/*
 * Intervals.java
 *
 * Copyright (C) 2002-2006 Alexei Drummond and Andrew Rambaut
 *
 * 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.evolution.coalescent;

import dr.evolution.util.Units;

import java.util.Arrays;

/**
 * A concrete class for a set of coalescent intevals.
 *
 * @version $Id: Intervals.java,v 1.19 2005/09/21 18:47:58 gerton Exp $
 *
 * @author Andrew Rambaut
 * @author Alexei Drummond
 */
public class Intervals implements IntervalList {

	public Intervals(int maxEventCount) {
		events = new Event[maxEventCount];
		for (int i = 0; i < maxEventCount; i++) {
			events[i] = new Event();
		}
		eventCount = 0;
		sampleCount = 0;

		intervals = new double[maxEventCount - 1];
		intervalTypes = new IntervalType[maxEventCount - 1];
		lineageCounts = new int[maxEventCount - 1];

		intervalsKnown = false;
	}

	public void copyIntervals(Intervals source) {
		intervalsKnown = source.intervalsKnown;
		eventCount = source.eventCount;
		sampleCount = source.sampleCount;

		//don't copy the actual events..
		/*
		for (int i = 0; i < events.length; i++) {
			events[i].time = source.events[i].time;
			events[i].type = source.events[i].type;
		}*/

		if (intervalsKnown) {
			System.arraycopy(source.intervals, 0, intervals, 0, intervals.length);
			System.arraycopy(source.intervalTypes, 0, intervalTypes, 0, intervals.length);
			System.arraycopy(source.lineageCounts, 0, lineageCounts, 0, intervals.length);
		}
	}

	public void resetEvents() {
		intervalsKnown = false;
		eventCount = 0;
		sampleCount = 0;
	}

	public void addSampleEvent(double time) {
		events[eventCount].time = time;
		events[eventCount].type = IntervalType.SAMPLE;
		eventCount++;
		sampleCount++;
		intervalsKnown = false;
	}

	public void addCoalescentEvent(double time) {
		events[eventCount].time = time;
		events[eventCount].type = IntervalType.COALESCENT;
		eventCount++;
		intervalsKnown = false;
	}

    public void addMigrationEvent(double time, int destination) {
        events[eventCount].time = time;
        events[eventCount].type = IntervalType.MIGRATION;
        events[eventCount].info = destination;
        eventCount++;
        intervalsKnown = false;
    }

	public void addNothingEvent(double time) {
		events[eventCount].time = time;
		events[eventCount].type = IntervalType.NOTHING;
		eventCount++;
		intervalsKnown = false;
	}

	public int getSampleCount() {
		return sampleCount;
	}

	public int getIntervalCount() {
		if (!intervalsKnown) calculateIntervals();
		return intervalCount;
	}

	public double getInterval(int i) {
		if (!intervalsKnown) calculateIntervals();
		return intervals[i];
	}

	public int getLineageCount(int i) {
		if (!intervalsKnown) calculateIntervals();
		return lineageCounts[i];
	}

	public int getCoalescentEvents(int i) {
		if (!intervalsKnown) calculateIntervals();
		if (i < intervalCount-1) {
			return lineageCounts[i]-lineageCounts[i+1];
		} else {
			return lineageCounts[i]-1;
		}
	}

	public IntervalType getIntervalType(int i)
	{
		if (!intervalsKnown) calculateIntervals();
		return intervalTypes[i];
	}

	public double getTotalDuration() {

		if (!intervalsKnown) calculateIntervals();
		return events[eventCount - 1].time;
	}

	public boolean isBinaryCoalescent() { return true; }
	public boolean isCoalescentOnly() { return true; }

	private void calculateIntervals() {

		if (eventCount < 2) {
			throw new IllegalArgumentException("Too few events to construct intervals");
		}

		Arrays.sort(events);

		if (events[0].type != IntervalType.SAMPLE) {
			throw new IllegalArgumentException("First event is not a sample event");
		}

		intervalCount = eventCount - 1;

		double lastTime = events[0].time;

		int lineages = 1;
		for (int i = 1; i < eventCount; i++) {

			intervals[i - 1] = events[i].time - lastTime;
			intervalTypes[i - 1] = events[i].type;
			lineageCounts[i - 1] = lineages;
			if (events[i].type == IntervalType.SAMPLE) {
				lineages++;
			} else if (events[i].type == IntervalType.COALESCENT) {
				lineages--;
			}
			lastTime = events[i].time;
		}
		intervalsKnown = true;
	}

	private Units.Type  units = Units.Type.GENERATIONS;

	public final Units.Type getUnits() {
		return units;
	}

	public final void setUnits(Type units) {
		this.units = units;
	}

	private class Event implements Comparable {

        public int compareTo(Object o) {
			double t = ((Event)o).time;
			if (t < time) {
				return 1;
			} else if (t > time) {
				return -1;
			} else {
				// events are at exact same time so sort by type
				return type.compareTo(((Event)o).type);
			}
		}

        /**
         * The type of event
         */
        IntervalType type;

        /**
         * The time of the event
         */
		double time;

        /**
         * Some extra information for the event (e.g., destination of a migration)
         */
        int info;

    }

	private Event[] events;
	private int eventCount;
	private int sampleCount;

	private boolean intervalsKnown = false;
	private double[] intervals;
	private int[] lineageCounts;
	private IntervalType[] intervalTypes;
	//private int[] destinations;
	private int intervalCount = 0;
}
@@ -4304,16 +4304,31 @@
 t(events
+, 0, eventCount
 );%0A%0A%09%09if

Fix for the Transmission History model.