org.biopax.validator.rules.EntityReferenceSamePhysicalEntitiesRule.java Source code

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Here is the source code for org.biopax.validator.rules.EntityReferenceSamePhysicalEntitiesRule.java

Source

package org.biopax.validator.rules;

/*
 * #%L
 * BioPAX Validator
 * %%
 * Copyright (C) 2008 - 2013 University of Toronto (baderlab.org) and Memorial Sloan-Kettering Cancer Center (cbio.mskcc.org)
 * %%
 * This program 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 3 of the 
 * License, or (at your option) any later version.
 * 
 * This program 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 General Lesser Public License for more details.
 * 
 * You should have received a copy of the GNU General Lesser Public 
 * License along with this program.  If not, see
 * <http://www.gnu.org/licenses/lgpl-3.0.html>.
 * #L%
 */

import org.biopax.paxtools.model.level3.EntityReference;
import org.biopax.paxtools.model.level3.SimplePhysicalEntity;
import org.biopax.validator.api.AbstractRule;
import org.biopax.validator.api.beans.Validation;
import org.biopax.validator.utils.Cluster;
import org.springframework.stereotype.Component;

import java.util.Set;

/**
 * Checks PhysicalEntities that reference the same EntityReference 
 * to be in different states (i.e. features on the PhysicalEntity can't be 
 * exactly the same on another PhysicalEntity, e.g. two proteins that 
 * reference the same ProteinReference must have different states.
 * 
 * @author rodche
 */
@Component
public class EntityReferenceSamePhysicalEntitiesRule extends AbstractRule<EntityReference> {

    Cluster<SimplePhysicalEntity> algorithm = new Cluster<SimplePhysicalEntity>() {
        @Override
        public boolean match(SimplePhysicalEntity e1, SimplePhysicalEntity e2) {
            return e1.hasEquivalentFeatures(e2) && e1.hasEquivalentCellularLocation(e2);
            //TODO add 'standardName' for comparison?
        }
    };

    public void check(final Validation validation, EntityReference eref) {

        Set<Set<SimplePhysicalEntity>> clasters = algorithm.cluster(eref.getEntityReferenceOf(), Integer.MAX_VALUE);

        // report the error case once per cluster
        for (Set<SimplePhysicalEntity> col : clasters) {
            if (col.size() > 1) {
                SimplePhysicalEntity u = col.iterator().next();
                col.remove(u);
                error(validation, eref, "same.state.entity", false, u, col);
            }
        }

    }

    public boolean canCheck(Object thing) {
        return thing instanceof EntityReference;
    }

}