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

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Here is the source code for org.biopax.validator.rules.SameNameDiffKindPhysEntitiesRule.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 java.util.HashSet;
import java.util.Set;

import org.apache.commons.collections15.CollectionUtils;
import org.biopax.paxtools.model.BioPAXLevel;
import org.biopax.paxtools.model.Model;
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;

/**
 * Checks that defferent kind physical entities 
 * (using different EntityReference) do not share
 * names.
 * 
 * @author rodche
 */
@Component
public class SameNameDiffKindPhysEntitiesRule extends AbstractRule<Model> {

    public void check(final Validation validation, Model model) {
        Set<SimplePhysicalEntity> peers = new HashSet<SimplePhysicalEntity>(
                model.getObjects(SimplePhysicalEntity.class));

        Cluster<SimplePhysicalEntity> groupping = new Cluster<SimplePhysicalEntity>() {
            @Override
            public boolean match(SimplePhysicalEntity a, SimplePhysicalEntity b) {
                return !a.equals(b) && a.getEntityReference() != null && !a.getName().isEmpty()
                        && !b.getName().isEmpty() && !a.getEntityReference().isEquivalent(b.getEntityReference())
                        && CollectionUtils.containsAny(a.getName(), b.getName());
            }
        };

        Set<Set<SimplePhysicalEntity>> sharedNamesClusters = groupping.cluster(peers, Integer.MAX_VALUE);

        // report the error once for each cluster
        for (Set<SimplePhysicalEntity> sharedNames : sharedNamesClusters) {
            if (sharedNames.size() > 1) {
                SimplePhysicalEntity a = sharedNames.iterator().next();
                error(validation, a, "diff.kind.same.name", false, sharedNames);
            }
        }
    }

    public boolean canCheck(Object thing) {
        return thing instanceof Model && ((Model) thing).getLevel() == BioPAXLevel.L3;
    }

}