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

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.CompositeCompositeMapImpl
All Implemented Interfaces:
DesignElementMap, BioEvent, Map, Describable, CompositeCompositeMap, Extendable, Identifiable, java.io.Serializable

public class CompositeCompositeMapImpl
extends DesignElementMapImpl
implements CompositeCompositeMap

A CompositeCompositeMap is the description of how source CompositeSequences are transformed into a target CompositeSequence. For instance, several CompositeSequences could represent different sequence regions for a Gene and could be mapped to different CompositeSequences, each representing a different splice variant for that Gene.

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

Field Summary
protected static java.util.ArrayList allAssociationMethods
           
protected static java.util.Hashtable associationMethods
           
protected  CompositePosition[] compositePositionSources
          DOCUMENT ME
protected  int compositePositionSourcesCount
          The count of CompositePosition objects.
protected  CompositeSequence compositeSequence
          DOCUMENT ME
protected  java.lang.Long compositeSequenceId
          The internal ID of the associated compositeSequence object.
 
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
CompositeCompositeMapImpl()
          Default constructor
 
Method Summary
 CompositePosition[] getCompositePositionSources()
          Returns the value of this CompositeCompositeMap object's compositePositionSources attribute.
 int getCompositePositionSourcesCount()
          Returns the count of all CompositePosition associated with this CompositeCompositeMap object.
 CompositeSequence getCompositeSequence()
          Returns the value of this CompositeCompositeMap object's compositeSequence attribute.
 java.util.Hashtable getXMLMethodDescriptors()
          Returns a Hashtable containing XMLMethodDescriptors descriptors of the association methods of this object.
protected  void init()
           
 CompositeCompositeMap[] searchCompositeCompositeMaps(CompositeCompositeMapSearchCriteria criteria)
          Returns an array of CompositeCompositeMap objects that satisfy the given CompositeCompositeMapSearchCriteria.
 void setCompositePositionSources(CompositePosition[] p_compositePositionSources)
          Sets the compositePositionSources attribute.
 void setCompositeSequence(CompositeSequence p_compositeSequence)
          Sets the compositeSequence 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

compositeSequence

protected CompositeSequence compositeSequence
DOCUMENT ME


compositeSequenceId

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


compositePositionSourcesCount

protected int compositePositionSourcesCount
The count of CompositePosition objects.


compositePositionSources

protected CompositePosition[] compositePositionSources
DOCUMENT ME

Constructor Detail

CompositeCompositeMapImpl

public CompositeCompositeMapImpl()
Default constructor

Method Detail

init

protected void init()
Overrides:
init in class DesignElementMapImpl

searchCompositeCompositeMaps

public CompositeCompositeMap[] searchCompositeCompositeMaps(CompositeCompositeMapSearchCriteria criteria)
                                                     throws gov.nih.nci.common.search.SearchException
Returns an array of CompositeCompositeMap objects that satisfy the given CompositeCompositeMapSearchCriteria.

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

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 CompositeCompositeMap object.

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

getCompositeSequence

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

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

setCompositePositionSources

public void setCompositePositionSources(CompositePosition[] p_compositePositionSources)
Sets the compositePositionSources attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a CompositeCompositeMap object.

Specified by:
setCompositePositionSources in interface CompositeCompositeMap
Parameters:
p_compositePositionSources - The new value for compositePositionSources.
See Also:
CompositeCompositeMap.getCompositePositionSources()

getCompositePositionSources

public CompositePosition[] getCompositePositionSources()
Description copied from interface: CompositeCompositeMap
Returns the value of this CompositeCompositeMap object's compositePositionSources attribute.

Specified by:
getCompositePositionSources in interface CompositeCompositeMap
Returns:
gov.nih.nci.mageom.bean.DesignElement.CompositePosition[] The value of compositePositionSources.
See Also:
CompositeCompositeMap.getCompositePositionSources()

getCompositePositionSourcesCount

public int getCompositePositionSourcesCount()
Returns the count of all CompositePosition associated with this CompositeCompositeMap object.

Returns:
the count
See Also:
CompositeCompositeMap.getCompositePositionSources()

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.