Package 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, 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
    Description
    static final Double
    UNKNOWN_DOUBLE
    Constant for representing unknown doubles.
    static final Float
    UNKNOWN_FLOAT
    Constant for representing unknown floats.
    static final Integer
    UNKNOWN_INT
    Constant for representing unknown integers.

  • Method Summary

    Modifier and Type
    Method
    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
    getUri()
    This method returns the absolute URI of the element.
    boolean
    isEquivalent(BioPAXElement element)
    This method compares the given element for equivalency.

  • Field Details

    • 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 Details

    • 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.

    • getUri

      String getUri()
      This method returns the absolute URI of the element. BioPAX data providers are responsible for generating globally unique and standard URIs for their BioPAX elements.
      Returns:
      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 URI. 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