org.biomage.BioAssay
Class BioAssayTreatment

java.lang.Object
  extended by org.biomage.Common.Extendable
      extended by org.biomage.Common.Describable
          extended by org.biomage.Common.Identifiable
              extended by org.biomage.BioEvent.BioEvent
                  extended by org.biomage.BioAssay.BioAssayTreatment
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasDescriptions, HasPhysicalBioAssay, HasPropertySets, HasProtocolApplications, HasSecurity, HasTarget
Direct Known Subclasses:
ImageAcquisition

public class BioAssayTreatment
extends BioEvent
implements java.io.Serializable, HasPhysicalBioAssay, HasTarget

The event which records the process by which PhysicalBioAssays are processed (typically washing, blocking, etc...).

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasProtocolApplications
HasProtocolApplications.ProtocolApplications_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAuditTrail
HasAuditTrail.AuditTrail_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDescriptions
HasDescriptions.Descriptions_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets
HasPropertySets.PropertySets_list
 
Field Summary
protected  java.lang.String ojbConcreteClass
           
protected  PhysicalBioAssay physicalBioAssay
          The set of treatments undergone by this PhysicalBioAssay.
protected  PhysicalBioAssay target
          The PhysicalBioAssay that was treated.
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
BioAssayTreatment()
          Default constructor.
BioAssayTreatment(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 boolean emptyMAGEobject()
           
 java.lang.String getModelClassName()
           
 PhysicalBioAssay getPhysicalBioAssay()
          Get method for physicalBioAssay
 PhysicalBioAssay getTarget()
          Get method for target
 void setAttributes(org.xml.sax.Attributes atts)
           
 void setPhysicalBioAssay(PhysicalBioAssay physicalBioAssay)
          Set method for physicalBioAssay
 void setTarget(PhysicalBioAssay target)
          Set method for target
 void writeAssociations(java.io.Writer out)
          writeAssociations This method is responsible for assembling the association data into XML.
 void writeAttributes(java.io.Writer out)
          writeAttributes This method is responsible for assembling the attribute data into XML.
 void writeMAGEML(java.io.Writer out)
          writeMAGEML This method is responsible for assembling the attribute and association data into XML.
 
Methods inherited from class org.biomage.BioEvent.BioEvent
addToProtocolApplications, addToProtocolApplications, getFromProtocolApplications, getProtocolApplications, removeElementAtFromProtocolApplications, removeFromProtocolApplications, setProtocolApplications
 
Methods inherited from class org.biomage.Common.Identifiable
getIdentifier, getName, setIdentifier, setName, toString
 
Methods inherited from class org.biomage.Common.Describable
addToAuditTrail, addToAuditTrail, addToDescriptions, addToDescriptions, getAuditTrail, getDescriptions, getFromAuditTrail, getFromDescriptions, getSecurity, removeElementAtFromAuditTrail, removeElementAtFromDescriptions, removeFromAuditTrail, removeFromDescriptions, setAuditTrail, setDescriptions, setSecurity
 
Methods inherited from class org.biomage.Common.Extendable
addToPropertySets, addToPropertySets, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setId, setIsEditable, setPropertySets, setSecuredElementId
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

ojbConcreteClass

protected java.lang.String ojbConcreteClass

physicalBioAssay

protected PhysicalBioAssay physicalBioAssay
The set of treatments undergone by this PhysicalBioAssay.


target

protected PhysicalBioAssay target
The PhysicalBioAssay that was treated.

Constructor Detail

BioAssayTreatment

public BioAssayTreatment()
Default constructor.


BioAssayTreatment

public BioAssayTreatment(org.xml.sax.Attributes atts)
Attribute constructor. Looks up the attributes in the parameter and casts them from strings appropriately

Parameters:
atts: - the attribute list.
Method Detail

setAttributes

public void setAttributes(org.xml.sax.Attributes atts)
Overrides:
setAttributes in class BioEvent

writeMAGEML

public void writeMAGEML(java.io.Writer out)
                 throws java.io.IOException
writeMAGEML This method is responsible for assembling the attribute and association data into XML. It creates the object tag and then calls the writeAttributes and writeAssociation methods.

Overrides:
writeMAGEML in class BioEvent
Throws:
java.io.IOException

emptyMAGEobject

public boolean emptyMAGEobject()

writeAttributes

public void writeAttributes(java.io.Writer out)
                     throws java.io.IOException
writeAttributes This method is responsible for assembling the attribute data into XML. It calls the super method to write out all attributes of this class and it's ancestors.

Overrides:
writeAttributes in class BioEvent
Throws:
java.io.IOException

writeAssociations

public void writeAssociations(java.io.Writer out)
                       throws java.io.IOException
writeAssociations This method is responsible for assembling the association data into XML. It calls the super method to write out all associations of this class's ancestors.

Overrides:
writeAssociations in class BioEvent
Throws:
java.io.IOException

getModelClassName

public java.lang.String getModelClassName()
Overrides:
getModelClassName in class BioEvent

setPhysicalBioAssay

public void setPhysicalBioAssay(PhysicalBioAssay physicalBioAssay)
Set method for physicalBioAssay

Specified by:
setPhysicalBioAssay in interface HasPhysicalBioAssay
Parameters:
value - to set

getPhysicalBioAssay

public PhysicalBioAssay getPhysicalBioAssay()
Get method for physicalBioAssay

Specified by:
getPhysicalBioAssay in interface HasPhysicalBioAssay
Returns:
value of the attribute

setTarget

public void setTarget(PhysicalBioAssay target)
Set method for target

Specified by:
setTarget in interface HasTarget
Parameters:
value - to set

getTarget

public PhysicalBioAssay getTarget()
Get method for target

Specified by:
getTarget in interface HasTarget
Returns:
value of the attribute