org.coode.matrix.model.helper.IndividualsHelper Maven / Gradle / Ivy

Go to download
Show more of this group Show more artifacts with this name
Show all versions of org.coode.matrix Show documentation
A Swing Component that combines a JTree and a JTable.
The newest version!
package org.coode.matrix.model.helper;

import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Set;

import org.semanticweb.owlapi.model.AddAxiom;
import org.semanticweb.owlapi.model.OWLAxiom;
import org.semanticweb.owlapi.model.OWLClass;
import org.semanticweb.owlapi.model.OWLClassAssertionAxiom;
import org.semanticweb.owlapi.model.OWLClassExpression;
import org.semanticweb.owlapi.model.OWLDataProperty;
import org.semanticweb.owlapi.model.OWLDataPropertyAssertionAxiom;
import org.semanticweb.owlapi.model.OWLIndividual;
import org.semanticweb.owlapi.model.OWLLiteral;
import org.semanticweb.owlapi.model.OWLNamedIndividual;
import org.semanticweb.owlapi.model.OWLObjectProperty;
import org.semanticweb.owlapi.model.OWLObjectPropertyAssertionAxiom;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyChange;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.model.RemoveAxiom;
import org.semanticweb.owlapi.search.EntitySearcher;

/*
* Copyright (C) 2007, University of Manchester
*
* Modifications to the initial code base are copyright of their
* respective authors, or their employers as appropriate.  Authorship
* of the modifications may be determined from the ChangeLog placed at
* the end of this file.
*
* This library is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public
* License as published by the Free Software Foundation; either
* version 2.1 of the License, or (at your option) any later version.

* This library is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
* Lesser General Public License for more details.

* You should have received a copy of the GNU Lesser General Public
* License along with this library; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
*/
/**
 * Author: Nick Drummond

 * http://www.cs.man.ac.uk/~drummond/

 * 

 * 
 * The University Of Manchester

 * Bio Health Informatics Group

 * Date: Jul 3, 2007

 * 

 */
public class IndividualsHelper {

    private OWLOntologyManager mngr;
    private Set onts;

    public IndividualsHelper(OWLOntologyManager mngr,
            Set ontologies) {
        this.mngr = mngr;
        this.onts = ontologies;
    }

    public void setOntologies(Set onts) {
        this.onts = onts;
    }

    public Collection getRelationships(OWLIndividual ind,
            OWLObjectProperty prop) {
        return EntitySearcher.getObjectPropertyValues(ind, onts).get(prop);
    }

    public Collection getRelationships(OWLIndividual ind,
            OWLDataProperty prop) {
        return EntitySearcher.getDataPropertyValues(ind, onts).get(prop);
    }

    public List setRelationships(OWLNamedIndividual subject,
            OWLObjectProperty p, Set objects,
            OWLOntology activeOnt) {
        List changes = new ArrayList();
        // generate the axioms that should be in the ontology after this has
        // completed
        Set axioms = new HashSet();
        for (OWLIndividual object : objects) {
            OWLObjectPropertyAssertionAxiom relationAxiom = mngr
                    .getOWLDataFactory()
                    .getOWLObjectPropertyAssertionAxiom(p, subject, object);
            axioms.add(relationAxiom);
        }
        // go through the ontologies removing appropriate relations not in this
        // set
        for (OWLOntology ont : onts) {
            for (OWLAxiom ax : ont.getReferencingAxioms(subject)) {
                if (ax instanceof OWLObjectPropertyAssertionAxiom
                        && ((OWLObjectPropertyAssertionAxiom) ax).getSubject()
                                .equals(subject)) {
                    if (axioms.contains(ax)) {
                        axioms.remove(ax); // we're satisfied this axiom is
                                           // already in the ontologies, no need
                                           // to create or check against it
                    } else {
                        if (((OWLObjectPropertyAssertionAxiom) ax).getProperty()
                                .equals(p)) {
                            // we already know the object does not match
                            // otherwise it would be in the "axioms" set
                            changes.add(new RemoveAxiom(ont, ax));
                        }
                    }
                }
            }
        }
        // add all remaining new axioms to the active ontology
        for (OWLAxiom ax : axioms) {
            changes.add(new AddAxiom(activeOnt, ax));
        }
        return changes;
    }

    public List setRelationships(OWLNamedIndividual subject,
            OWLDataProperty p, Set objects, OWLOntology activeOnt) {
        List changes = new ArrayList();
        // generate the axioms that should be in the ontology after this has
        // completed
        Set axioms = new HashSet();
        for (OWLLiteral object : objects) {
            OWLDataPropertyAssertionAxiom relationAxiom = mngr
                    .getOWLDataFactory()
                    .getOWLDataPropertyAssertionAxiom(p, subject, object);
            axioms.add(relationAxiom);
        }
        // go through the ontologies removing appropriate relations not in this
        // set
        for (OWLOntology ont : onts) {
            for (OWLAxiom ax : ont.getReferencingAxioms(subject)) {
                if (ax instanceof OWLDataPropertyAssertionAxiom
                        && ((OWLDataPropertyAssertionAxiom) ax).getSubject()
                                .equals(subject)) {
                    if (axioms.contains(ax)) {
                        axioms.remove(ax); // we're satisfied this axiom is
                                           // already in the ontologies, no need
                                           // to create or check against it
                    } else {
                        if (((OWLDataPropertyAssertionAxiom) ax).getProperty()
                                .equals(p)) {
                            // we already know the object does not match
                            // otherwise it would be in the "axioms" set
                            changes.add(new RemoveAxiom(ont, ax));
                        }
                    }
                }
            }
        }
        // add all remaining new axioms to the active ontology
        for (OWLAxiom ax : axioms) {
            changes.add(new AddAxiom(activeOnt, ax));
        }
        return changes;
    }

    public List addRelationships(OWLNamedIndividual subject,
            OWLObjectProperty p, Set objects,
            OWLOntology activeOnt) {
        List changes = new ArrayList();
        for (OWLIndividual object : objects) {
            OWLObjectPropertyAssertionAxiom ax = mngr.getOWLDataFactory()
                    .getOWLObjectPropertyAssertionAxiom(p, subject, object);
            if (!activeOnt.containsAxiom(ax)) {
                changes.add(new AddAxiom(activeOnt, ax));
            }
        }
        return changes;
    }

    public List addRelationships(OWLNamedIndividual subject,
            OWLDataProperty p, Set objects, OWLOntology activeOnt) {
        List changes = new ArrayList();
        for (OWLLiteral object : objects) {
            OWLDataPropertyAssertionAxiom ax = mngr.getOWLDataFactory()
                    .getOWLDataPropertyAssertionAxiom(p, subject, object);
            if (!activeOnt.containsAxiom(ax)) {
                changes.add(new AddAxiom(activeOnt, ax));
            }
        }
        return changes;
    }

    public Set getMembers(OWLClass cls) {
        Set instances = new HashSet();
        final OWLClass thing = mngr.getOWLDataFactory().getOWLThing();
        if (cls.equals(thing)) {
            for (OWLOntology ont : onts) {
                for (OWLIndividual ind : ont.getIndividualsInSignature()) {
                    if (!ind.isAnonymous()) {
                        Collection classes = EntitySearcher
                                .getTypes(ind, ont);
                        if (classes.contains(thing) || classes.isEmpty()) {
                            instances.add(ind.asOWLNamedIndividual());
                        }
                    }
                }
            }
        } else {
            for (OWLOntology ont : onts) {
                for (OWLClassAssertionAxiom ax : ont
                        .getClassAssertionAxioms(cls)) {
                    if (!ax.getIndividual().isAnonymous()) {
                        instances
                                .add(ax.getIndividual().asOWLNamedIndividual());
                    }
                }
            }
        }
        return instances;
    }

    public List addMembers(OWLClass cls,
            Set members, OWLOntology activeOnt) {
        List changes = new ArrayList();
        for (OWLIndividual member : members) {
            OWLClassAssertionAxiom axiom = mngr.getOWLDataFactory()
                    .getOWLClassAssertionAxiom(cls, member);
            if (!activeOnt.containsAxiom(axiom)) {
                changes.add(new AddAxiom(activeOnt, axiom));
            }
        }
        return changes;
    }

    public List setMembers(OWLClass cls,
            Set members, OWLOntology activeOnt) {
        List changes = new ArrayList();
        // generate the axioms that should be in the ontology after this has
        // completed
        Set axioms = new HashSet();
        for (OWLIndividual member : members) {
            OWLClassAssertionAxiom axiom = mngr.getOWLDataFactory()
                    .getOWLClassAssertionAxiom(cls, member);
            axioms.add(axiom);
        }
        // go through the ontologies removing appropriate relations not in this
        // set
        for (OWLOntology ont : onts) {
            for (OWLAxiom ax : ont.getReferencingAxioms(cls)) {
                if (ax instanceof OWLClassAssertionAxiom
                        && ((OWLClassAssertionAxiom) ax).getClassExpression()
                                .equals(cls)) {
                    if (axioms.contains(ax)) {
                        axioms.remove(ax); // we're satisfied this axiom is
                                           // already in the ontologies, no need
                                           // to create or check against it
                    } else {
                        // we already know the member does not match otherwise
                        // it would be in the "axioms" set
                        changes.add(new RemoveAxiom(ont, ax));
                    }
                }
            }
        }
        // add all remaining new axioms to the active ontology
        for (OWLAxiom ax : axioms) {
            changes.add(new AddAxiom(activeOnt, ax));
        }
        return changes;
    }

    public Collection getTypes(OWLIndividual individual) {
        return EntitySearcher.getTypes(individual, onts);
    }

    public Set getNamedTypes(OWLIndividual individual) {
        Set parents = Collections.emptySet();
        Collection types = getTypes(individual);
        if (types.size() > 0) {
            parents = new HashSet();
            for (OWLClassExpression type : types) {
                if (type instanceof OWLClass) {
                    parents.add((OWLClass) type);
                }
            }
        }
        return parents;
    }
}