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

Introduction

Here is the source code for org.biopax.validator.rules.NextStepShareParticipantsRule.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.*;

import org.biopax.paxtools.model.level3.BiochemicalPathwayStep;
import org.biopax.paxtools.model.level3.Conversion;
import org.biopax.paxtools.model.level3.Entity;
import org.biopax.paxtools.model.level3.Gene;
import org.biopax.paxtools.model.level3.Interaction;
import org.biopax.paxtools.model.level3.Pathway;
import org.biopax.paxtools.model.level3.PathwayStep;
import org.biopax.paxtools.model.level3.PhysicalEntity;
import org.biopax.paxtools.model.level3.Process;
import org.biopax.validator.api.AbstractRule;
import org.biopax.validator.api.beans.Validation;
import org.springframework.stereotype.Component;

/**
 * Checks:
 * PathwayStep (in Pathway.pathwayOrder), if listed in the 
 * nextStep property of another PathwayStep, must have 
 * not empty intersection of participants of their 
 * stepProcess-es (Process is an interaction or pathway) 
 *
 * @author rodche
 *
 */
@Component
public class NextStepShareParticipantsRule extends AbstractRule<PathwayStep> {
    public boolean canCheck(Object thing) {
        return thing instanceof PathwayStep && !((PathwayStep) thing).getNextStepOf().isEmpty();
    }

    public void check(final Validation validation, PathwayStep step) {
        if (step.getNextStepOf().isEmpty())
            return;

        // get all the participants
        Collection<Entity> thisStepParticipants = getParticipants(step);

        // now find participants intersection with each previous step:
        for (PathwayStep prevStep : step.getNextStepOf()) {
            Collection<Entity> participants = getParticipants(prevStep);
            // first set becomes the intersection of the two:
            participants.retainAll(thisStepParticipants);
            if (participants.isEmpty()) {
                error(validation, step, "empty.participants.intersection", false, prevStep);
            }
        }
    }

    Collection<Entity> getParticipants(PathwayStep step) {
        // this is a protection from an infinite loop 
        //(which normally should never occur; another rule will check that.)
        Collection<Process> processes = new HashSet<Process>();
        Set<Entity> ret = new HashSet<Entity>();
        if (step instanceof BiochemicalPathwayStep) {
            Conversion c = ((BiochemicalPathwayStep) step).getStepConversion();
            ret.addAll(getParticipants(c, processes));
        }
        for (Process p : step.getStepProcess()) {
            ret.addAll(getParticipants(p, processes));
        }
        return ret;
    }

    Collection<Entity> getParticipants(Process process, Collection<Process> visited) {
        Collection<Entity> ret = new HashSet<Entity>();

        // escape infinite loop
        if (visited.contains(process)) {
            //"Step Processes Form a Loop!"
            return ret; // empty
        }
        visited.add(process);

        if (process instanceof Interaction) {
            for (Entity pat : ((Interaction) process).getParticipant()) {
                if (pat instanceof PhysicalEntity || pat instanceof Gene)
                    ret.add(pat);
            }
        } else { // a pathway
            for (Process p : ((Pathway) process).getPathwayComponent()) {
                ret.addAll(getParticipants(p, visited));
            }
        }

        return ret;
    }

    private void fix(PathwayStep t, Object... values) {
        // is very difficult ;)
    }

}