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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:

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

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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.

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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.

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sourceBioMaterialMeasurements

private org.biomage.Interface.HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list sourceBioMaterialMeasurements

The BioSample and its amount used in the BioAssayCreation event.

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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.

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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.

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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.

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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.

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setArray

public void setArray(org.biomage.Array.Array array)

Set method for array

Specified by:

setArray in interface org.biomage.Interface.HasArray

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getArray

public org.biomage.Array.Array getArray()

Get method for array

Specified by:

getArray in interface org.biomage.Interface.HasArray

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setSourceBioMaterialMeasurements

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

Set method for sourceBioMaterialMeasurements

Specified by:

setSourceBioMaterialMeasurements in interface org.biomage.Interface.HasSourceBioMaterialMeasurements

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getSourceBioMaterialMeasurements

public org.biomage.Interface.HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list getSourceBioMaterialMeasurements()

Get method for sourceBioMaterialMeasurements

Specified by:

getSourceBioMaterialMeasurements in interface org.biomage.Interface.HasSourceBioMaterialMeasurements

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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

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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

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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

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removeElementAtFromSourceBioMaterialMeasurements

public void removeElementAtFromSourceBioMaterialMeasurements(int position)

Method to remove by position from SourceBioMaterialMeasurements_list

Specified by:

removeElementAtFromSourceBioMaterialMeasurements in interface org.biomage.Interface.HasSourceBioMaterialMeasurements

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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

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setPhysicalBioAssayTarget

public void setPhysicalBioAssayTarget(PhysicalBioAssay physicalBioAssayTarget)

Set method for physicalBioAssayTarget

Specified by:

setPhysicalBioAssayTarget in interface org.biomage.Interface.HasPhysicalBioAssayTarget

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getPhysicalBioAssayTarget

public PhysicalBioAssay getPhysicalBioAssayTarget()

Get method for physicalBioAssayTarget

Specified by:

getPhysicalBioAssayTarget in interface org.biomage.Interface.HasPhysicalBioAssayTarget

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> biomage >> [ BioAssay overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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