org.biomage.BioAssay
Class BioAssayCreation

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.BioEvent.BioEvent
                  extended by org.biomage.BioAssay.BioAssayCreation
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasArray, HasAuditTrail, HasDescriptions, HasPhysicalBioAssayTarget, HasPropertySets, HasProtocolApplications, HasSecurity, HasSourceBioMaterialMeasurements
Direct Known Subclasses:
Hybridization

public class BioAssayCreation
extends BioEvent
implements java.io.Serializable, HasArray, HasSourceBioMaterialMeasurements, HasPhysicalBioAssayTarget

The process by which an array and one or more biomaterials are combined to create a bioAssayCreation.

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasSourceBioMaterialMeasurements
HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasProtocolApplications
HasProtocolApplications.ProtocolApplications_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  Array array
          The array used in the BioAssayCreation event.
protected  java.lang.String ojbConcreteClass
           
protected  PhysicalBioAssay physicalBioAssayTarget
          The association between the BioAssayCreation event (typically Hybridization) and the PhysicalBioAssay and its annotation of this event.
protected  java.util.List sourceBioMaterialMeasurements
          The BioSample and its amount used in the BioAssayCreation event.
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
BioAssayCreation()
          Default constructor.
BioAssayCreation(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToSourceBioMaterialMeasurements(BioMaterialMeasurement bioMaterialMeasurement)
          Method to add BioMaterialMeasurement to SourceBioMaterialMeasurements_list
 void addToSourceBioMaterialMeasurements(int position, BioMaterialMeasurement bioMaterialMeasurement)
          Method to add BioMaterialMeasurement at position to SourceBioMaterialMeasurements_list
 boolean emptyMAGEobject()
           
 Array getArray()
          Get method for array
 BioMaterialMeasurement getFromSourceBioMaterialMeasurements(int position)
          Method to get BioMaterialMeasurement from SourceBioMaterialMeasurements_list
 java.lang.String getModelClassName()
           
 PhysicalBioAssay getPhysicalBioAssayTarget()
          Get method for physicalBioAssayTarget
 HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list getSourceBioMaterialMeasurements()
          Get method for sourceBioMaterialMeasurements
 void removeElementAtFromSourceBioMaterialMeasurements(int position)
          Method to remove by position from SourceBioMaterialMeasurements_list
 void removeFromSourceBioMaterialMeasurements(BioMaterialMeasurement bioMaterialMeasurement)
          Method to remove first BioMaterialMeasurement from SourceBioMaterialMeasurements_list
 void setArray(Array array)
          Set method for array
 void setAttributes(org.xml.sax.Attributes atts)
           
 void setPhysicalBioAssayTarget(PhysicalBioAssay physicalBioAssayTarget)
          Set method for physicalBioAssayTarget
 void setSourceBioMaterialMeasurements(HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list sourceBioMaterialMeasurements)
          Set method for sourceBioMaterialMeasurements
 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, 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

ojbConcreteClass

protected java.lang.String ojbConcreteClass

sourceBioMaterialMeasurements

protected java.util.List sourceBioMaterialMeasurements
The BioSample and its amount used in the BioAssayCreation event.


array

protected Array array
The array used in the BioAssayCreation event.


physicalBioAssayTarget

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

Constructor Detail

BioAssayCreation

public BioAssayCreation()
Default constructor.


BioAssayCreation

public BioAssayCreation(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 BioEvent

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
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 BioEvent
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 BioEvent
Throws:
java.io.IOException

getModelClassName

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

setSourceBioMaterialMeasurements

public void setSourceBioMaterialMeasurements(HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list sourceBioMaterialMeasurements)
Set method for sourceBioMaterialMeasurements

Specified by:
setSourceBioMaterialMeasurements in interface HasSourceBioMaterialMeasurements
Parameters:
value - to set

getSourceBioMaterialMeasurements

public HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list getSourceBioMaterialMeasurements()
Get method for sourceBioMaterialMeasurements

Specified by:
getSourceBioMaterialMeasurements in interface HasSourceBioMaterialMeasurements
Returns:
value of the attribute

addToSourceBioMaterialMeasurements

public void addToSourceBioMaterialMeasurements(BioMaterialMeasurement bioMaterialMeasurement)
Method to add BioMaterialMeasurement to SourceBioMaterialMeasurements_list

Specified by:
addToSourceBioMaterialMeasurements in interface HasSourceBioMaterialMeasurements

addToSourceBioMaterialMeasurements

public void addToSourceBioMaterialMeasurements(int position,
                                               BioMaterialMeasurement bioMaterialMeasurement)
Method to add BioMaterialMeasurement at position to SourceBioMaterialMeasurements_list

Specified by:
addToSourceBioMaterialMeasurements in interface HasSourceBioMaterialMeasurements

getFromSourceBioMaterialMeasurements

public BioMaterialMeasurement getFromSourceBioMaterialMeasurements(int position)
Method to get BioMaterialMeasurement from SourceBioMaterialMeasurements_list

Specified by:
getFromSourceBioMaterialMeasurements in interface HasSourceBioMaterialMeasurements

removeElementAtFromSourceBioMaterialMeasurements

public void removeElementAtFromSourceBioMaterialMeasurements(int position)
Method to remove by position from SourceBioMaterialMeasurements_list

Specified by:
removeElementAtFromSourceBioMaterialMeasurements in interface HasSourceBioMaterialMeasurements

removeFromSourceBioMaterialMeasurements

public void removeFromSourceBioMaterialMeasurements(BioMaterialMeasurement bioMaterialMeasurement)
Method to remove first BioMaterialMeasurement from SourceBioMaterialMeasurements_list

Specified by:
removeFromSourceBioMaterialMeasurements in interface HasSourceBioMaterialMeasurements

setArray

public void setArray(Array array)
Set method for array

Specified by:
setArray in interface HasArray
Parameters:
value - to set

getArray

public Array getArray()
Get method for array

Specified by:
getArray in interface HasArray
Returns:
value of the attribute

setPhysicalBioAssayTarget

public void setPhysicalBioAssayTarget(PhysicalBioAssay physicalBioAssayTarget)
Set method for physicalBioAssayTarget

Specified by:
setPhysicalBioAssayTarget in interface HasPhysicalBioAssayTarget
Parameters:
value - to set

getPhysicalBioAssayTarget

public PhysicalBioAssay getPhysicalBioAssayTarget()
Get method for physicalBioAssayTarget

Specified by:
getPhysicalBioAssayTarget in interface HasPhysicalBioAssayTarget
Returns:
value of the attribute