org.biomage.BioAssay
Class Hybridization

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

All Implemented Interfaces:

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

public class Hybridization

extends BioAssayCreation

implements java.io.Serializable

The archetypal bioAssayCreation event, whereby biomaterials are hybridized to an array.

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

Fields inherited from class org.biomage.BioAssay.BioAssayCreation

array, physicalBioAssayTarget, sourceBioMaterialMeasurements

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

Hybridization()
Default constructor.

Hybridization(org.xml.sax.Attributes atts)
Attribute constructor.

Method Summary

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.BioAssayCreation

addToSourceBioMaterialMeasurements, addToSourceBioMaterialMeasurements, getArray, getFromSourceBioMaterialMeasurements, getPhysicalBioAssayTarget, getSourceBioMaterialMeasurements, removeElementAtFromSourceBioMaterialMeasurements, removeFromSourceBioMaterialMeasurements, setArray, setPhysicalBioAssayTarget, setSourceBioMaterialMeasurements

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

Constructor Detail

Hybridization

public Hybridization()

Default constructor.

Hybridization

public Hybridization(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 BioAssayCreation

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 BioAssayCreation

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 BioAssayCreation

java.io.IOException