org.biopax.paxtools.model

Interface BioPAXElement

All Superinterfaces:

Cloneable, Serializable

All Known Subinterfaces:

BindingFeature, BiochemicalPathwayStep, biochemicalReaction, BiochemicalReaction, bioSource, BioSource, catalysis, Catalysis, CellularLocationVocabulary, CellVocabulary, ChemicalConstant, chemicalStructure, ChemicalStructure, complex, Complex, complexAssembly, ComplexAssembly, confidence, control, Control, ControlledVocabulary, Controller, conversion, Conversion, CovalentBindingFeature, dataSource, Degradation, DeltaG, deltaGprimeO, dna, Dna, DnaReference, DnaRegion, DnaRegionReference, entity, Entity, EntityFeature, EntityReference, EntityReferenceTypeVocabulary, evidence, Evidence, EvidenceCodeVocabulary, experimentalForm, ExperimentalForm, ExperimentalFormVocabulary, externalReferenceUtilityClass, FragmentFeature, Gene, GeneticInteraction, interaction, Interaction, InteractionParticipant, InteractionVocabulary, kPrime, KPrime, Level2Element, Level3Element, ModificationFeature, modulation, Modulation, MolecularInteraction, Named, NucleicAcid, NucleicAcidReference, NucleicAcidRegionReference, Observable, openControlledVocabulary, pathway, Pathway, pathwayComponent, pathwayStep, PathwayStep, PhenotypeVocabulary, physicalEntity, PhysicalEntity, physicalEntityParticipant, physicalInteraction, process, Process, protein, Protein, ProteinReference, Provenance, publicationXref, PublicationXref, RelationshipTypeVocabulary, relationshipXref, RelationshipXref, rna, Rna, RnaReference, RnaRegion, RnaRegionReference, Score, sequenceEntity, SequenceEntity, SequenceEntityReference, sequenceFeature, sequenceInterval, SequenceInterval, sequenceLocation, SequenceLocation, SequenceModificationVocabulary, sequenceParticipant, SequenceRegionVocabulary, sequenceSite, SequenceSite, SimplePhysicalEntity, smallMolecule, SmallMolecule, SmallMoleculeReference, Stoichiometry, TemplateReaction, TemplateReactionRegulation, TissueVocabulary, transport, Transport, transportWithBiochemicalReaction, TransportWithBiochemicalReaction, unificationXref, UnificationXref, utilityClass, UtilityClass, xref, Xref, XReferrable, XReferrable

All Known Implementing Classes:

BindingFeatureImpl, BiochemicalPathwayStepImpl, BiochemicalReactionImpl, BioPAXElementImpl, BioSourceImpl, CatalysisImpl, CellularLocationVocabularyImpl, CellVocabularyImpl, ChemicalConstantImpl, ChemicalStructureImpl, ComplexAssemblyImpl, ComplexImpl, ControlImpl, ControlledVocabularyImpl, ConversionImpl, CovalentBindingFeatureImpl, DegradationImpl, DeltaGImpl, DnaImpl, DnaReferenceImpl, DnaRegionImpl, DnaRegionReferenceImpl, EntityFeatureImpl, EntityImpl, EntityReferenceImpl, EntityReferenceTypeVocabularyImpl, EvidenceCodeVocabularyImpl, EvidenceImpl, ExperimentalFormImpl, ExperimentalFormVocabularyImpl, FragmentFeatureImpl, GeneImpl, GeneticInteractionImpl, Group, InteractionImpl, InteractionVocabularyImpl, KPrimeImpl, L3ElementImpl, ModificationFeatureImpl, ModulationImpl, MolecularInteractionImpl, NamedImpl, NucleicAcidImpl, NucleicAcidReferenceImpl, NucleicAcidRegionReferenceImpl, PathwayImpl, PathwayStepImpl, PhenotypeVocabularyImpl, PhysicalEntityImpl, ProcessImpl, ProteinImpl, ProteinReferenceImpl, ProvenanceImpl, PublicationXrefImpl, RelationshipTypeVocabularyImpl, RelationshipXrefImpl, RnaImpl, RnaReferenceImpl, RnaRegionImpl, RnaRegionReferenceImpl, ScoreImpl, SequenceEntityReferenceImpl, SequenceIntervalImpl, SequenceLocationImpl, SequenceModificationVocabularyImpl, SequenceRegionVocabularyImpl, SequenceSiteImpl, SimplePhysicalEntityImpl, SmallMoleculeImpl, SmallMoleculeReferenceImpl, StoichiometryImpl, TemplateReactionImpl, TemplateReactionRegulationImpl, TissueVocabularyImpl, TransportImpl, TransportWithBiochemicalReactionImpl, UnificationXrefImpl, XReferrableImpl, XrefImpl

public interface BioPAXElement
extends Serializable, Cloneable

This class represents a general BioPAXElement, regardless of Level.

Field Summary

Fields

Modifier and Type	Field and Description
static Double	UNKNOWN_DOUBLE Constant for representing unknown doubles.
static Float	UNKNOWN_FLOAT Constant for representing unknown floats.
static Integer	UNKNOWN_INT Constant for representing unknown integers.

Method Summary

Modifier and Type	Method and Description
int	equivalenceCode() If two elements are equivalent, then their equivalence code should be the same.
Map<String,Object>	getAnnotations() A general-purpose map to optionally store additional application-specific information about the BioPAX element, such as statistics, inferred fields, etc.
Class<? extends BioPAXElement>	getModelInterface() This method returns the actual model interface that a class implements.
String	getRDFId() This method returns the full URI of the element (despite it is called RDFId).
boolean	isEquivalent(BioPAXElement element) This method compares the given element for equivalency.

Field Detail

UNKNOWN_DOUBLE

static final Double UNKNOWN_DOUBLE

Constant for representing unknown doubles. This is required as by default java would assign 0.

UNKNOWN_FLOAT

static final Float UNKNOWN_FLOAT

Constant for representing unknown floats. This is required as by default java would assign 0.

UNKNOWN_INT

static final Integer UNKNOWN_INT

Constant for representing unknown integers. This is required as by default java would assign 0.

Method Detail

getModelInterface

Class<? extends BioPAXElement> getModelInterface()

This method returns the actual model interface that a class implements.

Returns:

an interface from org.biopax.paxtools.model package corresponding to a BioPAX class.

getRDFId

String getRDFId()

This method returns the full URI of the element (despite it is called RDFId). BioPAX data providers are responsible for generating globally unique and standard URIs for their BioPAX elements.

Returns:

the unique URI for this object.

isEquivalent

boolean isEquivalent(BioPAXElement element)

This method compares the given element for equivalency. This is different from equals(), as BioPAX elements resolve equality based on RDF ID. Equivalent returns true if elements are equal or if

• both elements implement the same model interface AND
• both elements have equivalent key properties

These key properties vary from class to class.

Parameters:

element - to be compared for equivalency

Returns:

true if the element equals to this, or has equivalent critical properties.

equivalenceCode

int equivalenceCode()

If two elements are equivalent, then their equivalence code should be the same.

Returns:

an integer that is same across all equivalent entities.

getAnnotations

Map<String,Object> getAnnotations()

A general-purpose map to optionally store additional application-specific information about the BioPAX element, such as statistics, inferred fields, etc.

Returns:

additional (not BioPAX standard) annotations