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org.biomage.BioAssay
Class BioAssayTreatment  view BioAssayTreatment download BioAssayTreatment.java

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

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

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


Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasProtocolApplications
org.biomage.Interface.HasProtocolApplications.ProtocolApplications_list
 
Nested classes inherited from class org.biomage.Interface.HasAuditTrail
org.biomage.Interface.HasAuditTrail.AuditTrail_list
 
Nested classes inherited from class org.biomage.Interface.HasDescriptions
org.biomage.Interface.HasDescriptions.Descriptions_list
 
Nested classes inherited from class org.biomage.Interface.HasPropertySets
org.biomage.Interface.HasPropertySets.PropertySets_list
 
Field Summary
private  PhysicalBioAssay physicalBioAssay
          The set of treatments undergone by this PhysicalBioAssay.
private  PhysicalBioAssay target
          The PhysicalBioAssay that was treated.
 
Fields inherited from class org.biomage.BioEvent.BioEvent
 
Fields inherited from class org.biomage.Common.Identifiable
 
Fields inherited from class org.biomage.Common.Describable
 
Fields inherited from class org.biomage.Common.Extendable
 
Constructor Summary
BioAssayTreatment()
          Default constructor.
BioAssayTreatment(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 PhysicalBioAssay getPhysicalBioAssay()
          Get method for physicalBioAssay
 PhysicalBioAssay getTarget()
          Get method for target
 void setPhysicalBioAssay(PhysicalBioAssay physicalBioAssay)
          Set method for physicalBioAssay
 void setTarget(PhysicalBioAssay target)
          Set method for target
 void writeAssociations(java.io.Writer out)
          writeAssociations
 void writeAttributes(java.io.Writer out)
          writeAttributes
 void writeMAGEML(java.io.Writer out)
          writeMAGEML
 
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
 
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, getFromPropertySets, getPropertySets, removeElementAtFromPropertySets, removeFromPropertySets, setPropertySets
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

physicalBioAssay

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


target

private 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

Method Detail

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.


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.


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.


setPhysicalBioAssay

public void setPhysicalBioAssay(PhysicalBioAssay physicalBioAssay)
Set method for physicalBioAssay

Specified by:
setPhysicalBioAssay in interface org.biomage.Interface.HasPhysicalBioAssay

getPhysicalBioAssay

public PhysicalBioAssay getPhysicalBioAssay()
Get method for physicalBioAssay

Specified by:
getPhysicalBioAssay in interface org.biomage.Interface.HasPhysicalBioAssay

setTarget

public void setTarget(PhysicalBioAssay target)
Set method for target

Specified by:
setTarget in interface org.biomage.Interface.HasTarget

getTarget

public PhysicalBioAssay getTarget()
Get method for target

Specified by:
getTarget in interface org.biomage.Interface.HasTarget