de.jstacs.motifDiscovery
Interface MotifDiscoverer

All Superinterfaces:

Cloneable, Storable

All Known Implementing Classes:

HiddenMotifMixture, SingleHiddenMotifMixture

public interface MotifDiscoverer
extends Cloneable, Storable

This is the interface that any tool for de novo motif discovery should implement.

Author:

Jan Grau, Jens Keilwagen

Nested Class Summary

static class

MotifDiscoverer.KindOfProfile This enum can be used to determine which kind of profile should be returned.

Method Summary

int	getGlobalIndexOfMotifInComponent(int component, int motif) Returns the global index of the motif used in component.
int	getIndexOfMaximalComponentFor(Sequence sequence) Returns the index of the component with the maximal score for the sequence sequence.
int	getMotifLength(int motif) This method returns the length of the motif with index motif.
int	getNumberOfComponents() Returns the number of components in this MotifDiscoverer.
int	getNumberOfMotifs() Returns the number of motifs for this MotifDiscoverer
int	getNumberOfMotifsInComponent(int component) Returns the number of motifs that are used in the component component of this motif discoverer.
double[]	getProfileOfScoresFor(int component, int motif, Sequence sequence, int startpos, MotifDiscoverer.KindOfProfile kind) Returns the profile of the scores for component component and motif motif at all possible start-positions of the motif in the sequence sequence.
StrandedLocatedSequenceAnnotationWithLength.Strand	getStrandFor(int component, int motif, Sequence sequence, int startpos) This method returns the strand for a given subsequence if it is consider as site of the motif model in a specific component.

Methods inherited from interface de.jstacs.Storable

toXML

Method Detail

getMotifLength

int getMotifLength(int motif)

This method returns the length of the motif with index motif.

Parameters:

motif - the index of the motif

Returns:

the length of the motif with index motif

getNumberOfComponents

int getNumberOfComponents()

Returns the number of components in this MotifDiscoverer.

Returns:

the number of components

getNumberOfMotifs

int getNumberOfMotifs()

Returns the number of motifs for this MotifDiscoverer

Returns:

the number of motifs

getNumberOfMotifsInComponent

int getNumberOfMotifsInComponent(int component)

Returns the number of motifs that are used in the component component of this motif discoverer.

Parameters:

component - the component

Returns:

the number of motifs

getIndexOfMaximalComponentFor

int getIndexOfMaximalComponentFor(Sequence sequence)
                                  throws Exception

Returns the index of the component with the maximal score for the sequence sequence.

Parameters:

sequence - the sequence

Returns:

the index of the maximal component

Throws:

Exception - if the index could not be computed for any reasons

getGlobalIndexOfMotifInComponent

int getGlobalIndexOfMotifInComponent(int component,
                                     int motif)

Returns the global index of the motif used in component. The index returned must be at least 0 and less than getNumberOfMotifs().

Parameters:

component - the component index

motif - the motif index in the component

Returns:

the global index of the motif in component

getProfileOfScoresFor

double[] getProfileOfScoresFor(int component,
                               int motif,
                               Sequence sequence,
                               int startpos,
                               MotifDiscoverer.KindOfProfile kind)
                               throws Exception

Returns the profile of the scores for component component and motif motif at all possible start-positions of the motif in the sequence sequence. This array should be of length sequence.length() - startpos - motifs[motif].length() + 1.
A high score should encode for a probable start position.

Parameters:

component - the component

motif - the index of the motif in the component

sequence - the sequence

startpos - the start position

kind - indicates the kind of profile

Returns:

the profile of scores

Throws:

Exception - if the score could not be computed for any reasons

getStrandFor

StrandedLocatedSequenceAnnotationWithLength.Strand getStrandFor(int component,
                                                                int motif,
                                                                Sequence sequence,
                                                                int startpos)
                                                                throws Exception

This method returns the strand for a given subsequence if it is consider as site of the motif model in a specific component.

Parameters:

component - the component

motif - the index of the motif in the component

sequence - the sequence

startpos - the start position in the sequence

Returns:

the predicted strand annotation

Throws:

Exception - if the strand could not be computed for any reasons