org.biomage.BioAssay
Class PhysicalBioAssay

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

All Implemented Interfaces:

HasAuditTrail, HasBioAssayCreation, HasBioAssayFactorValues, HasBioAssayTreatments, HasChannels, HasDescriptions, HasPhysicalBioAssayData, HasPropertySets, HasSecurity, java.io.Serializable

public class PhysicalBioAssay

extends BioAssay

implements java.io.Serializable, HasPhysicalBioAssayData, HasBioAssayCreation, HasBioAssayTreatments

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

See Also:

Serialized Form

Nested Class Summary

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

HasPhysicalBioAssayData.PhysicalBioAssayData_list

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

HasBioAssayTreatments.BioAssayTreatments_list

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

HasChannels.Channels_list

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

HasBioAssayFactorValues.BioAssayFactorValues_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 BioAssayCreation	bioAssayCreation The association between the BioAssayCreation event (typically Hybridization) and the PhysicalBioAssay and its annotation of this event.
protected HasBioAssayTreatments.BioAssayTreatments_list	bioAssayTreatments The set of treatments undergone by this PhysicalBioAssay.
protected HasPhysicalBioAssayData.PhysicalBioAssayData_list	physicalBioAssayData The Images associated with this PhysicalBioAssay by ImageAcquisition.

Fields inherited from class org.biomage.BioAssay.BioAssay

bioAssayFactorValues, channels

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

PhysicalBioAssay()
Default constructor.

PhysicalBioAssay(org.xml.sax.Attributes atts)
Attribute constructor.

Method Summary

void	addToBioAssayTreatments(BioAssayTreatment bioAssayTreatment) Method to add BioAssayTreatment to BioAssayTreatments_list
void	addToBioAssayTreatments(int position, BioAssayTreatment bioAssayTreatment) Method to add BioAssayTreatment at position to BioAssayTreatments_list
void	addToPhysicalBioAssayData(Image image) Method to add Image to PhysicalBioAssayData_list
void	addToPhysicalBioAssayData(int position, Image image) Method to add Image at position to PhysicalBioAssayData_list
BioAssayCreation	getBioAssayCreation() Get method for bioAssayCreation
HasBioAssayTreatments.BioAssayTreatments_list	getBioAssayTreatments() Get method for bioAssayTreatments
BioAssayTreatment	getFromBioAssayTreatments(int position) Method to get BioAssayTreatment from BioAssayTreatments_list
Image	getFromPhysicalBioAssayData(int position) Method to get Image from PhysicalBioAssayData_list
HasPhysicalBioAssayData.PhysicalBioAssayData_list	getPhysicalBioAssayData() Get method for physicalBioAssayData
void	removeElementAtFromBioAssayTreatments(int position) Method to remove by position from BioAssayTreatments_list
void	removeElementAtFromPhysicalBioAssayData(int position) Method to remove by position from PhysicalBioAssayData_list
void	removeFromBioAssayTreatments(BioAssayTreatment bioAssayTreatment) Method to remove first BioAssayTreatment from BioAssayTreatments_list
void	removeFromPhysicalBioAssayData(Image image) Method to remove first Image from PhysicalBioAssayData_list
void	setBioAssayCreation(BioAssayCreation bioAssayCreation) Set method for bioAssayCreation
void	setBioAssayTreatments(HasBioAssayTreatments.BioAssayTreatments_list bioAssayTreatments) Set method for bioAssayTreatments
void	setPhysicalBioAssayData(HasPhysicalBioAssayData.PhysicalBioAssayData_list physicalBioAssayData) Set method for physicalBioAssayData
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.BioAssay.BioAssay

addToBioAssayFactorValues, addToBioAssayFactorValues, addToChannels, addToChannels, getBioAssayFactorValues, getChannels, getFromBioAssayFactorValues, getFromChannels, removeElementAtFromBioAssayFactorValues, removeElementAtFromChannels, removeFromBioAssayFactorValues, removeFromChannels, setBioAssayFactorValues, setChannels

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

physicalBioAssayData

protected HasPhysicalBioAssayData.PhysicalBioAssayData_list physicalBioAssayData

The Images associated with this PhysicalBioAssay by ImageAcquisition.

bioAssayCreation

protected BioAssayCreation bioAssayCreation

The association between the BioAssayCreation event (typically Hybridization) and the PhysicalBioAssay and its annotation of this event.

bioAssayTreatments

protected HasBioAssayTreatments.BioAssayTreatments_list bioAssayTreatments

The set of treatments undergone by this PhysicalBioAssay.

Constructor Detail

PhysicalBioAssay

public PhysicalBioAssay()

Default constructor.

PhysicalBioAssay

public PhysicalBioAssay(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 BioAssay

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 BioAssay

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 BioAssay

java.io.IOException

setPhysicalBioAssayData

public void setPhysicalBioAssayData(HasPhysicalBioAssayData.PhysicalBioAssayData_list physicalBioAssayData)

Set method for physicalBioAssayData

Specified by:

setPhysicalBioAssayData in interface HasPhysicalBioAssayData

getPhysicalBioAssayData

public HasPhysicalBioAssayData.PhysicalBioAssayData_list getPhysicalBioAssayData()

Get method for physicalBioAssayData

Specified by:

getPhysicalBioAssayData in interface HasPhysicalBioAssayData

Returns:

value of the attribute

addToPhysicalBioAssayData

public void addToPhysicalBioAssayData(Image image)

Method to add Image to PhysicalBioAssayData_list

Specified by:

addToPhysicalBioAssayData in interface HasPhysicalBioAssayData

addToPhysicalBioAssayData

public void addToPhysicalBioAssayData(int position,
                                      Image image)

Method to add Image at position to PhysicalBioAssayData_list

Specified by:

addToPhysicalBioAssayData in interface HasPhysicalBioAssayData

getFromPhysicalBioAssayData

public Image getFromPhysicalBioAssayData(int position)

Method to get Image from PhysicalBioAssayData_list

Specified by:

getFromPhysicalBioAssayData in interface HasPhysicalBioAssayData

removeElementAtFromPhysicalBioAssayData

public void removeElementAtFromPhysicalBioAssayData(int position)

Method to remove by position from PhysicalBioAssayData_list

Specified by:

removeElementAtFromPhysicalBioAssayData in interface HasPhysicalBioAssayData

removeFromPhysicalBioAssayData

public void removeFromPhysicalBioAssayData(Image image)

Method to remove first Image from PhysicalBioAssayData_list

Specified by:

removeFromPhysicalBioAssayData in interface HasPhysicalBioAssayData

setBioAssayCreation

public void setBioAssayCreation(BioAssayCreation bioAssayCreation)

Set method for bioAssayCreation

Specified by:

setBioAssayCreation in interface HasBioAssayCreation

getBioAssayCreation

public BioAssayCreation getBioAssayCreation()

Get method for bioAssayCreation

Specified by:

getBioAssayCreation in interface HasBioAssayCreation

Returns:

value of the attribute

setBioAssayTreatments

public void setBioAssayTreatments(HasBioAssayTreatments.BioAssayTreatments_list bioAssayTreatments)

Set method for bioAssayTreatments

Specified by:

setBioAssayTreatments in interface HasBioAssayTreatments

getBioAssayTreatments

public HasBioAssayTreatments.BioAssayTreatments_list getBioAssayTreatments()

Get method for bioAssayTreatments

Specified by:

getBioAssayTreatments in interface HasBioAssayTreatments

Returns:

value of the attribute

addToBioAssayTreatments

public void addToBioAssayTreatments(BioAssayTreatment bioAssayTreatment)

Method to add BioAssayTreatment to BioAssayTreatments_list

Specified by:

addToBioAssayTreatments in interface HasBioAssayTreatments

addToBioAssayTreatments

public void addToBioAssayTreatments(int position,
                                    BioAssayTreatment bioAssayTreatment)

Method to add BioAssayTreatment at position to BioAssayTreatments_list

Specified by:

addToBioAssayTreatments in interface HasBioAssayTreatments

getFromBioAssayTreatments

public BioAssayTreatment getFromBioAssayTreatments(int position)

Method to get BioAssayTreatment from BioAssayTreatments_list

Specified by:

getFromBioAssayTreatments in interface HasBioAssayTreatments

removeElementAtFromBioAssayTreatments

public void removeElementAtFromBioAssayTreatments(int position)

Method to remove by position from BioAssayTreatments_list

Specified by:

removeElementAtFromBioAssayTreatments in interface HasBioAssayTreatments

removeFromBioAssayTreatments

public void removeFromBioAssayTreatments(BioAssayTreatment bioAssayTreatment)

Method to remove first BioAssayTreatment from BioAssayTreatments_list

Specified by:

removeFromBioAssayTreatments in interface HasBioAssayTreatments