gov.nih.nci.mageom.domain.BioMaterial.impl
Class TreatmentImpl

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.BioMaterial.impl.TreatmentImpl
All Implemented Interfaces:
BioEvent, Treatment, Describable, Extendable, Identifiable, java.io.Serializable

public class TreatmentImpl
extends BioEventImpl
implements Treatment

The process by which a biomaterial is created (from source biomaterials). Treatments have an order and an action.

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

Field Summary
protected  OntologyEntry action
          DOCUMENT ME
protected  java.lang.Long actionId
          The internal ID of the associated action object.
protected  Measurement actionMeasurement
          The measurement of an action, time exposed, speed of centrifuge, etc.
protected  java.lang.Long actionMeasurementId
          The internal ID of the associated actionMeasurement object.
protected static java.util.ArrayList allAssociationMethods
           
protected static java.util.Hashtable associationMethods
           
protected  CompoundMeasurement[] compoundMeasurements
          DOCUMENT ME
protected  int compoundMeasurementsCount
          The count of CompoundMeasurement objects.
protected  java.lang.Integer order
          The chronological order in which a treatment occurred (in relation to other treatments).
protected  BioMaterialMeasurement[] sourceBioMaterialMeasurements
          DOCUMENT ME
protected  int sourceBioMaterialMeasurementsCount
          The count of BioMaterialMeasurement 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
TreatmentImpl()
          Default constructor
 
Method Summary
 OntologyEntry getAction()
          Returns the value of this Treatment object's action attribute.
 Measurement getActionMeasurement()
          Returns the value of this Treatment object's actionMeasurement attribute.
 CompoundMeasurement[] getCompoundMeasurements()
          Returns the value of this Treatment object's compoundMeasurements attribute.
 int getCompoundMeasurementsCount()
          Returns the count of all CompoundMeasurement associated with this Treatment object.
 java.lang.Integer getOrder()
          Returns the value of this Treatment object's order attribute.
 BioMaterialMeasurement[] getSourceBioMaterialMeasurements()
          Returns the value of this Treatment object's sourceBioMaterialMeasurements attribute.
 int getSourceBioMaterialMeasurementsCount()
          Returns the count of all BioMaterialMeasurement associated with this Treatment object.
 java.util.Hashtable getXMLMethodDescriptors()
          Returns a Hashtable containing XMLMethodDescriptors descriptors of the association methods of this object.
protected  void init()
           
 Treatment[] searchTreatments(TreatmentSearchCriteria criteria)
          Returns an array of Treatment objects that satisfy the given TreatmentSearchCriteria.
 void setAction(OntologyEntry p_action)
          Sets the action attribute.
 void setActionMeasurement(Measurement p_actionMeasurement)
          Sets the actionMeasurement attribute.
 void setCompoundMeasurements(CompoundMeasurement[] p_compoundMeasurements)
          Sets the compoundMeasurements attribute.
 void setOrder(java.lang.Integer p_order)
          Sets the order attribute.
 void setSourceBioMaterialMeasurements(BioMaterialMeasurement[] p_sourceBioMaterialMeasurements)
          Sets the sourceBioMaterialMeasurements 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.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

order

protected java.lang.Integer order
The chronological order in which a treatment occurred (in relation to other treatments). More one treatment can have the same chronological order indicating that they happened (or were to happen) simultaneously.


actionMeasurement

protected Measurement actionMeasurement
The measurement of an action, time exposed, speed of centrifuge, etc.


actionMeasurementId

protected java.lang.Long actionMeasurementId
The internal ID of the associated actionMeasurement object.


sourceBioMaterialMeasurementsCount

protected int sourceBioMaterialMeasurementsCount
The count of BioMaterialMeasurement objects.


sourceBioMaterialMeasurements

protected BioMaterialMeasurement[] sourceBioMaterialMeasurements
DOCUMENT ME


compoundMeasurementsCount

protected int compoundMeasurementsCount
The count of CompoundMeasurement objects.


compoundMeasurements

protected CompoundMeasurement[] compoundMeasurements
DOCUMENT ME


action

protected OntologyEntry action
DOCUMENT ME


actionId

protected java.lang.Long actionId
The internal ID of the associated action object.

Constructor Detail

TreatmentImpl

public TreatmentImpl()
Default constructor

Method Detail

init

protected void init()
Overrides:
init in class BioEventImpl

searchTreatments

public Treatment[] searchTreatments(TreatmentSearchCriteria criteria)
                             throws gov.nih.nci.common.search.SearchException
Returns an array of Treatment objects that satisfy the given TreatmentSearchCriteria.

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

setOrder

public void setOrder(java.lang.Integer p_order)
Sets the order attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a Treatment object.

Specified by:
setOrder in interface Treatment
Parameters:
p_order - The new value for order.
See Also:
Treatment.getOrder()

getOrder

public java.lang.Integer getOrder()
Description copied from interface: Treatment
Returns the value of this Treatment object's order attribute. Description of order: The chronological order in which a treatment occurred (in relation to other treatments). More than one treatment can have the same chronological order indicating that they happened (or were caused to happen) simultaneously.

Specified by:
getOrder in interface Treatment
Returns:
int The value of order.
See Also:
Treatment.getOrder()

setActionMeasurement

public void setActionMeasurement(Measurement p_actionMeasurement)
Sets the actionMeasurement attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a Treatment object.

Specified by:
setActionMeasurement in interface Treatment
Parameters:
p_actionMeasurement - The new value for actionMeasurement.
See Also:
Treatment.getActionMeasurement()

getActionMeasurement

public Measurement getActionMeasurement()
Description copied from interface: Treatment
Returns the value of this Treatment object's actionMeasurement attribute.

Specified by:
getActionMeasurement in interface Treatment
Returns:
gov.nih.nci.mageom.bean.Measurement.Measurement The value of actionMeasurement.
See Also:
Treatment.getActionMeasurement()

setSourceBioMaterialMeasurements

public void setSourceBioMaterialMeasurements(BioMaterialMeasurement[] p_sourceBioMaterialMeasurements)
Sets the sourceBioMaterialMeasurements attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a Treatment object.

Specified by:
setSourceBioMaterialMeasurements in interface Treatment
Parameters:
p_sourceBioMaterialMeasurements - The new value for sourceBioMaterialMeasurements.
See Also:
Treatment.getSourceBioMaterialMeasurements()

getSourceBioMaterialMeasurements

public BioMaterialMeasurement[] getSourceBioMaterialMeasurements()
Description copied from interface: Treatment
Returns the value of this Treatment object's sourceBioMaterialMeasurements attribute.

Specified by:
getSourceBioMaterialMeasurements in interface Treatment
Returns:
gov.nih.nci.mageom.bean.BioMaterial.BioMaterialMeasurement[] The value of sourceBioMaterialMeasurements.
See Also:
Treatment.getSourceBioMaterialMeasurements()

setCompoundMeasurements

public void setCompoundMeasurements(CompoundMeasurement[] p_compoundMeasurements)
Sets the compoundMeasurements attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a Treatment object.

Specified by:
setCompoundMeasurements in interface Treatment
Parameters:
p_compoundMeasurements - The new value for compoundMeasurements.
See Also:
Treatment.getCompoundMeasurements()

getCompoundMeasurements

public CompoundMeasurement[] getCompoundMeasurements()
Description copied from interface: Treatment
Returns the value of this Treatment object's compoundMeasurements attribute.

Specified by:
getCompoundMeasurements in interface Treatment
Returns:
gov.nih.nci.mageom.bean.BioMaterial.CompoundMeasurement[] The value of compoundMeasurements.
See Also:
Treatment.getCompoundMeasurements()

setAction

public void setAction(OntologyEntry p_action)
Sets the action attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a Treatment object.

Specified by:
setAction in interface Treatment
Parameters:
p_action - The new value for action.
See Also:
Treatment.getAction()

getAction

public OntologyEntry getAction()
Description copied from interface: Treatment
Returns the value of this Treatment object's action attribute.

Specified by:
getAction in interface Treatment
Returns:
gov.nih.nci.mageom.bean.Description.OntologyEntry The value of action.
See Also:
Treatment.getAction()

getSourceBioMaterialMeasurementsCount

public int getSourceBioMaterialMeasurementsCount()
Returns the count of all BioMaterialMeasurement associated with this Treatment object.

Returns:
the count
See Also:
Treatment.getSourceBioMaterialMeasurements()

getCompoundMeasurementsCount

public int getCompoundMeasurementsCount()
Returns the count of all CompoundMeasurement associated with this Treatment object.

Returns:
the count
See Also:
Treatment.getCompoundMeasurements()

toXML

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

toXMLDoc

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

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 BioEventImpl
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 BioEventImpl
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 BioEventImpl
Returns:
the String representation.