org.biomage.Experiment
Class ExperimentDesign

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

All Implemented Interfaces:

HasAuditTrail, HasDescriptions, HasExperimentalFactors, HasNormalizationDescription, HasPropertySets, HasQualityControlDescription, HasReplicateDescription, HasSecurity, HasTopLevelBioAssays, HasTypes, java.io.Serializable

public class ExperimentDesign

extends Describable

implements java.io.Serializable, HasTopLevelBioAssays, HasExperimentalFactors, HasReplicateDescription, HasQualityControlDescription, HasNormalizationDescription, HasTypes

The ExperimentDesign is the description and collection of ExperimentalFactors and the hierarchy of BioAssays to which they pertain.

See Also:

Serialized Form

Nested Class Summary

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

HasTopLevelBioAssays.TopLevelBioAssays_list

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

HasExperimentalFactors.ExperimentalFactors_list

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

HasTypes.Types_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 HasExperimentalFactors.ExperimentalFactors_list	experimentalFactors The description of the factors (TimeCourse, Dosage, etc.) that group the BioAssays.
protected Description	normalizationDescription Description of the normalization strategy of the Experiment.
protected Description	qualityControlDescription Description of the quality control aspects of the Experiment.
protected Description	replicateDescription Description of the replicate strategy of the Experiment.
protected HasTopLevelBioAssays.TopLevelBioAssays_list	topLevelBioAssays The organization of the BioAssays as specified by the ExperimentDesign (TimeCourse, Dosage, etc.)
protected HasTypes.Types_list	types Classification of an experiment.

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

ExperimentDesign()
Default constructor.

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

Method Summary

void	addToExperimentalFactors(ExperimentalFactor experimentalFactor) Method to add ExperimentalFactor to ExperimentalFactors_list
void	addToExperimentalFactors(int position, ExperimentalFactor experimentalFactor) Method to add ExperimentalFactor at position to ExperimentalFactors_list
void	addToTopLevelBioAssays(BioAssay bioAssay) Method to add BioAssay to TopLevelBioAssays_list
void	addToTopLevelBioAssays(int position, BioAssay bioAssay) Method to add BioAssay at position to TopLevelBioAssays_list
void	addToTypes(int position, OntologyEntry ontologyEntry) Method to add OntologyEntry at position to Types_list
void	addToTypes(OntologyEntry ontologyEntry) Method to add OntologyEntry to Types_list
HasExperimentalFactors.ExperimentalFactors_list	getExperimentalFactors() Get method for experimentalFactors
ExperimentalFactor	getFromExperimentalFactors(int position) Method to get ExperimentalFactor from ExperimentalFactors_list
BioAssay	getFromTopLevelBioAssays(int position) Method to get BioAssay from TopLevelBioAssays_list
OntologyEntry	getFromTypes(int position) Method to get OntologyEntry from Types_list
Description	getNormalizationDescription() Get method for normalizationDescription
Description	getQualityControlDescription() Get method for qualityControlDescription
Description	getReplicateDescription() Get method for replicateDescription
HasTopLevelBioAssays.TopLevelBioAssays_list	getTopLevelBioAssays() Get method for topLevelBioAssays
HasTypes.Types_list	getTypes() Get method for types
void	removeElementAtFromExperimentalFactors(int position) Method to remove by position from ExperimentalFactors_list
void	removeElementAtFromTopLevelBioAssays(int position) Method to remove by position from TopLevelBioAssays_list
void	removeElementAtFromTypes(int position) Method to remove by position from Types_list
void	removeFromExperimentalFactors(ExperimentalFactor experimentalFactor) Method to remove first ExperimentalFactor from ExperimentalFactors_list
void	removeFromTopLevelBioAssays(BioAssay bioAssay) Method to remove first BioAssay from TopLevelBioAssays_list
void	removeFromTypes(OntologyEntry ontologyEntry) Method to remove first OntologyEntry from Types_list
void	setExperimentalFactors(HasExperimentalFactors.ExperimentalFactors_list experimentalFactors) Set method for experimentalFactors
void	setNormalizationDescription(Description normalizationDescription) Set method for normalizationDescription
void	setQualityControlDescription(Description qualityControlDescription) Set method for qualityControlDescription
void	setReplicateDescription(Description replicateDescription) Set method for replicateDescription
void	setTopLevelBioAssays(HasTopLevelBioAssays.TopLevelBioAssays_list topLevelBioAssays) Set method for topLevelBioAssays
void	setTypes(HasTypes.Types_list types) Set method for types
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.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

types

protected HasTypes.Types_list types

Classification of an experiment. For example 'normal vs. diseased', 'treated vs. untreated', 'time course', 'tiling', etc.

topLevelBioAssays

protected HasTopLevelBioAssays.TopLevelBioAssays_list topLevelBioAssays

The organization of the BioAssays as specified by the ExperimentDesign (TimeCourse, Dosage, etc.)

experimentalFactors

protected HasExperimentalFactors.ExperimentalFactors_list experimentalFactors

The description of the factors (TimeCourse, Dosage, etc.) that group the BioAssays.

qualityControlDescription

protected Description qualityControlDescription

Description of the quality control aspects of the Experiment.

normalizationDescription

protected Description normalizationDescription

Description of the normalization strategy of the Experiment.

replicateDescription

protected Description replicateDescription

Description of the replicate strategy of the Experiment.

Constructor Detail

ExperimentDesign

public ExperimentDesign()

Default constructor.

ExperimentDesign

public ExperimentDesign(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 Describable

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 Describable

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 Describable

java.io.IOException

setTypes

public void setTypes(HasTypes.Types_list types)

Set method for types

Specified by:

setTypes in interface HasTypes

getTypes

public HasTypes.Types_list getTypes()

Get method for types

Specified by:

getTypes in interface HasTypes

Returns:

value of the attribute

addToTypes

public void addToTypes(OntologyEntry ontologyEntry)

Method to add OntologyEntry to Types_list

Specified by:

addToTypes in interface HasTypes

addToTypes

public void addToTypes(int position,
                       OntologyEntry ontologyEntry)

Method to add OntologyEntry at position to Types_list

Specified by:

addToTypes in interface HasTypes

getFromTypes

public OntologyEntry getFromTypes(int position)

Method to get OntologyEntry from Types_list

Specified by:

getFromTypes in interface HasTypes

removeElementAtFromTypes

public void removeElementAtFromTypes(int position)

Method to remove by position from Types_list

Specified by:

removeElementAtFromTypes in interface HasTypes

removeFromTypes

public void removeFromTypes(OntologyEntry ontologyEntry)

Method to remove first OntologyEntry from Types_list

Specified by:

removeFromTypes in interface HasTypes

setTopLevelBioAssays

public void setTopLevelBioAssays(HasTopLevelBioAssays.TopLevelBioAssays_list topLevelBioAssays)

Set method for topLevelBioAssays

Specified by:

setTopLevelBioAssays in interface HasTopLevelBioAssays

getTopLevelBioAssays

public HasTopLevelBioAssays.TopLevelBioAssays_list getTopLevelBioAssays()

Get method for topLevelBioAssays

Specified by:

getTopLevelBioAssays in interface HasTopLevelBioAssays

Returns:

value of the attribute

addToTopLevelBioAssays

public void addToTopLevelBioAssays(BioAssay bioAssay)

Method to add BioAssay to TopLevelBioAssays_list

Specified by:

addToTopLevelBioAssays in interface HasTopLevelBioAssays

addToTopLevelBioAssays

public void addToTopLevelBioAssays(int position,
                                   BioAssay bioAssay)

Method to add BioAssay at position to TopLevelBioAssays_list

Specified by:

addToTopLevelBioAssays in interface HasTopLevelBioAssays

getFromTopLevelBioAssays

public BioAssay getFromTopLevelBioAssays(int position)

Method to get BioAssay from TopLevelBioAssays_list

Specified by:

getFromTopLevelBioAssays in interface HasTopLevelBioAssays

removeElementAtFromTopLevelBioAssays

public void removeElementAtFromTopLevelBioAssays(int position)

Method to remove by position from TopLevelBioAssays_list

Specified by:

removeElementAtFromTopLevelBioAssays in interface HasTopLevelBioAssays

removeFromTopLevelBioAssays

public void removeFromTopLevelBioAssays(BioAssay bioAssay)

Method to remove first BioAssay from TopLevelBioAssays_list

Specified by:

removeFromTopLevelBioAssays in interface HasTopLevelBioAssays

setExperimentalFactors

public void setExperimentalFactors(HasExperimentalFactors.ExperimentalFactors_list experimentalFactors)

Set method for experimentalFactors

Specified by:

setExperimentalFactors in interface HasExperimentalFactors

getExperimentalFactors

public HasExperimentalFactors.ExperimentalFactors_list getExperimentalFactors()

Get method for experimentalFactors

Specified by:

getExperimentalFactors in interface HasExperimentalFactors

Returns:

value of the attribute

addToExperimentalFactors

public void addToExperimentalFactors(ExperimentalFactor experimentalFactor)

Method to add ExperimentalFactor to ExperimentalFactors_list

Specified by:

addToExperimentalFactors in interface HasExperimentalFactors

addToExperimentalFactors

public void addToExperimentalFactors(int position,
                                     ExperimentalFactor experimentalFactor)

Method to add ExperimentalFactor at position to ExperimentalFactors_list

Specified by:

addToExperimentalFactors in interface HasExperimentalFactors

getFromExperimentalFactors

public ExperimentalFactor getFromExperimentalFactors(int position)

Method to get ExperimentalFactor from ExperimentalFactors_list

Specified by:

getFromExperimentalFactors in interface HasExperimentalFactors

removeElementAtFromExperimentalFactors

public void removeElementAtFromExperimentalFactors(int position)

Method to remove by position from ExperimentalFactors_list

Specified by:

removeElementAtFromExperimentalFactors in interface HasExperimentalFactors

removeFromExperimentalFactors

public void removeFromExperimentalFactors(ExperimentalFactor experimentalFactor)

Method to remove first ExperimentalFactor from ExperimentalFactors_list

Specified by:

removeFromExperimentalFactors in interface HasExperimentalFactors

setQualityControlDescription

public void setQualityControlDescription(Description qualityControlDescription)

Set method for qualityControlDescription

Specified by:

setQualityControlDescription in interface HasQualityControlDescription

getQualityControlDescription

public Description getQualityControlDescription()

Get method for qualityControlDescription

Specified by:

getQualityControlDescription in interface HasQualityControlDescription

Returns:

value of the attribute

setNormalizationDescription

public void setNormalizationDescription(Description normalizationDescription)

Set method for normalizationDescription

Specified by:

setNormalizationDescription in interface HasNormalizationDescription

getNormalizationDescription

public Description getNormalizationDescription()

Get method for normalizationDescription

Specified by:

getNormalizationDescription in interface HasNormalizationDescription

Returns:

value of the attribute

setReplicateDescription

public void setReplicateDescription(Description replicateDescription)

Set method for replicateDescription

Specified by:

setReplicateDescription in interface HasReplicateDescription

getReplicateDescription

public Description getReplicateDescription()

Get method for replicateDescription

Specified by:

getReplicateDescription in interface HasReplicateDescription

Returns:

value of the attribute