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

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

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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.Set;

import org.biopax.paxtools.model.level3.Complex;
import org.biopax.paxtools.model.level3.PhysicalEntity;
import org.biopax.paxtools.model.level3.Stoichiometry;
import org.biopax.validator.api.AbstractRule;
import org.biopax.validator.api.beans.Validation;
import org.springframework.stereotype.Component;

/**
 * Usually complexes have more than 1 component, unless stoichiometry of &gt;1
 * has been set on the single component, as would be done for a homodimer.
 * 
 * @author rodch
 *
 */
@Component
public class ComplexTwoOrMoreParticipantsRule extends AbstractRule<Complex> {

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

    public void check(final Validation validation, Complex thing) {
        Set<PhysicalEntity> components = thing.getComponent();

        if (components.isEmpty()) {
            error(validation, thing, "complex.incomplete", false, "no components");
        } else if (components.size() == 1) {
            // one component? - then stoi.coeff. must be > 1 (dimer, trimer,..)
            PhysicalEntity pe = components.iterator().next();
            Set<Stoichiometry> stoi = thing.getComponentStoichiometry();
            String msg = "has one component";
            if (stoi.isEmpty()) {
                error(validation, thing, "complex.incomplete", false, msg + ", but no stoichiometry defined.");
            } else {
                if (stoi.size() > 1)
                    msg += ", but multiple stoichiometries...";
                boolean ok = false;
                for (Stoichiometry s : stoi) {
                    if (pe.equals(s.getPhysicalEntity()) && s.getStoichiometricCoefficient() > 1) {
                        ok = true;
                        break;
                    }

                    if (!pe.equals(s.getPhysicalEntity()) && s.getPhysicalEntity() != null) {
                        error(validation, thing, "complex.stoichiometry.notcomponent", false, s,
                                s.getPhysicalEntity(), pe);
                    }
                }
                if (!ok) {
                    error(validation, thing, "complex.incomplete", false, msg + "; which stoichiometry < 2.");
                }
            }
        }

    }

}