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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:

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

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public class PhysicalBioAssay

extends BioAssay

implements java.io.Serializable, org.biomage.Interface.HasPhysicalBioAssayData, org.biomage.Interface.HasBioAssayCreation, org.biomage.Interface.HasBioAssayTreatments

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

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Nested Class Summary

 

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

org.biomage.Interface.HasPhysicalBioAssayData.PhysicalBioAssayData_list

 

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

org.biomage.Interface.HasBioAssayTreatments.BioAssayTreatments_list

 

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

org.biomage.Interface.HasChannels.Channels_list

 

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

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

 

Fields inherited from class org.biomage.BioAssay.BioAssay

 

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

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
org.biomage.Interface.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
org.biomage.Interface.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(org.biomage.Interface.HasBioAssayTreatments.BioAssayTreatments_list bioAssayTreatments)           Set method for bioAssayTreatments
void	setPhysicalBioAssayData(org.biomage.Interface.HasPhysicalBioAssayData.PhysicalBioAssayData_list physicalBioAssayData)           Set method for physicalBioAssayData
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.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

private org.biomage.Interface.HasPhysicalBioAssayData.PhysicalBioAssayData_list physicalBioAssayData

The Images associated with this PhysicalBioAssay by ImageAcquisition.

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bioAssayCreation

private BioAssayCreation bioAssayCreation

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

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bioAssayTreatments

private org.biomage.Interface.HasBioAssayTreatments.BioAssayTreatments_list bioAssayTreatments

The set of treatments undergone by this PhysicalBioAssay.

Constructor Detail

PhysicalBioAssay

public PhysicalBioAssay()

Default constructor.

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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

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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

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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

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setPhysicalBioAssayData

public void setPhysicalBioAssayData(org.biomage.Interface.HasPhysicalBioAssayData.PhysicalBioAssayData_list physicalBioAssayData)

Set method for physicalBioAssayData

Specified by:

setPhysicalBioAssayData in interface org.biomage.Interface.HasPhysicalBioAssayData

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getPhysicalBioAssayData

public org.biomage.Interface.HasPhysicalBioAssayData.PhysicalBioAssayData_list getPhysicalBioAssayData()

Get method for physicalBioAssayData

Specified by:

getPhysicalBioAssayData in interface org.biomage.Interface.HasPhysicalBioAssayData

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addToPhysicalBioAssayData

public void addToPhysicalBioAssayData(Image image)

Method to add Image to PhysicalBioAssayData_list

Specified by:

addToPhysicalBioAssayData in interface org.biomage.Interface.HasPhysicalBioAssayData

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addToPhysicalBioAssayData

public void addToPhysicalBioAssayData(int position,
                                      Image image)

Method to add Image at position to PhysicalBioAssayData_list

Specified by:

addToPhysicalBioAssayData in interface org.biomage.Interface.HasPhysicalBioAssayData

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getFromPhysicalBioAssayData

public Image getFromPhysicalBioAssayData(int position)

Method to get Image from PhysicalBioAssayData_list

Specified by:

getFromPhysicalBioAssayData in interface org.biomage.Interface.HasPhysicalBioAssayData

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removeElementAtFromPhysicalBioAssayData

public void removeElementAtFromPhysicalBioAssayData(int position)

Method to remove by position from PhysicalBioAssayData_list

Specified by:

removeElementAtFromPhysicalBioAssayData in interface org.biomage.Interface.HasPhysicalBioAssayData

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removeFromPhysicalBioAssayData

public void removeFromPhysicalBioAssayData(Image image)

Method to remove first Image from PhysicalBioAssayData_list

Specified by:

removeFromPhysicalBioAssayData in interface org.biomage.Interface.HasPhysicalBioAssayData

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setBioAssayCreation

public void setBioAssayCreation(BioAssayCreation bioAssayCreation)

Set method for bioAssayCreation

Specified by:

setBioAssayCreation in interface org.biomage.Interface.HasBioAssayCreation

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getBioAssayCreation

public BioAssayCreation getBioAssayCreation()

Get method for bioAssayCreation

Specified by:

getBioAssayCreation in interface org.biomage.Interface.HasBioAssayCreation

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setBioAssayTreatments

public void setBioAssayTreatments(org.biomage.Interface.HasBioAssayTreatments.BioAssayTreatments_list bioAssayTreatments)

Set method for bioAssayTreatments

Specified by:

setBioAssayTreatments in interface org.biomage.Interface.HasBioAssayTreatments

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getBioAssayTreatments

public org.biomage.Interface.HasBioAssayTreatments.BioAssayTreatments_list getBioAssayTreatments()

Get method for bioAssayTreatments

Specified by:

getBioAssayTreatments in interface org.biomage.Interface.HasBioAssayTreatments

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addToBioAssayTreatments

public void addToBioAssayTreatments(BioAssayTreatment bioAssayTreatment)

Method to add BioAssayTreatment to BioAssayTreatments_list

Specified by:

addToBioAssayTreatments in interface org.biomage.Interface.HasBioAssayTreatments

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addToBioAssayTreatments

public void addToBioAssayTreatments(int position,
                                    BioAssayTreatment bioAssayTreatment)

Method to add BioAssayTreatment at position to BioAssayTreatments_list

Specified by:

addToBioAssayTreatments in interface org.biomage.Interface.HasBioAssayTreatments

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getFromBioAssayTreatments

public BioAssayTreatment getFromBioAssayTreatments(int position)

Method to get BioAssayTreatment from BioAssayTreatments_list

Specified by:

getFromBioAssayTreatments in interface org.biomage.Interface.HasBioAssayTreatments

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removeElementAtFromBioAssayTreatments

public void removeElementAtFromBioAssayTreatments(int position)

Method to remove by position from BioAssayTreatments_list

Specified by:

removeElementAtFromBioAssayTreatments in interface org.biomage.Interface.HasBioAssayTreatments

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removeFromBioAssayTreatments

public void removeFromBioAssayTreatments(BioAssayTreatment bioAssayTreatment)

Method to remove first BioAssayTreatment from BioAssayTreatments_list

Specified by:

removeFromBioAssayTreatments in interface org.biomage.Interface.HasBioAssayTreatments

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> biomage >> [ BioAssay overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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