org.biomage.BioAssayData
Class Transformation

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Common.Describable
              |
              +--org.biomage.Common.Identifiable
                    |
                    +--org.biomage.BioEvent.BioEvent
                          |
                          +--org.biomage.BioAssayData.Transformation

All Implemented Interfaces:

HasAuditTrail, HasBioAssayDataSources, HasBioAssayMapping, HasDerivedBioAssayDataTarget, HasDescriptions, HasDesignElementMapping, HasPropertySets, HasProtocolApplications, HasQuantitationTypeMapping, HasSecurity, java.io.Serializable

public class Transformation

extends BioEvent

implements java.io.Serializable, HasBioAssayDataSources, HasBioAssayMapping, HasDerivedBioAssayDataTarget, HasQuantitationTypeMapping, HasDesignElementMapping

The process by which derivedBioAssays are created from measuredBioAssays and/or derivedBioAssays. It uses mappings to indicate the input and output dimensions.

See Also:

Serialized Form

Nested Class Summary

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

HasBioAssayDataSources.BioAssayDataSources_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 HasBioAssayDataSources.BioAssayDataSources_list	bioAssayDataSources The BioAssayData sources that the Transformation event uses to produce the target DerivedBioAssayData.
protected BioAssayMapping	bioAssayMapping The collection of mappings for the BioAssays.
protected DerivedBioAssayData	derivedBioAssayDataTarget The association between the DerivedBioAssayData and the Transformation event that produced it.
protected DesignElementMapping	designElementMapping The collection of mappings for the DesignElements.
protected QuantitationTypeMapping	quantitationTypeMapping The collection of mappings for the QuantitationTypes.

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

Transformation()
Default constructor.

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

Method Summary

void	addToBioAssayDataSources(BioAssayData bioAssayData) Method to add BioAssayData to BioAssayDataSources_list
void	addToBioAssayDataSources(int position, BioAssayData bioAssayData) Method to add BioAssayData at position to BioAssayDataSources_list
HasBioAssayDataSources.BioAssayDataSources_list	getBioAssayDataSources() Get method for bioAssayDataSources
BioAssayMapping	getBioAssayMapping() Get method for bioAssayMapping
DerivedBioAssayData	getDerivedBioAssayDataTarget() Get method for derivedBioAssayDataTarget
DesignElementMapping	getDesignElementMapping() Get method for designElementMapping
BioAssayData	getFromBioAssayDataSources(int position) Method to get BioAssayData from BioAssayDataSources_list
QuantitationTypeMapping	getQuantitationTypeMapping() Get method for quantitationTypeMapping
void	removeElementAtFromBioAssayDataSources(int position) Method to remove by position from BioAssayDataSources_list
void	removeFromBioAssayDataSources(BioAssayData bioAssayData) Method to remove first BioAssayData from BioAssayDataSources_list
void	setBioAssayDataSources(HasBioAssayDataSources.BioAssayDataSources_list bioAssayDataSources) Set method for bioAssayDataSources
void	setBioAssayMapping(BioAssayMapping bioAssayMapping) Set method for bioAssayMapping
void	setDerivedBioAssayDataTarget(DerivedBioAssayData derivedBioAssayDataTarget) Set method for derivedBioAssayDataTarget
void	setDesignElementMapping(DesignElementMapping designElementMapping) Set method for designElementMapping
void	setQuantitationTypeMapping(QuantitationTypeMapping quantitationTypeMapping) Set method for quantitationTypeMapping
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

bioAssayDataSources

protected HasBioAssayDataSources.BioAssayDataSources_list bioAssayDataSources

The BioAssayData sources that the Transformation event uses to produce the target DerivedBioAssayData.

derivedBioAssayDataTarget

protected DerivedBioAssayData derivedBioAssayDataTarget

The association between the DerivedBioAssayData and the Transformation event that produced it.

quantitationTypeMapping

protected QuantitationTypeMapping quantitationTypeMapping

The collection of mappings for the QuantitationTypes.

designElementMapping

protected DesignElementMapping designElementMapping

The collection of mappings for the DesignElements.

bioAssayMapping

protected BioAssayMapping bioAssayMapping

The collection of mappings for the BioAssays.

Constructor Detail

Transformation

public Transformation()

Default constructor.

Transformation

public Transformation(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

setBioAssayDataSources

public void setBioAssayDataSources(HasBioAssayDataSources.BioAssayDataSources_list bioAssayDataSources)

Set method for bioAssayDataSources

Specified by:

setBioAssayDataSources in interface HasBioAssayDataSources

getBioAssayDataSources

public HasBioAssayDataSources.BioAssayDataSources_list getBioAssayDataSources()

Get method for bioAssayDataSources

Specified by:

getBioAssayDataSources in interface HasBioAssayDataSources

Returns:

value of the attribute

addToBioAssayDataSources

public void addToBioAssayDataSources(BioAssayData bioAssayData)

Method to add BioAssayData to BioAssayDataSources_list

Specified by:

addToBioAssayDataSources in interface HasBioAssayDataSources

addToBioAssayDataSources

public void addToBioAssayDataSources(int position,
                                     BioAssayData bioAssayData)

Method to add BioAssayData at position to BioAssayDataSources_list

Specified by:

addToBioAssayDataSources in interface HasBioAssayDataSources

getFromBioAssayDataSources

public BioAssayData getFromBioAssayDataSources(int position)

Method to get BioAssayData from BioAssayDataSources_list

Specified by:

getFromBioAssayDataSources in interface HasBioAssayDataSources

removeElementAtFromBioAssayDataSources

public void removeElementAtFromBioAssayDataSources(int position)

Method to remove by position from BioAssayDataSources_list

Specified by:

removeElementAtFromBioAssayDataSources in interface HasBioAssayDataSources

removeFromBioAssayDataSources

public void removeFromBioAssayDataSources(BioAssayData bioAssayData)

Method to remove first BioAssayData from BioAssayDataSources_list

Specified by:

removeFromBioAssayDataSources in interface HasBioAssayDataSources

setDerivedBioAssayDataTarget

public void setDerivedBioAssayDataTarget(DerivedBioAssayData derivedBioAssayDataTarget)

Set method for derivedBioAssayDataTarget

Specified by:

setDerivedBioAssayDataTarget in interface HasDerivedBioAssayDataTarget

getDerivedBioAssayDataTarget

public DerivedBioAssayData getDerivedBioAssayDataTarget()

Get method for derivedBioAssayDataTarget

Specified by:

getDerivedBioAssayDataTarget in interface HasDerivedBioAssayDataTarget

Returns:

value of the attribute

setQuantitationTypeMapping

public void setQuantitationTypeMapping(QuantitationTypeMapping quantitationTypeMapping)

Set method for quantitationTypeMapping

Specified by:

setQuantitationTypeMapping in interface HasQuantitationTypeMapping

getQuantitationTypeMapping

public QuantitationTypeMapping getQuantitationTypeMapping()

Get method for quantitationTypeMapping

Specified by:

getQuantitationTypeMapping in interface HasQuantitationTypeMapping

Returns:

value of the attribute

setDesignElementMapping

public void setDesignElementMapping(DesignElementMapping designElementMapping)

Set method for designElementMapping

Specified by:

setDesignElementMapping in interface HasDesignElementMapping

getDesignElementMapping

public DesignElementMapping getDesignElementMapping()

Get method for designElementMapping

Specified by:

getDesignElementMapping in interface HasDesignElementMapping

Returns:

value of the attribute

setBioAssayMapping

public void setBioAssayMapping(BioAssayMapping bioAssayMapping)

Set method for bioAssayMapping

Specified by:

setBioAssayMapping in interface HasBioAssayMapping

getBioAssayMapping

public BioAssayMapping getBioAssayMapping()

Get method for bioAssayMapping

Specified by:

getBioAssayMapping in interface HasBioAssayMapping

Returns:

value of the attribute