Uses of Interface
org.biopax.paxtools.model.level3.XReferrable

Packages that use XReferrable

org.biopax.paxtools.controller
org.biopax.paxtools.impl.level3
org.biopax.paxtools.model.level3

Uses of XReferrable in org.biopax.paxtools.controller

Method parameters in org.biopax.paxtools.controller with type arguments of type XReferrable

java.util.Set<java.lang.String>

ModelUtils.getByXref(java.util.Set<? extends Xref> xrefs, java.lang.Class<? extends XReferrable> clazz) This is a special (not always applicable) utility method.

Uses of XReferrable in org.biopax.paxtools.impl.level3

Classes in org.biopax.paxtools.impl.level3 that implement XReferrable

class	BiochemicalReactionImpl
class	BioSourceImpl
class	CatalysisImpl
class	CellularLocationVocabularyImpl
class	CellVocabularyImpl
class	ComplexAssemblyImpl
class	ComplexImpl
class	ControlImpl
class	ControlledVocabularyImpl
class	ConversionImpl
class	DegradationImpl
class	DnaImpl
class	DnaReferenceImpl
class	DnaRegionImpl
class	DnaRegionReferenceImpl
class	EntityImpl
class	EntityReferenceImpl
class	EntityReferenceTypeVocabularyImpl
class	EvidenceCodeVocabularyImpl
class	EvidenceImpl
class	ExperimentalFormVocabularyImpl
class	GeneImpl
class	GeneticInteractionImpl
class	InteractionImpl
class	InteractionVocabularyImpl
class	ModulationImpl
class	MolecularInteractionImpl
class	NamedImpl
class	NucleicAcidImpl
class	NucleicAcidReferenceImpl
class	NucleicAcidRegionReferenceImpl
class	PathwayImpl
class	PhenotypeVocabularyImpl
class	PhysicalEntityImpl
class	ProcessImpl
class	ProteinImpl
class	ProteinReferenceImpl
class	ProvenanceImpl
class	RelationshipTypeVocabularyImpl
class	RnaImpl
class	RnaReferenceImpl
class	RnaRegionImpl
class	RnaRegionReferenceImpl
class	ScoreImpl
class	SequenceEntityReferenceImpl
class	SequenceModificationVocabularyImpl
class	SequenceRegionVocabularyImpl
class	SimplePhysicalEntityImpl
class	SmallMoleculeImpl
class	SmallMoleculeReferenceImpl
class	TemplateReactionImpl
class	TemplateReactionRegulationImpl
class	TissueVocabularyImpl
class	TransportImpl
class	TransportWithBiochemicalReactionImpl
class	XReferrableImpl This class helps with managing the bidirectional xref links.

Methods in org.biopax.paxtools.impl.level3 that return types with arguments of type XReferrable

java.util.Set<XReferrable>

XrefImpl.getXrefOf()

Methods in org.biopax.paxtools.impl.level3 with parameters of type XReferrable

protected boolean

XReferrableImpl.hasCommonUnificationXref(XReferrable xReferrable) Answers whether two BioPAX objects that implement

Method parameters in org.biopax.paxtools.impl.level3 with type arguments of type XReferrable

protected void

XrefImpl.setXrefOf(java.util.Set<XReferrable> xrefOf)

Uses of XReferrable in org.biopax.paxtools.model.level3

Subinterfaces of XReferrable in org.biopax.paxtools.model.level3

interface	BiochemicalReaction Definition: A conversion interaction in which one or more entities (substrates) undergo covalent changes to become one or more other entities (products).
interface	BioSource Definition: The biological source of an entity (e.g.
interface	Catalysis Definition: A control interaction in which a physical entity (a catalyst) increases the rate of a conversion interaction by lowering its activation energy.
interface	CellularLocationVocabulary Definition: A reference to the Gene Ontology Cellular Component (GO CC) ontology.
interface	CellVocabulary Definition: A reference to the Cell Type Ontology (CL).
interface	Complex Definition: A physical entity whose structure is comprised of other physical entities bound to each other non-covalently, at least one of which is a macromolecule (e.g.
interface	ComplexAssembly Definition: A conversion interaction in which a set of physical entities, at least one being a macromolecule (e.g.
interface	Control Definition: An interaction in which one entity regulates, modifies, or otherwise influences a continuant entity, i.e.
interface	ControlledVocabulary Definition: This class represents a term from an external controlled vocabulary (CV).
interface	Controller This is a role interface for pathway elements that can control processes, namely Pathway and PhysicalEntity.
interface	Conversion Definition: An interaction in which molecules of one or more PhysicalEntity pools are physically transformed and become a member of one or more other PhysicalEntity pools.
interface	Degradation Definition: A conversion in which a pool of macromolecules are degraded into their elementary units.
interface	Dna Definition: A physical entity consisting of a sequence of deoxyribonucleotide monophosphates; a deoxyribonucleic acid.
interface	DnaReference A DNA reference is a grouping of several DNA entities that are common in sequence and genomic position.
interface	DnaRegion Definition: A region on a DNA molecule.
interface	DnaRegionReference Definition: A DNARegionReference is a grouping of several DNARegion entities that are common in sequence and genomic position.
interface	Entity This class represents a discrete biological unit used when describing pathways.
interface	EntityReference Definition: An entity reference is a grouping of several physical entities across different contexts and molecular states, that share common physical properties and often named and treated as a single entity with multiple states by biologists.
interface	EntityReferenceTypeVocabulary Definiiton: A reference to a term from an entity reference group ontology.
interface	Evidence Definition: The support for a particular assertion, such as the existence of an interaction or pathway.
interface	EvidenceCodeVocabulary Definition: A reference to the PSI Molecular Interaction ontology experimental method types, including "interaction detection method", "participant identification method", "feature detection method".
interface	ExperimentalFormVocabulary Definition: A term that describes the form of the physical entity in the context of the experiment.
interface	Gene Definition: A continuant that encodes information that can be inherited through replication.
interface	GeneticInteraction Definition : Genetic interactions between genes occur when two genetic perturbations (e.g.
interface	Interaction Definition: A biological relationship between two or more entities.
interface	InteractionVocabulary A reference to the PSI Molecular Interaction ontology (MI) interaction type.
interface	Modulation Definition: An interaction in which one entity regulates, modifies, or otherwise influences another.
interface	MolecularInteraction Definition: An interaction in which at least one participant is a physical entity, e.g.
interface	Named Interface for all classes that can have names in BioPAX.
interface	NucleicAcid Tagger interface for DNA and RNA
interface	NucleicAcidReference Role interface for NucleicAcidReferences, namely DNA and RNA.
interface	NucleicAcidRegionReference
interface	Pathway
interface	PhenotypeVocabulary
interface	PhysicalEntity
interface	Process Tagging interface for entities that can participate in a pathway and can be targeted by a control : Pathway and Interaction
interface	Protein
interface	ProteinReference Description: A protein reference is a grouping of several protein entities that are encoded by the same genetic sequence.
interface	Provenance Definition: The direct source of a pathway data or score.
interface	RelationshipTypeVocabulary Vocabulary for defining relationship Xref types.
interface	Rna
interface	RnaReference
interface	RnaRegion Definition: A region on a RNA molecule.
interface	RnaRegionReference A RNA region reference
interface	Score Definition: A score associated with a publication reference describing how the score was determined, the name of the method and a comment briefly describing the method.
interface	SequenceEntityReference Tagger interface for protein, dna and rna entities
interface	SequenceModificationVocabulary Definition: A term that describes the covalent modifications to an amino acid or nucleic acid chain.
interface	SequenceRegionVocabulary Definition: A reference to a controlled vocabulary of sequence regions, such as InterPro or Sequence Ontology (SO) Homepage at http://www.sequenceontology.org.
interface	SimplePhysicalEntity Tagger interface for non-complex physical entities
interface	SmallMolecule
interface	SmallMoleculeReference
interface	TemplateReaction
interface	TemplateReactionRegulation
interface	TissueVocabulary Definition: A reference to the BRENDA
interface	Transport
interface	TransportWithBiochemicalReaction

Methods in org.biopax.paxtools.model.level3 that return types with arguments of type XReferrable

java.util.Set<XReferrable>

Xref.getXrefOf()