org.biopax.paxtools.model
Interface BioPAXElement

All Superinterfaces:

java.lang.Cloneable, java.io.Serializable

All Known Subinterfaces:

BindingFeature, BiochemicalPathwayStep, biochemicalReaction, BiochemicalReaction, bioSource, BioSource, catalysis, Catalysis, CellularLocationVocabulary, CellVocabulary, 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, 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, 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, ChemicalStructureImpl, ComplexAssemblyImpl, ComplexImpl, ControlImpl, ControlledVocabularyImpl, ConversionImpl, CovalentBindingFeatureImpl, DegradationImpl, DeltaGImpl, DnaImpl, DnaReferenceImpl, DnaRegionImpl, DnaRegionReferenceImpl, EntityFeatureImpl, EntityImpl, EntityReferenceImpl, EntityReferenceTypeVocabularyImpl, EvidenceCodeVocabularyImpl, EvidenceImpl, ExperimentalFormImpl, ExperimentalFormVocabularyImpl, FragmentFeatureImpl, GeneImpl, GeneticInteractionImpl, 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 java.io.Serializable, java.lang.Cloneable

This class represents a general BioPAXElement, regardless of Level.

Nested Class Summary

static interface

BioPAXElement.Key This annotation identifies properties that are

Field Summary

static java.lang.Double	UNKNOWN_DOUBLE Constant for representing unknown doubles.
static java.lang.Float	UNKNOWN_FLOAT Constant for representing unknown floats.
static java.lang.Integer	UNKNOWN_INT Constant for representing unknown integers.

Method Summary

int	equivalenceCode() If two elements are equivalent, then their equivalence code should be the same.
java.util.Map<java.lang.String,java.lang.Object>	getAnnotations() A general-purpose map to optionallly store additional application-specific information about the BioPAX element, such as statistics, inferred fields, etc.
java.lang.Class<? extends BioPAXElement>	getModelInterface() This method returns the actual model interface that a class implements.
java.lang.String	getRDFId() This method returns the RDF Id of the element.
boolean	isEquivalent(BioPAXElement element) This method compares the given element for equivalency.

Field Detail

UNKNOWN_DOUBLE

static final java.lang.Double UNKNOWN_DOUBLE

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

UNKNOWN_FLOAT

static final java.lang.Float UNKNOWN_FLOAT

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

UNKNOWN_INT

static final java.lang.Integer UNKNOWN_INT

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

Method Detail

getModelInterface

java.lang.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

java.lang.String getRDFId()

This method returns the RDF Id of the element. All data providers are responsible for generating unique ids.

Returns:

the unique rdf Id 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

java.util.Map<java.lang.String,java.lang.Object> getAnnotations()

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

Returns: