org.biopax.paxtools.model.level3

Interface Named

All Superinterfaces:

BioPAXElement, Cloneable, Level3Element, Serializable, XReferrable

All Known Subinterfaces:

BiochemicalReaction, BioSource, Catalysis, Complex, ComplexAssembly, Control, Controller, Conversion, Degradation, Dna, DnaReference, DnaRegion, DnaRegionReference, Entity, EntityReference, Gene, GeneticInteraction, Interaction, Modulation, MolecularInteraction, NucleicAcid, NucleicAcidReference, NucleicAcidRegionReference, Pathway, PhysicalEntity, Process, Protein, ProteinReference, Provenance, Rna, RnaReference, RnaRegion, RnaRegionReference, SequenceEntity, SequenceEntityReference, SimplePhysicalEntity, SmallMolecule, SmallMoleculeReference, TemplateReaction, TemplateReactionRegulation, Transport, TransportWithBiochemicalReaction

All Known Implementing Classes:

BiochemicalReactionImpl, BioSourceImpl, CatalysisImpl, ComplexAssemblyImpl, ComplexImpl, ControlImpl, ConversionImpl, DegradationImpl, DnaImpl, DnaReferenceImpl, DnaRegionImpl, DnaRegionReferenceImpl, EntityImpl, EntityReferenceImpl, GeneImpl, GeneticInteractionImpl, InteractionImpl, ModulationImpl, MolecularInteractionImpl, NamedImpl, NucleicAcidImpl, NucleicAcidReferenceImpl, NucleicAcidRegionReferenceImpl, PathwayImpl, PhysicalEntityImpl, ProcessImpl, ProteinImpl, ProteinReferenceImpl, ProvenanceImpl, RnaImpl, RnaReferenceImpl, RnaRegionImpl, RnaRegionReferenceImpl, SequenceEntityReferenceImpl, SimplePhysicalEntityImpl, SmallMoleculeImpl, SmallMoleculeReferenceImpl, TemplateReactionImpl, TemplateReactionRegulationImpl, TransportImpl, TransportWithBiochemicalReactionImpl

public interface Named
extends XReferrable

Interface for all classes that can have names in BioPAX. All named BioPAX elements can have multiple names, and exactly one standardName and exactly one shortName. standardName and shortName are OWL subproperties of name in BioPAX, so these are automatically considered as a name if defined. Paxtools refle Warning: There is a potential OWL-JAVA semantic mismatch when manipulating names. If a user decides to assign a different name to standardName or shortName, what happens to the old name is not well defined - they can be "demoted" to a regular name or removed from the names list altogether. Paxtools currently does the latter. If this is not the desired behaviour, the old name should be added manually back to the names list.

Field Summary

Fields inherited from interface org.biopax.paxtools.model.BioPAXElement

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Method Summary

Modifier and Type	Method and Description
void	addName(String name) This method adds the given value to the name set.
String	getDisplayName() An abbreviated name for this entity, preferably a name that is short enough to be used in a visualization application to label a graphical element that represents this entity.
Set<String>	getName() Names for this entity, including standardName and shortName if defined.
String	getStandardName() The preferred full name for this entity, if exists assigned by a standard nomenclature organization such as HUGO Gene Nomenclature Committee.
void	removeName(String name) This method removes the given value from the name set.
void	setDisplayName(String displayName) An abbreviated name for this entity, preferably a name that is short enough to be used in a visualization application to label a graphical element that represents this entity.
void	setName(Set<String> names) This method is reserved for batch operations and should not be used for normal use.
void	setStandardName(String standardName) The preferred full name for this entity, if exists assigned by a standard nomenclature organization such as HUGO Gene Nomenclature Committee.

Methods inherited from interface org.biopax.paxtools.model.level3.XReferrable

addXref, getXref, removeXref

Methods inherited from interface org.biopax.paxtools.model.level3.Level3Element

addComment, getComment, removeComment

Methods inherited from interface org.biopax.paxtools.model.BioPAXElement

equivalenceCode, getAnnotations, getModelInterface, getUri, isEquivalent

Method Detail

getName

Set<String> getName()

Names for this entity, including standardName and shortName if defined. The contents of this set can be modified directly but semantic consistency is not guaranteed. Using addName(java.lang.String) and removeName(java.lang.String) is recommended.

Returns:

Names for this entity, including standardName and shortName if defined.

setName

void setName(Set<String> names)

This method is reserved for batch operations and should not be used for normal use. Use add/remove name methods to manipulate the names instead.

Parameters:

names - new names to set (or replace all existing ones)

addName

void addName(String name)

This method adds the given value to the name set.

Parameters:

name - a new name to be added

removeName

void removeName(String name)

This method removes the given value from the name set.

Parameters:

name - a new name to be removed

getDisplayName

String getDisplayName()

An abbreviated name for this entity, preferably a name that is short enough to be used in a visualization application to label a graphical element that represents this entity. If no short name is available, an xref may be used for this purpose by the visualization application.

Returns:

An abbreviated name for this entity

setDisplayName

void setDisplayName(String displayName)

An abbreviated name for this entity, preferably a name that is short enough to be used in a visualization application to label a graphical element that represents this entity. If no short name is available, an xref may be used for this purpose by the visualization application.

Parameters:

displayName - new display name (preferably a short one)

getStandardName

String getStandardName()

The preferred full name for this entity, if exists assigned by a standard nomenclature organization such as HUGO Gene Nomenclature Committee.

Returns:

standard name for this entity

setStandardName

void setStandardName(String standardName)

The preferred full name for this entity, if exists assigned by a standard nomenclature organization such as HUGO Gene Nomenclature Committee.

Parameters:

standardName - standard name for this entity