Likelihood.java

/*
 * Likelihood.java
 *
 * Copyright (c) 2002-2015 Alexei Drummond, Andrew Rambaut and Marc Suchard
 *
 * This file is part of BEAST.
 * See the NOTICE file distributed with this work for additional
 * information regarding copyright ownership and licensing.
 *
 * BEAST 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 2
 * of the License, or (at your option) any later version.
 *
 *  BEAST 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 Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with BEAST; if not, write to the
 * Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
 * Boston, MA  02110-1301  USA
 */

package dr.inference.model;

import dr.inference.loggers.Loggable;
import dr.util.Identifiable;

import java.util.Arrays;
import java.util.HashSet;
import java.util.Set;

/**
 * classes that calculate likelihoods should implement this interface.
 *
 * @author Alexei Drummond
 * @author Andrew Rambaut
 * @version $Id: Likelihood.java,v 1.16 2005/05/24 20:26:00 rambaut Exp $
 */

public interface Likelihood extends Loggable, Identifiable {

    /**
     * Get the model.
     *
     * @return the model.
     */
    Model getModel();

    /**
     * Get the log likelihood.
     *
     * @return the log likelihood.
     */
    double getLogLikelihood();

    /**
     * Forces a complete recalculation of the likelihood next time getLikelihood is called
     */
    void makeDirty();

    /**
     * @return A detailed name of likelihood for debugging.
     */
    String prettyName();

    /**
     * Get the set of sub-component likelihoods that this likelihood uses
     *
     * @return
     */
    Set<Likelihood> getLikelihoodSet();

    /**
     * @return is the likelihood used in the MCMC?
     */
    boolean isUsed();

    void setUsed();

    /**
     * @return true if this likelihood should be evaluated early (if for example it may return a zero likelihood
     * and could terminate the evaluation early or is a required conditioning for another likelihood.
     */
    boolean evaluateEarly();

    /**
     * A simple abstract base class for likelihood functions
     */

    public abstract class Abstract implements Likelihood, ModelListener {

        public Abstract(Model model) {

            this.model = model;
            if (model != null) model.addModelListener(this);
        }

        public void modelChangedEvent(Model model, Object object, int index) {
            makeDirty();
        }

        // by default restore is the same as changed
        public void modelRestored(Model model) {
            makeDirty();
        }

        // **************************************************************
        // Likelihood IMPLEMENTATION
        // **************************************************************

        /**
         * Get the model.
         *
         * @return the model.
         */
        public Model getModel() {
            return model;
        }

        public final double getLogLikelihood() {
            if (!getLikelihoodKnown()) {
                logLikelihood = calculateLogLikelihood();
                likelihoodKnown = true;
            }
            return logLikelihood;
        }

        public void makeDirty() {
            likelihoodKnown = false;
        }

        /**
         * Called to decide if the likelihood must be calculated. Can be overridden
         * (for example, to always return false).
         *
         * @return true if no need to recompute likelihood
         */
        protected boolean getLikelihoodKnown() {
            return likelihoodKnown;
        }

        protected abstract double calculateLogLikelihood();

        public Set<Likelihood> getLikelihoodSet() {
            return new HashSet<Likelihood>(Arrays.asList(this));
        }

        public String toString() {
            // don't call any "recalculating" stuff like getLogLikelihood() in toString -
            // this interferes with the debugger.

            //return getClass().getName() + "(" + getLogLikelihood() + ")";
            return getClass().getName() + "(" + (getLikelihoodKnown() ? logLikelihood : "??") + ")";
        }

        static public String getPrettyName(Likelihood l) {
            final Model m = l.getModel();
            String s = l.getClass().getName();
            String[] parts = s.split("\\.");
            s = parts[parts.length - 1];
            if (m != null) {
                final String modelName = m.getModelName();
                final String i = m.getId();
                s = s + "(" + modelName;
                if (i != null && !i.equals(modelName)) {
                    s = s + '[' + i + ']';
                }
                s = s + ")";
            }
            return s;
        }

        public String prettyName() {
            return getPrettyName(this);
        }

        public boolean isUsed() {
            return used;
        }

        public void setUsed() {
            this.used = true;
        }

        public boolean evaluateEarly() {
            return false;
        }

        // **************************************************************
        // Loggable IMPLEMENTATION
        // **************************************************************

        /**
         * @return the log columns.
         */
        public dr.inference.loggers.LogColumn[] getColumns() {
            return new dr.inference.loggers.LogColumn[]{
                    new LikelihoodColumn(getId())
            };
        }

        private class LikelihoodColumn extends dr.inference.loggers.NumberColumn {
            public LikelihoodColumn(String label) {
                super(label);
            }

            public double getDoubleValue() {
                return getLogLikelihood();
            }
        }

        // **************************************************************
        // Identifiable IMPLEMENTATION
        // **************************************************************

        private String id = null;

        public void setId(String id) {
            this.id = id;
        }

        public String getId() {
            return id;
        }

        private final Model model;
        private double logLikelihood;
        private boolean likelihoodKnown = false;

        private boolean used = false;
    }


    // set to store all created likelihoods
    final static Set<Likelihood> FULL_LIKELIHOOD_SET = new HashSet<Likelihood>();
    final static Set<Likelihood> CONNECTED_LIKELIHOOD_SET = new HashSet<Likelihood>();

}