org.biomage.BioAssay
Class PhysicalBioAssay

java.lang.Object
  extended by org.biomage.Common.Extendable
      extended by org.biomage.Common.Describable
          extended by org.biomage.Common.Identifiable
              extended by org.biomage.BioAssay.BioAssay
                  extended by org.biomage.BioAssay.PhysicalBioAssay
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasBioAssayCreation, HasBioAssayFactorValues, HasBioAssayTreatments, HasChannels, HasDescriptions, HasPhysicalBioAssayData, HasPropertySets, HasSecurity

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/interfaces inherited from interface org.biomage.Interface.HasPhysicalBioAssayData
HasPhysicalBioAssayData.PhysicalBioAssayData_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasBioAssayTreatments
HasBioAssayTreatments.BioAssayTreatments_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasChannels
HasChannels.Channels_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasBioAssayFactorValues
HasBioAssayFactorValues.BioAssayFactorValues_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAuditTrail
HasAuditTrail.AuditTrail_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDescriptions
HasDescriptions.Descriptions_list
 
Nested classes/interfaces inherited from interface 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  java.util.List bioAssayTreatments
          The set of treatments undergone by this PhysicalBioAssay.
protected  java.util.List physicalBioAssayData
          The Images associated with this PhysicalBioAssay by ImageAcquisition.
 
Fields inherited from class org.biomage.BioAssay.BioAssay
bioAssayFactorValues, channels, deleted, ojbConcreteClass
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
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
 boolean emptyMAGEobject()
           
 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
 java.lang.String getModelClassName()
           
 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 setAttributes(org.xml.sax.Attributes atts)
           
 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, isDeleted, removeElementAtFromBioAssayFactorValues, removeElementAtFromChannels, removeFromBioAssayFactorValues, removeFromChannels, setBioAssayFactorValues, setChannels, setDeleted
 
Methods inherited from class org.biomage.Common.Identifiable
getIdentifier, getName, setIdentifier, setName, toString
 
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, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setId, setIsEditable, setPropertySets, setSecuredElementId
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

physicalBioAssayData

protected java.util.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 java.util.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

Parameters:
atts: - the attribute list.
Method Detail

setAttributes

public void setAttributes(org.xml.sax.Attributes atts)
Overrides:
setAttributes in class BioAssay

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
Throws:
java.io.IOException

emptyMAGEobject

public boolean emptyMAGEobject()

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
Throws:
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
Throws:
java.io.IOException

getModelClassName

public java.lang.String getModelClassName()
Overrides:
getModelClassName in class BioAssay

setPhysicalBioAssayData

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

Specified by:
setPhysicalBioAssayData in interface HasPhysicalBioAssayData
Parameters:
value - to set

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
Parameters:
value - to set

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
Parameters:
value - to set

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