Package ubic.gemma.model.expression.arrayDesign

Class ArrayDesign

java.lang.Object

ubic.gemma.model.common.AbstractDescribable

ubic.gemma.model.common.auditAndSecurity.AbstractAuditable

ubic.gemma.model.expression.arrayDesign.ArrayDesign

All Implemented Interfaces:

gemma.gsec.model.Securable, gemma.gsec.model.SecuredNotChild, Serializable, Auditable, Curatable, Securable, SecuredNotChild, Describable, Identifiable

@Indexed
public class ArrayDesign
extends AbstractAuditable
implements Curatable, SecuredNotChild

Represents an assembly of design elements that are assayed all at once.

Author:

Paul

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	ArrayDesign.Factory

Constructor Summary

Constructors

Constructor	Description
ArrayDesign()	No-arg constructor added to satisfy javabean contract

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object object)	Returns true if the argument is an Describable instance and all identifiers for this entity equal the identifiers of the argument entity.
Integer	getAdvertisedNumberOfDesignElements()
Set<AlternateName>	getAlternateNames()
ArrayDesign	getAlternativeTo()
Set<CompositeSequence>	getCompositeSequences()
CurationDetails	getCurationDetails()
String	getDescription()	Obtain a human-readable description of the object
Contact	getDesignProvider()
Set<DatabaseEntry>	getExternalReferences()
Long	getId()
ArrayDesign	getMergedInto()
Set<ArrayDesign>	getMergees()
String	getName()	Obtain the name of an object is a possibly ambiguous human-readable identifier that need not be an external database reference.
Taxon	getPrimaryTaxon()
String	getShortName()
Set<ArrayDesign>	getSubsumedArrayDesigns()
ArrayDesign	getSubsumingArrayDesign()
TechnologyType	getTechnologyType()
int	hashCode()	Returns a hash code based on this entity's identifiers.
void	setAdvertisedNumberOfDesignElements(Integer advertisedNumberOfDesignElements)
void	setAlternateNames(Set<AlternateName> alternateNames)
void	setAlternativeTo(ArrayDesign alternativeTo)
void	setCompositeSequences(Set<CompositeSequence> compositeSequences)
void	setCurationDetails(CurationDetails curationDetails)
void	setDesignProvider(Contact designProvider)
void	setExternalReferences(Set<DatabaseEntry> externalReferences)
void	setMergedInto(ArrayDesign mergedInto)
void	setMergees(Set<ArrayDesign> mergees)
void	setPrimaryTaxon(Taxon primaryTaxon)
void	setShortName(String shortName)
void	setSubsumedArrayDesigns(Set<ArrayDesign> subsumedArrayDesigns)
void	setSubsumingArrayDesign(ArrayDesign subsumingArrayDesign)
void	setTechnologyType(TechnologyType technologyType)
String	toString()

Methods inherited from class ubic.gemma.model.common.auditAndSecurity.AbstractAuditable

getAuditTrail, setAuditTrail

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

setDescription, setId, setName

Methods inherited from class java.lang.Object

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

Methods inherited from interface ubic.gemma.model.common.auditAndSecurity.Auditable

getAuditTrail, setAuditTrail

Constructor Detail

ArrayDesign

public ArrayDesign()

No-arg constructor added to satisfy javabean contract

Method Detail

equals

public boolean equals(Object object)

Description copied from class: AbstractDescribable

Returns true if the argument is an Describable instance and all identifiers for this entity equal the identifiers of the argument entity. Returns false otherwise.

Overrides:

equals in class AbstractDescribable

getId

@DocumentId
public Long getId()

Specified by:

getId in interface Identifiable

Specified by:

getId in interface gemma.gsec.model.Securable

Overrides:

getId in class AbstractDescribable

getName

@Field
public String getName()

Description copied from interface: Describable

Obtain the name of an object is a possibly ambiguous human-readable identifier that need not be an external database reference.

Specified by:

getName in interface Describable

Overrides:

getName in class AbstractDescribable

getDescription

@Field(store=YES)
public String getDescription()

Description copied from interface: Describable

Obtain a human-readable description of the object

Specified by:

getDescription in interface Describable

Overrides:

getDescription in class AbstractDescribable

getAdvertisedNumberOfDesignElements

public Integer getAdvertisedNumberOfDesignElements()

Returns:

The number of design elements, according to the manufactuerer or determined at the time the array design was entered into the system. The actual number of design elements can only be determined by looking at the associated Set of DesignElements.

getAlternateNames

@IndexedEmbedded
public Set<AlternateName> getAlternateNames()

getAlternativeTo

public ArrayDesign getAlternativeTo()

Returns:

true if this is an Affymetrix platform that has a related "canonical" platform we use instead.

getCompositeSequences

public Set<CompositeSequence> getCompositeSequences()

getCurationDetails

public CurationDetails getCurationDetails()

Specified by:

getCurationDetails in interface Curatable

getDesignProvider

public Contact getDesignProvider()

getExternalReferences

@IndexedEmbedded
public Set<DatabaseEntry> getExternalReferences()

Returns:

Accessions for this array design in other databases, e.g., GEO, ArrayExpression.

getMergedInto

public ArrayDesign getMergedInto()

getMergees

public Set<ArrayDesign> getMergees()

getPrimaryTaxon

public Taxon getPrimaryTaxon()

Returns:

The taxon the array design is for. This could be a non-specific taxon ("salmonid"). It may not match the sequences on the array exactly. For example, a mouse array might have some non-mouse sequences as controls, but the primary taxon is still mouse.

getShortName

@Field(analyze=NO)
public String getShortName()

Returns:

A brief unique (but optional) human-readable name for the expression experiment. For example in the past we often used names like "HG-U95A".

getSubsumedArrayDesigns

public Set<ArrayDesign> getSubsumedArrayDesigns()

Returns:

Array designs that this array design "covers". For example, the HG-U133_Plus_2 array includes all the elements that are on the HG-U133A and HG-U133B, so they are subsumed by the HG-U133_Plus_2.

getSubsumingArrayDesign

public ArrayDesign getSubsumingArrayDesign()

Returns:

An array design that subsumes this one (contains DesignElements that are equivalent to the ones on this arraydesign).

getTechnologyType

public TechnologyType getTechnologyType()

hashCode

public int hashCode()

Description copied from class: AbstractDescribable

Returns a hash code based on this entity's identifiers.

Overrides:

hashCode in class AbstractDescribable

setAdvertisedNumberOfDesignElements

public void setAdvertisedNumberOfDesignElements(Integer advertisedNumberOfDesignElements)

setAlternateNames

public void setAlternateNames(Set<AlternateName> alternateNames)

setAlternativeTo

public void setAlternativeTo(ArrayDesign alternativeTo)

setCompositeSequences

public void setCompositeSequences(Set<CompositeSequence> compositeSequences)

setCurationDetails

public void setCurationDetails(CurationDetails curationDetails)

Specified by:

setCurationDetails in interface Curatable

setDesignProvider

public void setDesignProvider(Contact designProvider)

setExternalReferences

public void setExternalReferences(Set<DatabaseEntry> externalReferences)

setMergedInto

public void setMergedInto(ArrayDesign mergedInto)

setMergees

public void setMergees(Set<ArrayDesign> mergees)

setPrimaryTaxon

public void setPrimaryTaxon(Taxon primaryTaxon)

setShortName

public void setShortName(String shortName)

setSubsumedArrayDesigns

public void setSubsumedArrayDesigns(Set<ArrayDesign> subsumedArrayDesigns)

setSubsumingArrayDesign

public void setSubsumingArrayDesign(ArrayDesign subsumingArrayDesign)

setTechnologyType

public void setTechnologyType(TechnologyType technologyType)

toString

public String toString()

Overrides:

toString in class AbstractDescribable

See Also:

AbstractDescribable.toString()