

Manually modifies the motif model with index motifIndex. The two offsets offsetLeft and offsetRight define how many positions the left or right border positions shall be moved. Negative numbers indicate moves to the left while positive numbers correspond to moves to the right. The distribution for sequences to the left and right side of the motif shall be computed internally.

Parameters:

motifIndex - the index of the motif in the motif discoverer

offsetLeft - the offset on the left side

offsetRight - the offset on the right side

Returns:

true if the motif model was modified otherwise false

Throws:

Exception - if some unexpected error occurred during the modification

See Also:

modifyMotif(int, int, int), Mutable.modify(int, int)

initializeMotif

void initializeMotif(int motifIndex,
                   DataSet data,
                   double[] weights)
                     throws Exception

This method allows to initialize the model of a motif manually using a weighted data set.

Parameters:

motifIndex - the index of the motif in the motif discoverer

data - the data set of sequences

weights - either null or an array of length data.getNumberofElements() with non-negative weights.

Throws:

Exception - if initialize was not possible

initializeMotifRandomly

void initializeMotifRandomly(int motif)
                             throws Exception

This method initializes the motif with index motif randomly using for instance DifferentiableSequenceScore.initializeFunctionRandomly(boolean). Furthermore, if available, it also initializes the positional distribution.

Parameters:

motif - the index of the motif

Throws:

Exception - either if the index is wrong or if it is thrown by the method DifferentiableSequenceScore.initializeFunctionRandomly(boolean)

adjustHiddenParameters

void adjustHiddenParameters(int index,
                          DataSet[] data,
                          double[][] weights)
                            throws Exception

Adjusts all hidden parameters including duration and mixture parameters according to the current values of the remaining parameters.

Parameters:

index - the index of the class of this MutableMotifDiscoverer

data - the array of data for all classes

weights - the weights for all sequences in data

Throws:

Exception - thrown if the hidden parameters could not be adjusted