gov.nih.nci.mageom.domain.DesignElement.impl
Class ReporterCompositeMapImpl

java.lang.Object
  extended by gov.nih.nci.mageom.domain.impl.MAGEOMObject
      extended by gov.nih.nci.mageom.domain.impl.ExtendableImpl
          extended by gov.nih.nci.mageom.domain.impl.DescribableImpl
              extended by gov.nih.nci.mageom.domain.impl.IdentifiableImpl
                  extended by gov.nih.nci.mageom.domain.BioEvent.impl.BioEventImpl
                      extended by gov.nih.nci.mageom.domain.BioEvent.impl.MapImpl
                          extended by gov.nih.nci.mageom.domain.BioAssayData.impl.DesignElementMapImpl
                              extended by gov.nih.nci.mageom.domain.DesignElement.impl.ReporterCompositeMapImpl
All Implemented Interfaces:
DesignElementMap, BioEvent, Map, Describable, ReporterCompositeMap, Extendable, Identifiable, java.io.Serializable

public class ReporterCompositeMapImpl
extends DesignElementMapImpl
implements ReporterCompositeMap

A ReporterCompositeMap is the description of how source Reporters are transformed into a target CompositeSequences. For instance, several reporters that tile across a section of a chromosome could be mapped to a CompositeSequence.

Version:
%I%, %G%
See Also:
Serialized Form

Field Summary
protected static java.util.ArrayList allAssociationMethods
           
protected static java.util.Hashtable associationMethods
           
protected  CompositeSequence compositeSequence
          DOCUMENT ME
protected  java.lang.Long compositeSequenceId
          The internal ID of the associated compositeSequence object.
protected  ReporterPosition[] reporterPositionSources
          DOCUMENT ME
protected  int reporterPositionSourcesCount
          The count of ReporterPosition objects.
 
Fields inherited from class gov.nih.nci.mageom.domain.BioEvent.impl.BioEventImpl
protocolApplications, protocolApplicationsCount
 
Fields inherited from class gov.nih.nci.mageom.domain.impl.IdentifiableImpl
identifier, name
 
Fields inherited from class gov.nih.nci.mageom.domain.impl.DescribableImpl
auditTrail, auditTrailCount, descriptions, descriptionsCount, security, securityId
 
Fields inherited from class gov.nih.nci.mageom.domain.impl.ExtendableImpl
propertySets, propertySetsCount, securedElementId
 
Constructor Summary
ReporterCompositeMapImpl()
          Default constructor
 
Method Summary
 CompositeSequence getCompositeSequence()
          Returns the value of this ReporterCompositeMap object's compositeSequence attribute.
 ReporterPosition[] getReporterPositionSources()
          Returns the value of this ReporterCompositeMap object's reporterPositionSources attribute.
 int getReporterPositionSourcesCount()
          Returns the count of all ReporterPosition associated with this ReporterCompositeMap object.
 java.util.Hashtable getXMLMethodDescriptors()
          Returns a Hashtable containing XMLMethodDescriptors descriptors of the association methods of this object.
protected  void init()
           
 ReporterCompositeMap[] searchReporterCompositeMaps(ReporterCompositeMapSearchCriteria criteria)
          Returns an array of ReporterCompositeMap objects that satisfy the given ReporterCompositeMapSearchCriteria.
 void setCompositeSequence(CompositeSequence p_compositeSequence)
          Sets the compositeSequence attribute.
 void setReporterPositionSources(ReporterPosition[] p_reporterPositionSources)
          Sets the reporterPositionSources attribute.
 java.lang.String toString()
          Returns a String representation of this object suitable for console display.
 org.w3c.dom.Element toXML(org.w3c.dom.Document doc)
           
 org.w3c.dom.Element toXMLDoc(org.w3c.dom.Document doc)
           
 org.w3c.dom.Element toXMLProcessor(org.w3c.dom.Document doc, java.util.ArrayList fillOutValues)
          Returns an XML representation of the object.
 
Methods inherited from class gov.nih.nci.mageom.domain.BioAssayData.impl.DesignElementMapImpl
searchDesignElementMaps
 
Methods inherited from class gov.nih.nci.mageom.domain.BioEvent.impl.MapImpl
searchMaps
 
Methods inherited from class gov.nih.nci.mageom.domain.BioEvent.impl.BioEventImpl
getProtocolApplications, getProtocolApplicationsCount, searchBioEvents, setProtocolApplications
 
Methods inherited from class gov.nih.nci.mageom.domain.impl.IdentifiableImpl
getIdentifier, getName, searchIdentifiables, setIdentifier, setName
 
Methods inherited from class gov.nih.nci.mageom.domain.impl.DescribableImpl
getAuditTrail, getAuditTrailCount, getDescriptions, getDescriptionsCount, getSecurity, searchDescribables, setAuditTrail, setDescriptions, setSecurity
 
Methods inherited from class gov.nih.nci.mageom.domain.impl.ExtendableImpl
getPropertySets, getPropertySetsCount, getSecuredElementId, searchExtendables, setPropertySets, setSecuredElementId
 
Methods inherited from class gov.nih.nci.mageom.domain.impl.MAGEOMObject
getId, getIsEditable, setId
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 
Methods inherited from interface gov.nih.nci.mageom.domain.BioEvent.BioEvent
getProtocolApplications, setProtocolApplications
 
Methods inherited from interface gov.nih.nci.mageom.domain.Identifiable
getIdentifier, getName, setIdentifier, setName
 
Methods inherited from interface gov.nih.nci.mageom.domain.Describable
getAuditTrail, getDescriptions, getSecurity, setAuditTrail, setDescriptions, setSecurity
 
Methods inherited from interface gov.nih.nci.mageom.domain.Extendable
getPropertySets, setPropertySets
 

Field Detail

allAssociationMethods

protected static java.util.ArrayList allAssociationMethods

associationMethods

protected static java.util.Hashtable associationMethods

reporterPositionSourcesCount

protected int reporterPositionSourcesCount
The count of ReporterPosition objects.


reporterPositionSources

protected ReporterPosition[] reporterPositionSources
DOCUMENT ME


compositeSequence

protected CompositeSequence compositeSequence
DOCUMENT ME


compositeSequenceId

protected java.lang.Long compositeSequenceId
The internal ID of the associated compositeSequence object.

Constructor Detail

ReporterCompositeMapImpl

public ReporterCompositeMapImpl()
Default constructor

Method Detail

init

protected void init()
Overrides:
init in class DesignElementMapImpl

searchReporterCompositeMaps

public ReporterCompositeMap[] searchReporterCompositeMaps(ReporterCompositeMapSearchCriteria criteria)
                                                   throws gov.nih.nci.common.search.SearchException
Returns an array of ReporterCompositeMap objects that satisfy the given ReporterCompositeMapSearchCriteria.

Parameters:
criteria - The ReporterCompositeMapSearchCriteria which represents a query for ReporterCompositeMap objects.
Returns:
An array of ReporterCompositeMap objects.
Throws:
A - gov.nih.nci.common.search.SearchException if there is a problem searching.
gov.nih.nci.common.search.SearchException

setReporterPositionSources

public void setReporterPositionSources(ReporterPosition[] p_reporterPositionSources)
Sets the reporterPositionSources attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a ReporterCompositeMap object.

Specified by:
setReporterPositionSources in interface ReporterCompositeMap
Parameters:
p_reporterPositionSources - The new value for reporterPositionSources.
See Also:
ReporterCompositeMap.getReporterPositionSources()

getReporterPositionSources

public ReporterPosition[] getReporterPositionSources()
Description copied from interface: ReporterCompositeMap
Returns the value of this ReporterCompositeMap object's reporterPositionSources attribute.

Specified by:
getReporterPositionSources in interface ReporterCompositeMap
Returns:
gov.nih.nci.mageom.bean.DesignElement.ReporterPosition[] The value of reporterPositionSources.
See Also:
ReporterCompositeMap.getReporterPositionSources()

setCompositeSequence

public void setCompositeSequence(CompositeSequence p_compositeSequence)
Sets the compositeSequence attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a ReporterCompositeMap object.

Specified by:
setCompositeSequence in interface ReporterCompositeMap
Parameters:
p_compositeSequence - The new value for compositeSequence.
See Also:
ReporterCompositeMap.getCompositeSequence()

getCompositeSequence

public CompositeSequence getCompositeSequence()
Description copied from interface: ReporterCompositeMap
Returns the value of this ReporterCompositeMap object's compositeSequence attribute.

Specified by:
getCompositeSequence in interface ReporterCompositeMap
Returns:
gov.nih.nci.mageom.bean.DesignElement.CompositeSequence The value of compositeSequence.
See Also:
ReporterCompositeMap.getCompositeSequence()

getReporterPositionSourcesCount

public int getReporterPositionSourcesCount()
Returns the count of all ReporterPosition associated with this ReporterCompositeMap object.

Returns:
the count
See Also:
ReporterCompositeMap.getReporterPositionSources()

toXML

public org.w3c.dom.Element toXML(org.w3c.dom.Document doc)
Overrides:
toXML in class DesignElementMapImpl

toXMLDoc

public org.w3c.dom.Element toXMLDoc(org.w3c.dom.Document doc)
Overrides:
toXMLDoc in class DesignElementMapImpl

toXMLProcessor

public org.w3c.dom.Element toXMLProcessor(org.w3c.dom.Document doc,
                                          java.util.ArrayList fillOutValues)
Returns an XML representation of the object. The document is not modified.

Overrides:
toXMLProcessor in class DesignElementMapImpl
Parameters:
doc - the working document
fillOutValues - a list of attribute names that should have full XML for their values.
Returns:
org.w3c.dom.Element an XML representation

getXMLMethodDescriptors

public java.util.Hashtable getXMLMethodDescriptors()
Returns a Hashtable containing XMLMethodDescriptors descriptors of the association methods of this object.

Overrides:
getXMLMethodDescriptors in class DesignElementMapImpl
Returns:
Hashtable The Hashtable of descriptors.

toString

public java.lang.String toString()
Returns a String representation of this object suitable for console display.

Overrides:
toString in class DesignElementMapImpl
Returns:
the String representation.