de.jstacs.data.sequences.annotation
Class CisRegulatoryModuleAnnotation

java.lang.Object
  de.jstacs.results.ResultSet
      de.jstacs.data.sequences.annotation.SequenceAnnotation
          de.jstacs.data.sequences.annotation.CisRegulatoryModuleAnnotation

All Implemented Interfaces:

Storable

public class CisRegulatoryModuleAnnotation
extends SequenceAnnotation

Annotation for a cis-regulatory module as defined by a set of MotifAnnotations of the motifs in the module.

Author:

Jan Grau

See Also:

MotifAnnotation

Field Summary

Fields inherited from class de.jstacs.results.ResultSet

results

Constructor Summary

CisRegulatoryModuleAnnotation(StringBuffer representation)
The standard constructor for the interface Storable.

CisRegulatoryModuleAnnotation(String identifier, MotifAnnotation[] motifs, Result... additionalAnnotation)
Creates a new CisRegulatoryModuleAnnotation from a set of motifs and possibly additional annotations.

Method Summary

Methods inherited from class de.jstacs.data.sequences.annotation.SequenceAnnotation

fromXML, getAnnotations, getIdentifier, getSubAnnotations, getType, hashCode, toString, toXML

Methods inherited from class de.jstacs.results.ResultSet

findColumn, getNumberOfResults, getResultAt, getResultForName, getResults

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

CisRegulatoryModuleAnnotation

public CisRegulatoryModuleAnnotation(String identifier,
                                     MotifAnnotation[] motifs,
                                     Result... additionalAnnotation)

Creates a new CisRegulatoryModuleAnnotation from a set of motifs and possibly additional annotations.

Parameters:

identifier - the identifier of this annotation

motifs - the motifs in the module

additionalAnnotation - the additional annotations

See Also:

SequenceAnnotation.SequenceAnnotation(String, String, SequenceAnnotation[], Result...)

CisRegulatoryModuleAnnotation

public CisRegulatoryModuleAnnotation(StringBuffer representation)
                              throws NonParsableException

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

Parameters:

representation - the XML representation as StringBuffer

Throws:

NonParsableException - if the CisRegulatoryModuleAnnotation could not be reconstructed out of the XML representation (the StringBuffer representation could not be parsed)

See Also:

SequenceAnnotation.SequenceAnnotation(StringBuffer), Storable