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

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Common.Describable
          extended byorg.biomage.Common.Identifiable
              extended byorg.biomage.BioAssay.BioAssay
                  extended byorg.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

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).


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.


bioAssayCreation

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


bioAssayTreatments

private org.biomage.Interface.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

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

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

setPhysicalBioAssayData

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

Specified by:
setPhysicalBioAssayData in interface org.biomage.Interface.HasPhysicalBioAssayData

getPhysicalBioAssayData

public org.biomage.Interface.HasPhysicalBioAssayData.PhysicalBioAssayData_list getPhysicalBioAssayData()
Get method for physicalBioAssayData

Specified by:
getPhysicalBioAssayData in interface org.biomage.Interface.HasPhysicalBioAssayData

addToPhysicalBioAssayData

public void addToPhysicalBioAssayData(Image image)
Method to add Image to PhysicalBioAssayData_list

Specified by:
addToPhysicalBioAssayData in interface org.biomage.Interface.HasPhysicalBioAssayData

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

getFromPhysicalBioAssayData

public Image getFromPhysicalBioAssayData(int position)
Method to get Image from PhysicalBioAssayData_list

Specified by:
getFromPhysicalBioAssayData in interface org.biomage.Interface.HasPhysicalBioAssayData

removeElementAtFromPhysicalBioAssayData

public void removeElementAtFromPhysicalBioAssayData(int position)
Method to remove by position from PhysicalBioAssayData_list

Specified by:
removeElementAtFromPhysicalBioAssayData in interface org.biomage.Interface.HasPhysicalBioAssayData

removeFromPhysicalBioAssayData

public void removeFromPhysicalBioAssayData(Image image)
Method to remove first Image from PhysicalBioAssayData_list

Specified by:
removeFromPhysicalBioAssayData in interface org.biomage.Interface.HasPhysicalBioAssayData

setBioAssayCreation

public void setBioAssayCreation(BioAssayCreation bioAssayCreation)
Set method for bioAssayCreation

Specified by:
setBioAssayCreation in interface org.biomage.Interface.HasBioAssayCreation

getBioAssayCreation

public BioAssayCreation getBioAssayCreation()
Get method for bioAssayCreation

Specified by:
getBioAssayCreation in interface org.biomage.Interface.HasBioAssayCreation

setBioAssayTreatments

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

Specified by:
setBioAssayTreatments in interface org.biomage.Interface.HasBioAssayTreatments

getBioAssayTreatments

public org.biomage.Interface.HasBioAssayTreatments.BioAssayTreatments_list getBioAssayTreatments()
Get method for bioAssayTreatments

Specified by:
getBioAssayTreatments in interface org.biomage.Interface.HasBioAssayTreatments

addToBioAssayTreatments

public void addToBioAssayTreatments(BioAssayTreatment bioAssayTreatment)
Method to add BioAssayTreatment to BioAssayTreatments_list

Specified by:
addToBioAssayTreatments in interface org.biomage.Interface.HasBioAssayTreatments

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

getFromBioAssayTreatments

public BioAssayTreatment getFromBioAssayTreatments(int position)
Method to get BioAssayTreatment from BioAssayTreatments_list

Specified by:
getFromBioAssayTreatments in interface org.biomage.Interface.HasBioAssayTreatments

removeElementAtFromBioAssayTreatments

public void removeElementAtFromBioAssayTreatments(int position)
Method to remove by position from BioAssayTreatments_list

Specified by:
removeElementAtFromBioAssayTreatments in interface org.biomage.Interface.HasBioAssayTreatments

removeFromBioAssayTreatments

public void removeFromBioAssayTreatments(BioAssayTreatment bioAssayTreatment)
Method to remove first BioAssayTreatment from BioAssayTreatments_list

Specified by:
removeFromBioAssayTreatments in interface org.biomage.Interface.HasBioAssayTreatments