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

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Here is the source code for org.biopax.validator.rules.ClonedUtilityClassRule.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.HashMap;
import java.util.Map;
import java.util.Set;

import org.biopax.paxtools.controller.ModelUtils;
import org.biopax.paxtools.model.BioPAXLevel;
import org.biopax.paxtools.model.Model;
import org.biopax.paxtools.model.level3.UtilityClass;
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 equivalent (duplicated) UtilityClass instances.
 * It collects/reports all duplicates. 
 * 
 * @author rodche
 */
@Component
public class ClonedUtilityClassRule extends AbstractRule<Model> {

    public void check(final Validation validation, Model model) {
        Cluster<UtilityClass> algorithm = new Cluster<UtilityClass>() {
            @Override
            public boolean match(UtilityClass a, UtilityClass b) {
                return !a.equals(b) && a.isEquivalent(b);
            }
        };

        Set<Set<UtilityClass>> clusters = algorithm.cluster(model.getObjects(UtilityClass.class),
                Integer.MAX_VALUE);

        Map<UtilityClass, UtilityClass> replacementMap = new HashMap<UtilityClass, UtilityClass>();

        // report the error once for each cluster
        for (Set<UtilityClass> clones : clusters) {
            if (clones.size() < 2)
                continue; //skip unique individuals

            UtilityClass first = clones.iterator().next();
            clones.remove(first); // pop the first element from the clones collection

            if (validation.isFix()) {
                // set "fixed" in advance... fix below
                error(validation, first, "cloned.utility.class", true, clones,
                        first.getModelInterface().getSimpleName());

                for (UtilityClass clone : clones)
                    replacementMap.put(clone, first);

            } else {
                // report the problem (not fixed)
                error(validation, first, "cloned.utility.class", false, clones,
                        first.getModelInterface().getSimpleName());
            }
        }

        if (validation.isFix())
            ModelUtils.replace(model, replacementMap);

    }

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