org.biomage.BioAssay
Class BioAssayTreatment

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Common.Describable
              |
              +--org.biomage.Common.Identifiable
                    |
                    +--org.biomage.BioEvent.BioEvent
                          |
                          +--org.biomage.BioAssay.BioAssayTreatment

All Implemented Interfaces:

HasAuditTrail, HasDescriptions, HasPhysicalBioAssay, HasPropertySets, HasProtocolApplications, HasSecurity, HasTarget, java.io.Serializable

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 inherited from class org.biomage.Interface.HasProtocolApplications

HasProtocolApplications.ProtocolApplications_list

Nested classes inherited from class org.biomage.Interface.HasAuditTrail

HasAuditTrail.AuditTrail_list

Nested classes inherited from class org.biomage.Interface.HasDescriptions

HasDescriptions.Descriptions_list

Nested classes inherited from class org.biomage.Interface.HasPropertySets

HasPropertySets.PropertySets_list

Field Summary

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.BioEvent.BioEvent

protocolApplications

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

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 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

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

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

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.

Overrides:

writeMAGEML in class BioEvent

java.io.IOException

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

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

java.io.IOException

setPhysicalBioAssay

public void setPhysicalBioAssay(PhysicalBioAssay physicalBioAssay)

Set method for physicalBioAssay

Specified by:

setPhysicalBioAssay in interface HasPhysicalBioAssay

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

getTarget

public PhysicalBioAssay getTarget()

Get method for target

Specified by:

getTarget in interface HasTarget

Returns:

value of the attribute