Package ubic.gemma.model.expression.experiment

Class ExperimentalDesignValueObject

java.lang.Object

ubic.gemma.model.common.IdentifiableValueObject<ExperimentalDesign>

ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject

All Implemented Interfaces:

Serializable, Identifiable

public class ExperimentalDesignValueObject
extends IdentifiableValueObject<ExperimentalDesign>

Full structural representation of an ExperimentalDesign: factors, their factor values (with statements carrying stable database IDs), and the assignment of biomaterials to factor values.

The shape is intended for client-side editing flows that need to round-trip individual statements/factor values by ID rather than by content. Sample identity is keyed by BioMaterial ID; clients can join to the result of /datasets/{id}/samples via BioAssayValueObject.sample.id.

Author:

ogan

See Also:

• Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	ExperimentalDesignValueObject.BioMaterialFactorValueAssignment	Assignment of a single BioMaterial (sample) to its assigned FactorValues.
static class	ExperimentalDesignValueObject.ExperimentalFactorEntry	One ExperimentalFactor, with its factor values inlined.

Field Summary

Fields inherited from class ubic.gemma.model.common.IdentifiableValueObject

id

Constructor Summary

Constructors

Constructor	Description
ExperimentalDesignValueObject()
ExperimentalDesignValueObject(ExperimentalDesign ed, Collection<BioAssay> bioAssays)	Build the design VO from an ExperimentalDesign and the BioAssays of the owning experiment.

Method Summary

Modifier and Type	Method	Description
List<ExperimentalDesignValueObject.BioMaterialFactorValueAssignment>	getBioMaterialAssignments()	Many-to-many assignment of BioMaterials to FactorValues, materialized as a flat list.
String	getDescription()
List<ExperimentalDesignValueObject.ExperimentalFactorEntry>	getExperimentalFactors()
String	getName()
String	getNormalizationDescription()
String	getQualityControlDescription()
String	getReplicateDescription()
void	setBioMaterialAssignments(List<ExperimentalDesignValueObject.BioMaterialFactorValueAssignment> bioMaterialAssignments)	Many-to-many assignment of BioMaterials to FactorValues, materialized as a flat list.
void	setDescription(String description)
void	setExperimentalFactors(List<ExperimentalDesignValueObject.ExperimentalFactorEntry> experimentalFactors)
void	setName(String name)
void	setNormalizationDescription(String normalizationDescription)
void	setQualityControlDescription(String qualityControlDescription)
void	setReplicateDescription(String replicateDescription)

Methods inherited from class ubic.gemma.model.common.IdentifiableValueObject

canEqual, equals, getId, hashCode, setId, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Details

ExperimentalDesignValueObject

public ExperimentalDesignValueObject()

ExperimentalDesignValueObject

public ExperimentalDesignValueObject(ExperimentalDesign ed,
 Collection<BioAssay> bioAssays)

Build the design VO from an ExperimentalDesign and the BioAssays of the owning experiment.

Must be invoked while a Hibernate session is open, since factor-value characteristics and biomaterial factor value collections are lazily loaded.

Method Details

getName

@Nullable
public String getName()

getDescription

@Nullable
public String getDescription()

getReplicateDescription

@Nullable
public String getReplicateDescription()

getQualityControlDescription

@Nullable
public String getQualityControlDescription()

getNormalizationDescription

@Nullable
public String getNormalizationDescription()

getExperimentalFactors

public List<ExperimentalDesignValueObject.ExperimentalFactorEntry> getExperimentalFactors()

getBioMaterialAssignments

public List<ExperimentalDesignValueObject.BioMaterialFactorValueAssignment> getBioMaterialAssignments()

Many-to-many assignment of BioMaterials to FactorValues, materialized as a flat list.

setName

public void setName(@Nullable
 String name)

setDescription

public void setDescription(@Nullable
 String description)

setReplicateDescription

public void setReplicateDescription(@Nullable
 String replicateDescription)

setQualityControlDescription

public void setQualityControlDescription(@Nullable
 String qualityControlDescription)

setNormalizationDescription

public void setNormalizationDescription(@Nullable
 String normalizationDescription)

setExperimentalFactors

public void setExperimentalFactors(List<ExperimentalDesignValueObject.ExperimentalFactorEntry> experimentalFactors)

setBioMaterialAssignments

public void setBioMaterialAssignments(List<ExperimentalDesignValueObject.BioMaterialFactorValueAssignment> bioMaterialAssignments)

Many-to-many assignment of BioMaterials to FactorValues, materialized as a flat list.