org.biopax.paxtools.model.level3

Interface Entity

All Superinterfaces:

BioPAXElement, Cloneable, Level3Element, Named, Observable, Serializable, XReferrable

All Known Subinterfaces:

BiochemicalReaction, Catalysis, Complex, ComplexAssembly, Control, Controller, Conversion, Degradation, Dna, DnaRegion, Gene, GeneticInteraction, Interaction, Modulation, MolecularInteraction, NucleicAcid, Pathway, PhysicalEntity, Process, Protein, Rna, RnaRegion, SequenceEntity, SimplePhysicalEntity, SmallMolecule, TemplateReaction, TemplateReactionRegulation, Transport, TransportWithBiochemicalReaction

All Known Implementing Classes:

BiochemicalReactionImpl, CatalysisImpl, ComplexAssemblyImpl, ComplexImpl, ControlImpl, ConversionImpl, DegradationImpl, DnaImpl, DnaRegionImpl, EntityImpl, GeneImpl, GeneticInteractionImpl, InteractionImpl, ModulationImpl, MolecularInteractionImpl, NucleicAcidImpl, PathwayImpl, PhysicalEntityImpl, ProcessImpl, ProteinImpl, RnaImpl, RnaRegionImpl, SimplePhysicalEntityImpl, SmallMoleculeImpl, TemplateReactionImpl, TemplateReactionRegulationImpl, TransportImpl, TransportWithBiochemicalReactionImpl

public interface Entity
extends Level3Element, Observable, Named

This class represents a discrete biological unit used when describing pathways. This is the root class for all biological concepts in the ontology, which include pathways, interactions and physical entities. As the most abstract class in the ontology, instances of the entity class should never be created. Instead, more specific classes should be used. Synonyms: thing, object, bioentity.

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	addAvailability(String availability) This method adds the given text to the avaialability set.
void	addDataSource(Provenance dataSource) This method adds the given value to the DATA_SOURCE set.
Set<String>	getAvailability() The contents of this set can be modified but semantic consistency is not guaranteed.
Set<Provenance>	getDataSource() This method returns a set of free text descriptions of the source of this data, e.g.
Set<Interaction>	getParticipantOf() This method returns the interaction that this entity/pep takes part in.
void	removeAvailability(String availability) This method removes the given text from the avaialability set.
void	removeDataSource(Provenance dataSource) This method removes the given value from the DATA_SOURCE set.

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

addEvidence, getEvidence, removeEvidence

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

addName, getDisplayName, getName, getStandardName, removeName, setDisplayName, setName, setStandardName

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

getAvailability

Set<String> getAvailability()

The contents of this set can be modified but semantic consistency is not guaranteed. Using addAvailability(String) and removeAvailability(String) is recommended.

Returns:

a set of strings describing the availability of this data (e.g. a copyright statement).

addAvailability

void addAvailability(String availability)

This method adds the given text to the avaialability set.

Parameters:

availability - a string describing the availability of this data (e.g. a copyright statement).

removeAvailability

void removeAvailability(String availability)

This method removes the given text from the avaialability set.

Parameters:

availability - a string describing the availability of this data (e.g. a copyright statement).

getDataSource

Set<Provenance> getDataSource()

This method returns a set of free text descriptions of the source of this data, e.g. a database or person name. This property should be used to describe the source of the data. This is meant to be used by databases that export their data to the BioPAX format or by systems that are integrating data from multiple sources. The granularity of use (specifying the data source in many or few instances) is up to the user. It is intended that this property report the last data source, not all data sources that the data has passed through from creation. The contents of this set can be modified but semantic consistency is not guaranteed. Using addDataSource(Provenance) and removeDataSource(Provenance) is recommended.

Returns:

a set of free text descriptions of the source of this data, e.g. a database or person name.

addDataSource

void addDataSource(Provenance dataSource)

This method adds the given value to the DATA_SOURCE set.

Parameters:

dataSource - a free text description of the source of this data, e.g. a database or person name.

removeDataSource

void removeDataSource(Provenance dataSource)

This method removes the given value from the DATA_SOURCE set.

Parameters:

dataSource - a free text description of the source of this data, e.g. a database or person name.

getParticipantOf

Set<Interaction> getParticipantOf()

This method returns the interaction that this entity/pep takes part in. Contents of this set should not be modified. Reverse of Interaction.getParticipant()

Returns:

a set of interactions that