gov.nih.nci.mageom.domain.BioAssay.impl
Class PhysicalBioAssayImpl

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.BioAssay.impl.BioAssayImpl
                      extended by gov.nih.nci.mageom.domain.BioAssay.impl.PhysicalBioAssayImpl
All Implemented Interfaces:
BioAssay, PhysicalBioAssay, Describable, Extendable, Identifiable, java.io.Serializable

public class PhysicalBioAssayImpl
extends BioAssayImpl
implements PhysicalBioAssay

A bioAssay created by the bioAssayCreation event (e.g. in gene expression analysis this event is represented by the hybridization event).

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

Field Summary
protected static java.util.ArrayList allAssociationMethods
           
protected static java.util.Hashtable associationMethods
           
protected  BioAssayCreation bioAssayCreation
          DOCUMENT ME
protected  java.lang.Long bioAssayCreationId
          The internal ID of the associated bioAssayCreation object.
protected  BioAssayTreatment[] bioAssayTreatments
          DOCUMENT ME
protected  int bioAssayTreatmentsCount
          The count of BioAssayTreatment objects.
protected  Image[] physicalBioAssayData
          DOCUMENT ME
protected  int physicalBioAssayDataCount
          The count of Image objects.
 
Fields inherited from class gov.nih.nci.mageom.domain.BioAssay.impl.BioAssayImpl
bioAssayFactorValues, bioAssayFactorValuesCount, channels, channelsCount
 
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
PhysicalBioAssayImpl()
          Default constructor
 
Method Summary
 BioAssayCreation getBioAssayCreation()
          Returns the value of this PhysicalBioAssay object's bioAssayCreation attribute.
 BioAssayTreatment[] getBioAssayTreatments()
          Returns the value of this PhysicalBioAssay object's bioAssayTreatments attribute.
 int getBioAssayTreatmentsCount()
          Returns the count of all BioAssayTreatment associated with this PhysicalBioAssay object.
 Image[] getPhysicalBioAssayData()
          Returns the value of this PhysicalBioAssay object's physicalBioAssayData attribute.
 int getPhysicalBioAssayDataCount()
          Returns the count of all Image associated with this PhysicalBioAssay object.
 java.util.Hashtable getXMLMethodDescriptors()
          Returns a Hashtable containing XMLMethodDescriptors descriptors of the association methods of this object.
protected  void init()
           
 PhysicalBioAssay[] searchPhysicalBioAssays(PhysicalBioAssaySearchCriteria criteria)
          Returns an array of PhysicalBioAssay objects that satisfy the given PhysicalBioAssaySearchCriteria.
 void setBioAssayCreation(BioAssayCreation p_bioAssayCreation)
          Sets the bioAssayCreation attribute.
 void setBioAssayTreatments(BioAssayTreatment[] p_bioAssayTreatments)
          Sets the bioAssayTreatments attribute.
 void setPhysicalBioAssayData(Image[] p_physicalBioAssayData)
          Sets the physicalBioAssayData 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.BioAssay.impl.BioAssayImpl
getBioAssayFactorValues, getBioAssayFactorValuesCount, getChannels, getChannelsCount, searchBioAssays, setBioAssayFactorValues, setChannels
 
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.BioAssay.BioAssay
getBioAssayFactorValues, getChannels, setBioAssayFactorValues, setChannels
 
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

physicalBioAssayDataCount

protected int physicalBioAssayDataCount
The count of Image objects.


physicalBioAssayData

protected Image[] physicalBioAssayData
DOCUMENT ME


bioAssayCreation

protected BioAssayCreation bioAssayCreation
DOCUMENT ME


bioAssayCreationId

protected java.lang.Long bioAssayCreationId
The internal ID of the associated bioAssayCreation object.


bioAssayTreatmentsCount

protected int bioAssayTreatmentsCount
The count of BioAssayTreatment objects.


bioAssayTreatments

protected BioAssayTreatment[] bioAssayTreatments
DOCUMENT ME

Constructor Detail

PhysicalBioAssayImpl

public PhysicalBioAssayImpl()
Default constructor

Method Detail

init

protected void init()
Overrides:
init in class BioAssayImpl

searchPhysicalBioAssays

public PhysicalBioAssay[] searchPhysicalBioAssays(PhysicalBioAssaySearchCriteria criteria)
                                           throws gov.nih.nci.common.search.SearchException
Returns an array of PhysicalBioAssay objects that satisfy the given PhysicalBioAssaySearchCriteria.

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

setPhysicalBioAssayData

public void setPhysicalBioAssayData(Image[] p_physicalBioAssayData)
Sets the physicalBioAssayData attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a PhysicalBioAssay object.

Specified by:
setPhysicalBioAssayData in interface PhysicalBioAssay
Parameters:
p_physicalBioAssayData - The new value for physicalBioAssayData.
See Also:
PhysicalBioAssay.getPhysicalBioAssayData()

getPhysicalBioAssayData

public Image[] getPhysicalBioAssayData()
Description copied from interface: PhysicalBioAssay
Returns the value of this PhysicalBioAssay object's physicalBioAssayData attribute.

Specified by:
getPhysicalBioAssayData in interface PhysicalBioAssay
Returns:
gov.nih.nci.mageom.bean.BioAssay.Image[] The value of physicalBioAssayData.
See Also:
PhysicalBioAssay.getPhysicalBioAssayData()

setBioAssayCreation

public void setBioAssayCreation(BioAssayCreation p_bioAssayCreation)
Sets the bioAssayCreation attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a PhysicalBioAssay object.

Specified by:
setBioAssayCreation in interface PhysicalBioAssay
Parameters:
p_bioAssayCreation - The new value for bioAssayCreation.
See Also:
PhysicalBioAssay.getBioAssayCreation()

getBioAssayCreation

public BioAssayCreation getBioAssayCreation()
Description copied from interface: PhysicalBioAssay
Returns the value of this PhysicalBioAssay object's bioAssayCreation attribute.

Specified by:
getBioAssayCreation in interface PhysicalBioAssay
Returns:
gov.nih.nci.mageom.bean.BioAssay.BioAssayCreation The value of bioAssayCreation.
See Also:
PhysicalBioAssay.getBioAssayCreation()

setBioAssayTreatments

public void setBioAssayTreatments(BioAssayTreatment[] p_bioAssayTreatments)
Sets the bioAssayTreatments attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a PhysicalBioAssay object.

Specified by:
setBioAssayTreatments in interface PhysicalBioAssay
Parameters:
p_bioAssayTreatments - The new value for bioAssayTreatments.
See Also:
PhysicalBioAssay.getBioAssayTreatments()

getBioAssayTreatments

public BioAssayTreatment[] getBioAssayTreatments()
Description copied from interface: PhysicalBioAssay
Returns the value of this PhysicalBioAssay object's bioAssayTreatments attribute.

Specified by:
getBioAssayTreatments in interface PhysicalBioAssay
Returns:
gov.nih.nci.mageom.bean.BioAssay.BioAssayTreatment[] The value of bioAssayTreatments.
See Also:
PhysicalBioAssay.getBioAssayTreatments()

getPhysicalBioAssayDataCount

public int getPhysicalBioAssayDataCount()
Returns the count of all Image associated with this PhysicalBioAssay object.

Returns:
the count
See Also:
PhysicalBioAssay.getPhysicalBioAssayData()

getBioAssayTreatmentsCount

public int getBioAssayTreatmentsCount()
Returns the count of all BioAssayTreatment associated with this PhysicalBioAssay object.

Returns:
the count
See Also:
PhysicalBioAssay.getBioAssayTreatments()

toXML

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

toXMLDoc

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

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 BioAssayImpl
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 BioAssayImpl
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 BioAssayImpl
Returns:
the String representation.