Package org.phyloref.jphyloref.helpers

Class PhylorefHelper

java.lang.Object
org.phyloref.jphyloref.helpers.PhylorefHelper
public class PhylorefHelper extends Object
A Phyloreference helper class. It consists of common terms and helper functions to make writing about Phyloreferences easier.

Eventually, this will be reorganized into a Phyloreferencing Java library, but we don't need that level of sophistication just yet.

Author:
Gaurav Vaidya

  • Nested Class Summary

    Nested Classes
    Modifier and Type
    Class
    Description
    static class 
    PhylorefHelper.PhylorefStatus
    A wrapper for a phyloref status at a particular point in time.

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static org.semanticweb.owlapi.model.IRI
    IRI_CDAO_NODE
    IRI for OWL class Phylogeny
    static org.semanticweb.owlapi.model.IRI
    IRI_OBI_HAS_SPECIFIED_INPUT
    IRI for the OBI has_specified_input property.
    static org.semanticweb.owlapi.model.IRI
    IRI_OBI_IS_SPECIFIED_OUTPUT_OF
    IRI for the OBI is_specified_output_of property.
    static org.semanticweb.owlapi.model.IRI
    IRI_PHYLOREFERENCE
    IRI for OWL class Phyloreference
    static org.semanticweb.owlapi.model.IRI
    IRI_PSO_DRAFT
    IRI for the publication status of "Draft"
    static org.semanticweb.owlapi.model.IRI
    IRI_PSO_HOLDS_STATUS_IN_TIME
    IRI for the OWL object property that associates a publication with its publication status at a particular time.
    static org.semanticweb.owlapi.model.IRI
    IRI_PSO_PUBLISHED
    IRI for the publication status of "Published"
    static org.semanticweb.owlapi.model.IRI
    IRI_PSO_SUBMITTED
    IRI for the publication status of "Submitted"
    static org.semanticweb.owlapi.model.IRI
    IRI_PSO_WITH_STATUS
    IRI for the OWL object property that indicates the publication status of a publication status at a particular time.
    static org.semanticweb.owlapi.model.IRI
    IRI_TIMEINT_HAS_INTERVAL_END_DATE
    IRI for the OWL data property that indicates when a publication status time ends
    static org.semanticweb.owlapi.model.IRI
    IRI_TIMEINT_HAS_INTERVAL_START_DATE
    IRI for the OWL data property that indicates when a publication status time begins
    static org.semanticweb.owlapi.model.IRI
    IRI_TVC_AT_TIME
    IRI for the OWL object property that associates a publication status at a particular time with a particular time.

  • Constructor Summary

    Constructors
    Constructor
    Description
    PhylorefHelper()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    static Set<org.semanticweb.owlapi.model.OWLNamedIndividual>
    getNodesInClass​(org.semanticweb.owlapi.model.OWLClass owlClass, org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.reasoner.OWLReasoner reasoner)
    Get the set of named individuals in a particular OWL class.
    static Set<org.semanticweb.owlapi.model.OWLClass>
    getPhyloreferences​(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.reasoner.OWLReasoner reasoner)
    Get a list of phyloreferences in this ontology.
    static Set<org.semanticweb.owlapi.model.OWLClass>
    getPhyloreferencesWithoutReasoning​(org.semanticweb.owlapi.model.OWLOntology ontology)
    Get a list of phyloreferences in this ontology without reasoning.
    static List<PhylorefHelper.PhylorefStatus>
    getStatusesForPhyloref​(org.semanticweb.owlapi.model.OWLClass phyloref, org.semanticweb.owlapi.model.OWLOntology ontology)
    Return a list of PhylorefStatuses associated with a particular phyloreference in the provided ontology.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Field Details

    • IRI_CDAO_NODE

      public static final org.semanticweb.owlapi.model.IRI IRI_CDAO_NODE
      IRI for OWL class Phylogeny

    • IRI_PHYLOREFERENCE

      public static final org.semanticweb.owlapi.model.IRI IRI_PHYLOREFERENCE
      IRI for OWL class Phyloreference

    • IRI_OBI_IS_SPECIFIED_OUTPUT_OF

      public static final org.semanticweb.owlapi.model.IRI IRI_OBI_IS_SPECIFIED_OUTPUT_OF
      IRI for the OBI is_specified_output_of property.

    • IRI_OBI_HAS_SPECIFIED_INPUT

      public static final org.semanticweb.owlapi.model.IRI IRI_OBI_HAS_SPECIFIED_INPUT
      IRI for the OBI has_specified_input property.

    • IRI_PSO_HOLDS_STATUS_IN_TIME

      public static final org.semanticweb.owlapi.model.IRI IRI_PSO_HOLDS_STATUS_IN_TIME
      IRI for the OWL object property that associates a publication with its publication status at a particular time.

    • IRI_PSO_WITH_STATUS

      public static final org.semanticweb.owlapi.model.IRI IRI_PSO_WITH_STATUS
      IRI for the OWL object property that indicates the publication status of a publication status at a particular time.

    • IRI_TVC_AT_TIME

      public static final org.semanticweb.owlapi.model.IRI IRI_TVC_AT_TIME
      IRI for the OWL object property that associates a publication status at a particular time with a particular time.

    • IRI_TIMEINT_HAS_INTERVAL_START_DATE

      public static final org.semanticweb.owlapi.model.IRI IRI_TIMEINT_HAS_INTERVAL_START_DATE
      IRI for the OWL data property that indicates when a publication status time begins

    • IRI_TIMEINT_HAS_INTERVAL_END_DATE

      public static final org.semanticweb.owlapi.model.IRI IRI_TIMEINT_HAS_INTERVAL_END_DATE
      IRI for the OWL data property that indicates when a publication status time ends

    • IRI_PSO_DRAFT

      public static final org.semanticweb.owlapi.model.IRI IRI_PSO_DRAFT
      IRI for the publication status of "Draft"

    • IRI_PSO_SUBMITTED

      public static final org.semanticweb.owlapi.model.IRI IRI_PSO_SUBMITTED
      IRI for the publication status of "Submitted"

    • IRI_PSO_PUBLISHED

      public static final org.semanticweb.owlapi.model.IRI IRI_PSO_PUBLISHED
      IRI for the publication status of "Published"

  • Constructor Details

    • PhylorefHelper

      public PhylorefHelper()

  • Method Details

    • getPhyloreferencesWithoutReasoning

      public static Set<org.semanticweb.owlapi.model.OWLClass> getPhyloreferencesWithoutReasoning​(org.semanticweb.owlapi.model.OWLOntology ontology)
      Get a list of phyloreferences in this ontology without reasoning. This method does not use the reasoner, and so will only find classes asserted to be subclasses of phyloref:Phyloreference.

    • getPhyloreferences

      public static Set<org.semanticweb.owlapi.model.OWLClass> getPhyloreferences​(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.reasoner.OWLReasoner reasoner)
      Get a list of phyloreferences in this ontology. This method uses the reasoner, and so will find all classes reasoned to be subclasses of class phyloref:Phyloreference.
      Parameters:
      ontology - The OWL Ontology within with we should look for phylorefs
      reasoner - The reasoner to use. May be null.

    • getNodesInClass

      public static Set<org.semanticweb.owlapi.model.OWLNamedIndividual> getNodesInClass​(org.semanticweb.owlapi.model.OWLClass owlClass, org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.reasoner.OWLReasoner reasoner)
      Get the set of named individuals in a particular OWL class. If `reasoner` is set to null, this will return all individuals asserted as belonging to the provided class, allowing it to be used on precomputed OWL ontologies.
      Parameters:
      owlClass - The OWL class to retrieve instances from.
      ontology - The ontology containing the OWL class and its instances.
      reasoner - The reasoner to use. May be set to null if no reasoner if available.
      Returns:
      A set of OWLNamedIndividuals asserted directly or indirectly as belonging to the provided class.

    • getStatusesForPhyloref

      public static List<PhylorefHelper.PhylorefStatus> getStatusesForPhyloref​(org.semanticweb.owlapi.model.OWLClass phyloref, org.semanticweb.owlapi.model.OWLOntology ontology)
      Return a list of PhylorefStatuses associated with a particular phyloreference in the provided ontology.
      Parameters:
      phyloref - The phyloreference whose statuses are being queried.
      ontology - The ontology within which this phyloreference is defined.
      Returns:
      A list of phyloref statuses.