MockConsistencyModel.java

/*
 * This file is part of ADDIS (Aggregate Data Drug Information System).
 * ADDIS is distributed from http://drugis.org/.
 * Copyright © 2009 Gert van Valkenhoef, Tommi Tervonen.
 * Copyright © 2010 Gert van Valkenhoef, Tommi Tervonen, Tijs Zwinkels,
 * Maarten Jacobs, Hanno Koeslag, Florin Schimbinschi, Ahmad Kamal, Daniel
 * Reid.
 * Copyright © 2011 Gert van Valkenhoef, Ahmad Kamal, Daniel Reid, Florin
 * Schimbinschi.
 * Copyright © 2012 Gert van Valkenhoef, Daniel Reid, Joël Kuiper, Wouter
 * Reckman.
 * Copyright © 2013 Gert van Valkenhoef, Joël Kuiper.
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU 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 Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */

package org.drugis.addis.mocks;

import java.util.ArrayList;
import java.util.Collections;
import java.util.List;

import org.drugis.common.threading.SimpleSuspendableTask;
import org.drugis.common.threading.Task;
import org.drugis.common.threading.activity.ActivityModel;
import org.drugis.common.threading.activity.ActivityTask;
import org.drugis.common.threading.activity.DirectTransition;
import org.drugis.mtc.ConsistencyModel;
import org.drugis.mtc.MCMCResults;
import org.drugis.mtc.Parameter;
import org.drugis.mtc.model.Treatment;
import org.drugis.mtc.parameterization.BasicParameter;
import org.drugis.mtc.yadas.YadasConsistencyModel;
import org.drugis.mtc.yadas.YadasModelFactory;
import org.drugis.mtc.yadas.YadasResults;

public class MockConsistencyModel extends YadasConsistencyModel implements ConsistencyModel {

	@Deprecated
	public static ConsistencyModel buildMockSimulationConsistencyModel(List<Treatment> ts) {
		return new MockConsistencyModel(ts);
	}

	boolean d_ready = false;
	private ActivityTask d_task;
	private YadasResults d_results;

	private static final int BURNIN_ITER = 1000;
	private static final int SIMULATION_ITER = 10000;

	private MockConsistencyModel(List<Treatment> ts) {
		super(null, new YadasModelFactory().getDefaults());
		Task start = new SimpleSuspendableTask(new Runnable() { public void run() {} });
		Task end = new SimpleSuspendableTask(new Runnable() { public void run() { finished(); } });
		d_task = new ActivityTask(new ActivityModel(start, end,
				Collections.singleton(new DirectTransition(start, end))));
		d_results = new YadasResults();
		d_results.setNumberOfIterations(SIMULATION_ITER);
		d_results.setNumberOfChains(1);
		d_results.setDirectParameters(createParameters(ts));
	}

	private List<Parameter> createParameters(List<Treatment> ts) {
		List<Parameter> parameters = new ArrayList<Parameter>();
		for (Treatment t1: ts) {
			for (Treatment t2: ts) {
				if (!t1.equals(t2)) {
					parameters.add(new BasicParameter(t1, t2));
				}
			}
		}
		return parameters;
	}

	public BasicParameter getRelativeEffect(Treatment base, Treatment subj) {
		return new BasicParameter(base, subj);
	}

	public boolean isReady() {
		return d_task.isFinished();
	}

	public int getBurnInIterations() {
		return BURNIN_ITER;
	}

	public int getSimulationIterations() {
		return SIMULATION_ITER;
	}

	public void setBurnInIterations(int it) {
	}

	public void setSimulationIterations(int it) {
	}

	public ActivityTask getActivityTask() {
		return d_task;
	}

	public Parameter getRandomEffectsStandardDeviation() {
		return null;
	}

	public MCMCResults getResults() {
		return d_results;
	}

	protected void finished() {
		d_results.simulationFinished();
	}
}