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

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Common.Describable
          extended byorg.biomage.Common.Identifiable
              extended byorg.biomage.BioEvent.BioEvent
                  extended byorg.biomage.BioAssay.BioAssayCreation
All Implemented Interfaces:
org.biomage.Interface.HasArray, org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasPhysicalBioAssayTarget, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasProtocolApplications, org.biomage.Interface.HasSecurity, org.biomage.Interface.HasSourceBioMaterialMeasurements, java.io.Serializable
Direct Known Subclasses:
Hybridization

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

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


Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasSourceBioMaterialMeasurements
org.biomage.Interface.HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list
 
Nested classes inherited from class org.biomage.Interface.HasProtocolApplications
org.biomage.Interface.HasProtocolApplications.ProtocolApplications_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  org.biomage.Array.Array array
          The array used in the BioAssayCreation event.
private  PhysicalBioAssay physicalBioAssayTarget
          The association between the BioAssayCreation event (typically Hybridization) and the PhysicalBioAssay and its annotation of this event.
private  org.biomage.Interface.HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list sourceBioMaterialMeasurements
          The BioSample and its amount used in the BioAssayCreation event.
 
Fields inherited from class org.biomage.BioEvent.BioEvent
 
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
BioAssayCreation()
          Default constructor.
BioAssayCreation(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToSourceBioMaterialMeasurements(org.biomage.BioMaterial.BioMaterialMeasurement bioMaterialMeasurement)
          Method to add BioMaterialMeasurement to SourceBioMaterialMeasurements_list
 void addToSourceBioMaterialMeasurements(int position, org.biomage.BioMaterial.BioMaterialMeasurement bioMaterialMeasurement)
          Method to add BioMaterialMeasurement at position to SourceBioMaterialMeasurements_list
 org.biomage.Array.Array getArray()
          Get method for array
 org.biomage.BioMaterial.BioMaterialMeasurement getFromSourceBioMaterialMeasurements(int position)
          Method to get BioMaterialMeasurement from SourceBioMaterialMeasurements_list
 PhysicalBioAssay getPhysicalBioAssayTarget()
          Get method for physicalBioAssayTarget
 org.biomage.Interface.HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list getSourceBioMaterialMeasurements()
          Get method for sourceBioMaterialMeasurements
 void removeElementAtFromSourceBioMaterialMeasurements(int position)
          Method to remove by position from SourceBioMaterialMeasurements_list
 void removeFromSourceBioMaterialMeasurements(org.biomage.BioMaterial.BioMaterialMeasurement bioMaterialMeasurement)
          Method to remove first BioMaterialMeasurement from SourceBioMaterialMeasurements_list
 void setArray(org.biomage.Array.Array array)
          Set method for array
 void setPhysicalBioAssayTarget(PhysicalBioAssay physicalBioAssayTarget)
          Set method for physicalBioAssayTarget
 void setSourceBioMaterialMeasurements(org.biomage.Interface.HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list sourceBioMaterialMeasurements)
          Set method for sourceBioMaterialMeasurements
 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.BioEvent.BioEvent
addToProtocolApplications, addToProtocolApplications, getFromProtocolApplications, getProtocolApplications, removeElementAtFromProtocolApplications, removeFromProtocolApplications, setProtocolApplications
 
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

array

private org.biomage.Array.Array array
The array used in the BioAssayCreation event.


sourceBioMaterialMeasurements

private org.biomage.Interface.HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list sourceBioMaterialMeasurements
The BioSample and its amount used in the BioAssayCreation event.


physicalBioAssayTarget

private 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

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.


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.


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.


setArray

public void setArray(org.biomage.Array.Array array)
Set method for array

Specified by:
setArray in interface org.biomage.Interface.HasArray

getArray

public org.biomage.Array.Array getArray()
Get method for array

Specified by:
getArray in interface org.biomage.Interface.HasArray

setSourceBioMaterialMeasurements

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

Specified by:
setSourceBioMaterialMeasurements in interface org.biomage.Interface.HasSourceBioMaterialMeasurements

getSourceBioMaterialMeasurements

public org.biomage.Interface.HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list getSourceBioMaterialMeasurements()
Get method for sourceBioMaterialMeasurements

Specified by:
getSourceBioMaterialMeasurements in interface org.biomage.Interface.HasSourceBioMaterialMeasurements

addToSourceBioMaterialMeasurements

public void addToSourceBioMaterialMeasurements(org.biomage.BioMaterial.BioMaterialMeasurement bioMaterialMeasurement)
Method to add BioMaterialMeasurement to SourceBioMaterialMeasurements_list

Specified by:
addToSourceBioMaterialMeasurements in interface org.biomage.Interface.HasSourceBioMaterialMeasurements

addToSourceBioMaterialMeasurements

public void addToSourceBioMaterialMeasurements(int position,
                                               org.biomage.BioMaterial.BioMaterialMeasurement bioMaterialMeasurement)
Method to add BioMaterialMeasurement at position to SourceBioMaterialMeasurements_list

Specified by:
addToSourceBioMaterialMeasurements in interface org.biomage.Interface.HasSourceBioMaterialMeasurements

getFromSourceBioMaterialMeasurements

public org.biomage.BioMaterial.BioMaterialMeasurement getFromSourceBioMaterialMeasurements(int position)
Method to get BioMaterialMeasurement from SourceBioMaterialMeasurements_list

Specified by:
getFromSourceBioMaterialMeasurements in interface org.biomage.Interface.HasSourceBioMaterialMeasurements

removeElementAtFromSourceBioMaterialMeasurements

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

Specified by:
removeElementAtFromSourceBioMaterialMeasurements in interface org.biomage.Interface.HasSourceBioMaterialMeasurements

removeFromSourceBioMaterialMeasurements

public void removeFromSourceBioMaterialMeasurements(org.biomage.BioMaterial.BioMaterialMeasurement bioMaterialMeasurement)
Method to remove first BioMaterialMeasurement from SourceBioMaterialMeasurements_list

Specified by:
removeFromSourceBioMaterialMeasurements in interface org.biomage.Interface.HasSourceBioMaterialMeasurements

setPhysicalBioAssayTarget

public void setPhysicalBioAssayTarget(PhysicalBioAssay physicalBioAssayTarget)
Set method for physicalBioAssayTarget

Specified by:
setPhysicalBioAssayTarget in interface org.biomage.Interface.HasPhysicalBioAssayTarget

getPhysicalBioAssayTarget

public PhysicalBioAssay getPhysicalBioAssayTarget()
Get method for physicalBioAssayTarget

Specified by:
getPhysicalBioAssayTarget in interface org.biomage.Interface.HasPhysicalBioAssayTarget