org.biomage.BioAssay
Class BioAssayCreation

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Common.Describable
              |
              +--org.biomage.Common.Identifiable
                    |
                    +--org.biomage.BioEvent.BioEvent
                          |
                          +--org.biomage.BioAssay.BioAssayCreation

All Implemented Interfaces:

HasArray, HasAuditTrail, HasDescriptions, HasPhysicalBioAssayTarget, HasPropertySets, HasProtocolApplications, HasSecurity, HasSourceBioMaterialMeasurements, java.io.Serializable

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 inherited from class org.biomage.Interface.HasSourceBioMaterialMeasurements

HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list

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

HasProtocolApplications.ProtocolApplications_list

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

HasAuditTrail.AuditTrail_list

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

HasDescriptions.Descriptions_list

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

HasPropertySets.PropertySets_list

Field Summary

protected Array	array The array used in the BioAssayCreation event.
protected PhysicalBioAssay	physicalBioAssayTarget The association between the BioAssayCreation event (typically Hybridization) and the PhysicalBioAssay and its annotation of this event.
protected HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list	sourceBioMaterialMeasurements The BioSample and its amount used in the BioAssayCreation event.

Fields inherited from class org.biomage.BioEvent.BioEvent

protocolApplications

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

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
Array	getArray() Get method for array
BioMaterialMeasurement	getFromSourceBioMaterialMeasurements(int position) Method to get BioMaterialMeasurement from SourceBioMaterialMeasurements_list
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	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

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

sourceBioMaterialMeasurements

protected HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_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

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 BioEvent

java.io.IOException

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

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

java.io.IOException

setSourceBioMaterialMeasurements

public void setSourceBioMaterialMeasurements(HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list sourceBioMaterialMeasurements)

Set method for sourceBioMaterialMeasurements

Specified by:

setSourceBioMaterialMeasurements in interface HasSourceBioMaterialMeasurements

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

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

getPhysicalBioAssayTarget

public PhysicalBioAssay getPhysicalBioAssayTarget()

Get method for physicalBioAssayTarget

Specified by:

getPhysicalBioAssayTarget in interface HasPhysicalBioAssayTarget

Returns:

value of the attribute