org.biomage.Experiment
Class Experiment

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Common.Describable
              |
              +--org.biomage.Common.Identifiable
                    |
                    +--org.biomage.Experiment.Experiment

All Implemented Interfaces:

HasAnalysisResults, HasAuditTrail, HasBioAssayData, HasBioAssays, HasDescriptions, HasExperimentDesign, HasPropertySets, HasProviders, HasSecurity, java.io.Serializable

public class Experiment

extends Identifiable

implements java.io.Serializable, HasAnalysisResults, HasBioAssays, HasProviders, HasBioAssayData, HasExperimentDesign

The Experiment is the collection of all the BioAssays that are related by the ExperimentDesign.

See Also:

Serialized Form

Nested Class Summary

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

HasAnalysisResults.AnalysisResults_list

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

HasBioAssays.BioAssays_list

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

HasProviders.Providers_list

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

HasBioAssayData.BioAssayData_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 HasAnalysisResults.AnalysisResults_list	analysisResults The results of analyzing the data, typically with a clustering algorithm.
protected HasBioAssayData.BioAssayData_list	bioAssayData The collection of BioAssayDatas for this Experiment.
protected HasBioAssays.BioAssays_list	bioAssays The collection of BioAssays for this Experiment.
protected ExperimentDesign	experimentDesign The association to the description and annotation of the Experiment, along with the grouping of the top-level BioAssays.
protected HasProviders.Providers_list	providers The providers of the Experiment, its data and annotation.

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

Experiment()
Default constructor.

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

Method Summary

void	addToAnalysisResults(BioAssayDataCluster bioAssayDataCluster) Method to add BioAssayDataCluster to AnalysisResults_list
void	addToAnalysisResults(int position, BioAssayDataCluster bioAssayDataCluster) Method to add BioAssayDataCluster at position to AnalysisResults_list
void	addToBioAssayData(BioAssayData bioAssayData) Method to add BioAssayData to BioAssayData_list
void	addToBioAssayData(int position, BioAssayData bioAssayData) Method to add BioAssayData at position to BioAssayData_list
void	addToBioAssays(BioAssay bioAssay) Method to add BioAssay to BioAssays_list
void	addToBioAssays(int position, BioAssay bioAssay) Method to add BioAssay at position to BioAssays_list
void	addToProviders(Contact contact) Method to add Contact to Providers_list
void	addToProviders(int position, Contact contact) Method to add Contact at position to Providers_list
HasAnalysisResults.AnalysisResults_list	getAnalysisResults() Get method for analysisResults
HasBioAssayData.BioAssayData_list	getBioAssayData() Get method for bioAssayData
HasBioAssays.BioAssays_list	getBioAssays() Get method for bioAssays
ExperimentDesign	getExperimentDesign() Get method for experimentDesign
BioAssayDataCluster	getFromAnalysisResults(int position) Method to get BioAssayDataCluster from AnalysisResults_list
BioAssayData	getFromBioAssayData(int position) Method to get BioAssayData from BioAssayData_list
BioAssay	getFromBioAssays(int position) Method to get BioAssay from BioAssays_list
Contact	getFromProviders(int position) Method to get Contact from Providers_list
HasProviders.Providers_list	getProviders() Get method for providers
void	removeElementAtFromAnalysisResults(int position) Method to remove by position from AnalysisResults_list
void	removeElementAtFromBioAssayData(int position) Method to remove by position from BioAssayData_list
void	removeElementAtFromBioAssays(int position) Method to remove by position from BioAssays_list
void	removeElementAtFromProviders(int position) Method to remove by position from Providers_list
void	removeFromAnalysisResults(BioAssayDataCluster bioAssayDataCluster) Method to remove first BioAssayDataCluster from AnalysisResults_list
void	removeFromBioAssayData(BioAssayData bioAssayData) Method to remove first BioAssayData from BioAssayData_list
void	removeFromBioAssays(BioAssay bioAssay) Method to remove first BioAssay from BioAssays_list
void	removeFromProviders(Contact contact) Method to remove first Contact from Providers_list
void	setAnalysisResults(HasAnalysisResults.AnalysisResults_list analysisResults) Set method for analysisResults
void	setBioAssayData(HasBioAssayData.BioAssayData_list bioAssayData) Set method for bioAssayData
void	setBioAssays(HasBioAssays.BioAssays_list bioAssays) Set method for bioAssays
void	setExperimentDesign(ExperimentDesign experimentDesign) Set method for experimentDesign
void	setProviders(HasProviders.Providers_list providers) Set method for providers
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.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

providers

protected HasProviders.Providers_list providers

The providers of the Experiment, its data and annotation.

analysisResults

protected HasAnalysisResults.AnalysisResults_list analysisResults

The results of analyzing the data, typically with a clustering algorithm.

bioAssayData

protected HasBioAssayData.BioAssayData_list bioAssayData

The collection of BioAssayDatas for this Experiment.

bioAssays

protected HasBioAssays.BioAssays_list bioAssays

The collection of BioAssays for this Experiment.

experimentDesign

protected ExperimentDesign experimentDesign

The association to the description and annotation of the Experiment, along with the grouping of the top-level BioAssays.

Constructor Detail

Experiment

public Experiment()

Default constructor.

Experiment

public Experiment(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 Identifiable

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 Identifiable

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 Identifiable

java.io.IOException

setProviders

public void setProviders(HasProviders.Providers_list providers)

Set method for providers

Specified by:

setProviders in interface HasProviders

getProviders

public HasProviders.Providers_list getProviders()

Get method for providers

Specified by:

getProviders in interface HasProviders

Returns:

value of the attribute

addToProviders

public void addToProviders(Contact contact)

Method to add Contact to Providers_list

Specified by:

addToProviders in interface HasProviders

addToProviders

public void addToProviders(int position,
                           Contact contact)

Method to add Contact at position to Providers_list

Specified by:

addToProviders in interface HasProviders

getFromProviders

public Contact getFromProviders(int position)

Method to get Contact from Providers_list

Specified by:

getFromProviders in interface HasProviders

removeElementAtFromProviders

public void removeElementAtFromProviders(int position)

Method to remove by position from Providers_list

Specified by:

removeElementAtFromProviders in interface HasProviders

removeFromProviders

public void removeFromProviders(Contact contact)

Method to remove first Contact from Providers_list

Specified by:

removeFromProviders in interface HasProviders

setAnalysisResults

public void setAnalysisResults(HasAnalysisResults.AnalysisResults_list analysisResults)

Set method for analysisResults

Specified by:

setAnalysisResults in interface HasAnalysisResults

getAnalysisResults

public HasAnalysisResults.AnalysisResults_list getAnalysisResults()

Get method for analysisResults

Specified by:

getAnalysisResults in interface HasAnalysisResults

Returns:

value of the attribute

addToAnalysisResults

public void addToAnalysisResults(BioAssayDataCluster bioAssayDataCluster)

Method to add BioAssayDataCluster to AnalysisResults_list

Specified by:

addToAnalysisResults in interface HasAnalysisResults

addToAnalysisResults

public void addToAnalysisResults(int position,
                                 BioAssayDataCluster bioAssayDataCluster)

Method to add BioAssayDataCluster at position to AnalysisResults_list

Specified by:

addToAnalysisResults in interface HasAnalysisResults

getFromAnalysisResults

public BioAssayDataCluster getFromAnalysisResults(int position)

Method to get BioAssayDataCluster from AnalysisResults_list

Specified by:

getFromAnalysisResults in interface HasAnalysisResults

removeElementAtFromAnalysisResults

public void removeElementAtFromAnalysisResults(int position)

Method to remove by position from AnalysisResults_list

Specified by:

removeElementAtFromAnalysisResults in interface HasAnalysisResults

removeFromAnalysisResults

public void removeFromAnalysisResults(BioAssayDataCluster bioAssayDataCluster)

Method to remove first BioAssayDataCluster from AnalysisResults_list

Specified by:

removeFromAnalysisResults in interface HasAnalysisResults

setBioAssayData

public void setBioAssayData(HasBioAssayData.BioAssayData_list bioAssayData)

Set method for bioAssayData

Specified by:

setBioAssayData in interface HasBioAssayData

getBioAssayData

public HasBioAssayData.BioAssayData_list getBioAssayData()

Get method for bioAssayData

Specified by:

getBioAssayData in interface HasBioAssayData

Returns:

value of the attribute

addToBioAssayData

public void addToBioAssayData(BioAssayData bioAssayData)

Method to add BioAssayData to BioAssayData_list

Specified by:

addToBioAssayData in interface HasBioAssayData

addToBioAssayData

public void addToBioAssayData(int position,
                              BioAssayData bioAssayData)

Method to add BioAssayData at position to BioAssayData_list

Specified by:

addToBioAssayData in interface HasBioAssayData

getFromBioAssayData

public BioAssayData getFromBioAssayData(int position)

Method to get BioAssayData from BioAssayData_list

Specified by:

getFromBioAssayData in interface HasBioAssayData

removeElementAtFromBioAssayData

public void removeElementAtFromBioAssayData(int position)

Method to remove by position from BioAssayData_list

Specified by:

removeElementAtFromBioAssayData in interface HasBioAssayData

removeFromBioAssayData

public void removeFromBioAssayData(BioAssayData bioAssayData)

Method to remove first BioAssayData from BioAssayData_list

Specified by:

removeFromBioAssayData in interface HasBioAssayData

setBioAssays

public void setBioAssays(HasBioAssays.BioAssays_list bioAssays)

Set method for bioAssays

Specified by:

setBioAssays in interface HasBioAssays

getBioAssays

public HasBioAssays.BioAssays_list getBioAssays()

Get method for bioAssays

Specified by:

getBioAssays in interface HasBioAssays

Returns:

value of the attribute

addToBioAssays

public void addToBioAssays(BioAssay bioAssay)

Method to add BioAssay to BioAssays_list

Specified by:

addToBioAssays in interface HasBioAssays

addToBioAssays

public void addToBioAssays(int position,
                           BioAssay bioAssay)

Method to add BioAssay at position to BioAssays_list

Specified by:

addToBioAssays in interface HasBioAssays

getFromBioAssays

public BioAssay getFromBioAssays(int position)

Method to get BioAssay from BioAssays_list

Specified by:

getFromBioAssays in interface HasBioAssays

removeElementAtFromBioAssays

public void removeElementAtFromBioAssays(int position)

Method to remove by position from BioAssays_list

Specified by:

removeElementAtFromBioAssays in interface HasBioAssays

removeFromBioAssays

public void removeFromBioAssays(BioAssay bioAssay)

Method to remove first BioAssay from BioAssays_list

Specified by:

removeFromBioAssays in interface HasBioAssays

setExperimentDesign

public void setExperimentDesign(ExperimentDesign experimentDesign)

Set method for experimentDesign

Specified by:

setExperimentDesign in interface HasExperimentDesign

getExperimentDesign

public ExperimentDesign getExperimentDesign()

Get method for experimentDesign

Specified by:

getExperimentDesign in interface HasExperimentDesign

Returns:

value of the attribute