Class MIOlsOntology

  • All Implemented Interfaces:
    MIOntologyAccess, psidev.psi.tools.ontology_manager.interfaces.OntologyAccessTemplate<MIOntologyTermI>

    public class MIOlsOntology
    extends AbstractMIOntologyAccess
    jami extension for OlsOntology
    Since:
    01/11/11
    Version:
    $Id$
    Author:
    Marine Dumousseau (marine@ebi.ac.uk)
    • Field Detail

      • log

        public static final org.apache.commons.logging.Log log
        Constant log
    • Constructor Detail

      • MIOlsOntology

        public MIOlsOntology()
                      throws psidev.psi.tools.ontology_manager.impl.local.OntologyLoaderException

        Constructor for MIOlsOntology.

        Throws:
        psidev.psi.tools.ontology_manager.impl.local.OntologyLoaderException - if any.
      • MIOlsOntology

        public MIOlsOntology​(OntologyTermFetcher termBuilder)
                      throws psidev.psi.tools.ontology_manager.impl.local.OntologyLoaderException

        Constructor for MIOlsOntology.

        Parameters:
        termBuilder - a OntologyTermFetcher object.
        Throws:
        psidev.psi.tools.ontology_manager.impl.local.OntologyLoaderException - if any.
      • MIOlsOntology

        public MIOlsOntology​(String dbName,
                             String dbIdentifier,
                             Pattern dbRegexp,
                             String parent)
                      throws psidev.psi.tools.ontology_manager.impl.local.OntologyLoaderException

        Constructor for MIOlsOntology.

        Parameters:
        dbName - a String object.
        dbIdentifier - a String object.
        dbRegexp - a Pattern object.
        parent - a String object.
        Throws:
        psidev.psi.tools.ontology_manager.impl.local.OntologyLoaderException - if any.
      • MIOlsOntology

        public MIOlsOntology​(OntologyTermFetcher termBuilder,
                             String dbName,
                             String dbIdentifier,
                             Pattern dbRegexp,
                             String parent)
                      throws psidev.psi.tools.ontology_manager.impl.local.OntologyLoaderException

        Constructor for MIOlsOntology.

        Parameters:
        termBuilder - a OntologyTermFetcher object.
        dbName - a String object.
        dbIdentifier - a String object.
        dbRegexp - a Pattern object.
        parent - a String object.
        Throws:
        psidev.psi.tools.ontology_manager.impl.local.OntologyLoaderException - if any.
    • Method Detail

      • loadOntology

        public void loadOntology​(String ontologyID,
                                 String name,
                                 String version,
                                 String format,
                                 URI uri)
                          throws psidev.psi.tools.ontology_manager.impl.local.OntologyLoaderException
        Specified by:
        loadOntology in interface psidev.psi.tools.ontology_manager.interfaces.OntologyAccessTemplate<MIOntologyTermI>
        Specified by:
        loadOntology in class AbstractMIOntologyAccess
        Throws:
        psidev.psi.tools.ontology_manager.impl.local.OntologyLoaderException
      • isOntologyUpToDate

        public boolean isOntologyUpToDate()
                                   throws psidev.psi.tools.ontology_manager.impl.local.OntologyLoaderException

        isOntologyUpToDate.

        Specified by:
        isOntologyUpToDate in interface psidev.psi.tools.ontology_manager.interfaces.OntologyAccessTemplate<MIOntologyTermI>
        Specified by:
        isOntologyUpToDate in class AbstractMIOntologyAccess
        Returns:
        a boolean.
        Throws:
        psidev.psi.tools.ontology_manager.impl.local.OntologyLoaderException - if any.