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

Packages that use UtilityClass

Package	Description
org.biopax.paxtools.impl.level3	This package contains the default implementation for BioPAX Level 3.
org.biopax.paxtools.model.level3	This package contains the interfaces that maps classes defined in the BioPAX Level 3 specification.

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

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

Modifier and Type	Class	Description
class	BindingFeatureImpl
class	BiochemicalPathwayStepImpl
class	BioSourceImpl
class	CellularLocationVocabularyImpl
class	CellVocabularyImpl
class	ChemicalConstantImpl
class	ChemicalStructureImpl
class	ControlledVocabularyImpl
class	CovalentBindingFeatureImpl
class	DeltaGImpl
class	DnaReferenceImpl
class	DnaRegionReferenceImpl
class	EntityFeatureImpl
class	EntityReferenceImpl
class	EntityReferenceTypeVocabularyImpl
class	EvidenceCodeVocabularyImpl
class	EvidenceImpl
class	ExperimentalFormImpl
class	ExperimentalFormVocabularyImpl
class	FragmentFeatureImpl
class	InteractionVocabularyImpl
class	KPrimeImpl
class	ModificationFeatureImpl
class	NucleicAcidReferenceImpl
class	NucleicAcidRegionReferenceImpl
class	PathwayStepImpl
class	PhenotypeVocabularyImpl
class	ProteinReferenceImpl
class	ProvenanceImpl
class	PublicationXrefImpl
class	RelationshipTypeVocabularyImpl
class	RelationshipXrefImpl
class	RnaReferenceImpl
class	RnaRegionReferenceImpl
class	ScoreImpl
class	SequenceEntityReferenceImpl
class	SequenceIntervalImpl
class	SequenceLocationImpl
class	SequenceModificationVocabularyImpl
class	SequenceRegionVocabularyImpl
class	SequenceSiteImpl
class	SmallMoleculeReferenceImpl
class	StoichiometryImpl
class	TissueVocabularyImpl
class	UnificationXrefImpl
class	XrefImpl

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

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

Modifier and Type	Interface	Description
interface	BindingFeature
interface	BiochemicalPathwayStep	Definition: Imposes ordering on a step in a biochemical pathway.
interface	BioSource	Definition: The biological source of an entity (e.g.
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	ChemicalConstant
interface	ChemicalStructure	Definition: The chemical structure of a small molecule.
interface	ControlledVocabulary	Definition: This class represents a term from an external controlled vocabulary (CV).
interface	CovalentBindingFeature	Definition: An entity feature that represent the covalently bound state of a physical entity.
interface	DeltaG	Standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants (sums of species), delta-G'o.
interface	DnaReference	A DNA reference is a grouping of several DNA entities that are common in sequence and genomic position.
interface	DnaRegionReference	Definition: A DNARegionReference is a grouping of several DNARegion entities that are common in sequence and genomic position.
interface	EntityFeature	Description: A characteristic of a physical entity that can change while the entity still retains its biological identity.
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	ExperimentalForm	Definition: The form of a physical entity in a particular experiment, as it may be modified for purposes of experimental design.
interface	ExperimentalFormVocabulary	Definition: A term that describes the form of the physical entity in the context of the experiment.
interface	FragmentFeature	Definition: An entity feature that represents the resulting physical entity subsequent to a cleavage or degradation event.
interface	InteractionVocabulary	A reference to the PSI Molecular Interaction ontology (MI) interaction type.
interface	KPrime	The apparent equilibrium constant, K', and associated values.
interface	ModificationFeature	Definition: A covalently modified feature on a sequence, relevant to an interaction, such as a post-translational modification.
interface	NucleicAcidReference	Role interface for NucleicAcidReferences, namely DNA and RNA.
interface	NucleicAcidRegionReference
interface	PathwayStep	This represents a set of pathway events.
interface	PhenotypeVocabulary
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	PublicationXref
interface	RelationshipTypeVocabulary	Vocabulary for defining relationship Xref types.
interface	RelationshipXref	Definition: An xref that defines a reference to an entity in an external resource that does not have the same biological identity as the referring entity.
interface	RnaReference
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	SequenceInterval
interface	SequenceLocation	Definition: A location on a nucleotide or amino acid sequence.
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	SequenceSite
interface	SmallMoleculeReference
interface	Stoichiometry	Stoichiometric coefficient of a physical entity in the context of a conversion or complex.
interface	TissueVocabulary	Definition: A reference to the BRENDA
interface	UnificationXref	Definition: A unification xref defines a reference to an entity in an external resource that has the same biological identity as the referring entity.
interface	Xref