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

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.DesignElement.impl.DesignElementImpl
                      extended by gov.nih.nci.mageom.domain.DesignElement.impl.CompositeSequenceImpl
All Implemented Interfaces:
Describable, CompositeSequence, DesignElement, Extendable, Identifiable, java.io.Serializable

public class CompositeSequenceImpl
extends DesignElementImpl
implements CompositeSequence

A collection of Reporter or CompositeSequence Design Elements, annotated through the association to BioSequence.

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

Field Summary
protected static java.util.ArrayList allAssociationMethods
           
protected static java.util.Hashtable associationMethods
           
protected  BioSequence[] biologicalCharacteristics
          DOCUMENT ME
protected  int biologicalCharacteristicsCount
          The count of BioSequence objects.
protected  CompositeCompositeMap[] compositeCompositeMaps
          DOCUMENT ME
protected  int compositeCompositeMapsCount
          The count of CompositeCompositeMap objects.
protected  ReporterCompositeMap[] reporterCompositeMaps
          DOCUMENT ME
protected  int reporterCompositeMapsCount
          The count of ReporterCompositeMap objects.
 
Fields inherited from class gov.nih.nci.mageom.domain.DesignElement.impl.DesignElementImpl
controlType, controlTypeId
 
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
CompositeSequenceImpl()
          Default constructor
 
Method Summary
 BioSequence[] getBiologicalCharacteristics()
          Returns the value of this CompositeSequence object's biologicalCharacteristics attribute.
 int getBiologicalCharacteristicsCount()
          Returns the count of all BioSequence associated with this CompositeSequence object.
 CompositeCompositeMap[] getCompositeCompositeMaps()
          Returns the value of this CompositeSequence object's compositeCompositeMaps attribute.
 int getCompositeCompositeMapsCount()
          Returns the count of all CompositeCompositeMap associated with this CompositeSequence object.
 ReporterCompositeMap[] getReporterCompositeMaps()
          Returns the value of this CompositeSequence object's reporterCompositeMaps attribute.
 int getReporterCompositeMapsCount()
          Returns the count of all ReporterCompositeMap associated with this CompositeSequence object.
 java.util.Hashtable getXMLMethodDescriptors()
          Returns a Hashtable containing XMLMethodDescriptors descriptors of the association methods of this object.
protected  void init()
           
 CompositeSequence[] searchCompositeSequences(CompositeSequenceSearchCriteria criteria)
          Returns an array of CompositeSequence objects that satisfy the given CompositeSequenceSearchCriteria.
 void setBiologicalCharacteristics(BioSequence[] p_biologicalCharacteristics)
          Sets the biologicalCharacteristics attribute.
 void setCompositeCompositeMaps(CompositeCompositeMap[] p_compositeCompositeMaps)
          Sets the compositeCompositeMaps attribute.
 void setReporterCompositeMaps(ReporterCompositeMap[] p_reporterCompositeMaps)
          Sets the reporterCompositeMaps 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.DesignElement.impl.DesignElementImpl
getControlType, searchDesignElements, setControlType
 
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.DesignElement.DesignElement
getControlType, setControlType
 
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

biologicalCharacteristicsCount

protected int biologicalCharacteristicsCount
The count of BioSequence objects.


biologicalCharacteristics

protected BioSequence[] biologicalCharacteristics
DOCUMENT ME


reporterCompositeMapsCount

protected int reporterCompositeMapsCount
The count of ReporterCompositeMap objects.


reporterCompositeMaps

protected ReporterCompositeMap[] reporterCompositeMaps
DOCUMENT ME


compositeCompositeMapsCount

protected int compositeCompositeMapsCount
The count of CompositeCompositeMap objects.


compositeCompositeMaps

protected CompositeCompositeMap[] compositeCompositeMaps
DOCUMENT ME

Constructor Detail

CompositeSequenceImpl

public CompositeSequenceImpl()
Default constructor

Method Detail

init

protected void init()
Overrides:
init in class DesignElementImpl

searchCompositeSequences

public CompositeSequence[] searchCompositeSequences(CompositeSequenceSearchCriteria criteria)
                                             throws gov.nih.nci.common.search.SearchException
Returns an array of CompositeSequence objects that satisfy the given CompositeSequenceSearchCriteria.

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

setBiologicalCharacteristics

public void setBiologicalCharacteristics(BioSequence[] p_biologicalCharacteristics)
Sets the biologicalCharacteristics attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a CompositeSequence object.

Specified by:
setBiologicalCharacteristics in interface CompositeSequence
Parameters:
p_biologicalCharacteristics - The new value for biologicalCharacteristics.
See Also:
CompositeSequence.getBiologicalCharacteristics()

getBiologicalCharacteristics

public BioSequence[] getBiologicalCharacteristics()
Description copied from interface: CompositeSequence
Returns the value of this CompositeSequence object's biologicalCharacteristics attribute.

Specified by:
getBiologicalCharacteristics in interface CompositeSequence
Returns:
gov.nih.nci.mageom.bean.BioSequence.BioSequence[] The value of biologicalCharacteristics.
See Also:
CompositeSequence.getBiologicalCharacteristics()

setReporterCompositeMaps

public void setReporterCompositeMaps(ReporterCompositeMap[] p_reporterCompositeMaps)
Sets the reporterCompositeMaps attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a CompositeSequence object.

Specified by:
setReporterCompositeMaps in interface CompositeSequence
Parameters:
p_reporterCompositeMaps - The new value for reporterCompositeMaps.
See Also:
CompositeSequence.getReporterCompositeMaps()

getReporterCompositeMaps

public ReporterCompositeMap[] getReporterCompositeMaps()
Description copied from interface: CompositeSequence
Returns the value of this CompositeSequence object's reporterCompositeMaps attribute.

Specified by:
getReporterCompositeMaps in interface CompositeSequence
Returns:
gov.nih.nci.mageom.bean.DesignElement.ReporterCompositeMap[] The value of reporterCompositeMaps.
See Also:
CompositeSequence.getReporterCompositeMaps()

setCompositeCompositeMaps

public void setCompositeCompositeMaps(CompositeCompositeMap[] p_compositeCompositeMaps)
Sets the compositeCompositeMaps attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a CompositeSequence object.

Specified by:
setCompositeCompositeMaps in interface CompositeSequence
Parameters:
p_compositeCompositeMaps - The new value for compositeCompositeMaps.
See Also:
CompositeSequence.getCompositeCompositeMaps()

getCompositeCompositeMaps

public CompositeCompositeMap[] getCompositeCompositeMaps()
Description copied from interface: CompositeSequence
Returns the value of this CompositeSequence object's compositeCompositeMaps attribute.

Specified by:
getCompositeCompositeMaps in interface CompositeSequence
Returns:
gov.nih.nci.mageom.bean.DesignElement.CompositeCompositeMap[] The value of compositeCompositeMaps.
See Also:
CompositeSequence.getCompositeCompositeMaps()

getBiologicalCharacteristicsCount

public int getBiologicalCharacteristicsCount()
Returns the count of all BioSequence associated with this CompositeSequence object.

Returns:
the count
See Also:
CompositeSequence.getBiologicalCharacteristics()

getReporterCompositeMapsCount

public int getReporterCompositeMapsCount()
Returns the count of all ReporterCompositeMap associated with this CompositeSequence object.

Returns:
the count
See Also:
CompositeSequence.getReporterCompositeMaps()

getCompositeCompositeMapsCount

public int getCompositeCompositeMapsCount()
Returns the count of all CompositeCompositeMap associated with this CompositeSequence object.

Returns:
the count
See Also:
CompositeSequence.getCompositeCompositeMaps()

toXML

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

toXMLDoc

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

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 DesignElementImpl
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 DesignElementImpl
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 DesignElementImpl
Returns:
the String representation.