Taxon.java

/*
 * Taxon.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.evolution.util;

import dr.util.Attributable;
import dr.util.Identifiable;

import java.util.ArrayList;
import java.util.Iterator;

/**
 * Class for data about a taxon.
 *
 * @version $Id: Taxon.java,v 1.24 2006/09/05 13:29:34 rambaut Exp $
 *
 * @author Andrew Rambaut
 * @author Alexei Drummond
 */
public class Taxon implements Attributable, Identifiable, Comparable<Taxon> {

    public Taxon(String id) {
        setId(id);
    }

    /**
     * Sets a date for this taxon.
     */
    public void setDate(Date date) {
        setAttribute("date", date);
        addDateToTimeScale(date);
    }

    /**
     * @return a date for this taxon.
     */
    public Date getDate() {
        Object date = getAttribute("date");
        if (date != null && date instanceof Date) {
            return (Date)date;
        }
        return null;
    }

    /**
     * @return a height for this taxon.
     * This gets the height from the globally defined timescale of dates for all Taxa.
     */
    public double getHeight() {
        Object date = getAttribute("date");
        if (date != null && date instanceof Date) {
            return getHeightFromDate((Date)date);
        }
        return 0.0;
    }

    /**
     * Sets a location for this taxon.
     */
    public void setLocation(Location location) {
        setAttribute("location", location);
    }

    /**
     * @return a location for this taxon.
     */
    public Location getLocation() {
        Object location = getAttribute("location");
        if (location != null && location instanceof Location) {
            return (Location)location;
        }
        return null;
    }
    // **************************************************************
    // Attributable IMPLEMENTATION
    // **************************************************************

    private Attributable.AttributeHelper attributes = null;

    /**
     * Sets an named attribute for this object.
     * @param name the name of the attribute.
     * @param value the new value of the attribute.
     */
    public void setAttribute(String name, Object value) {
        if (attributes == null)
            attributes = new Attributable.AttributeHelper();
        attributes.setAttribute(name, value);
    }

    /**
     * @return an object representing the named attributed for this object.
     * @param name the name of the attribute of interest.
     */
    public Object getAttribute(String name) {
        if (attributes == null)
            return null;
        else
            return attributes.getAttribute(name);
    }

    /**
     * if attributes == null, return false
     * @param name attribute name
     * @return boolean whether contains attribute by given its name
     */
    public boolean containsAttribute(String name) {
        return attributes != null && attributes.containsAttribute(name);
    }

    /**
     * @return an iterator of the attributes that this object has.
     */
    public Iterator<String> getAttributeNames() {
        if (attributes == null)
            return new ArrayList<String>().iterator();
        else
            return attributes.getAttributeNames();
    }

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

    protected String id = null;

    /**
     * @return the id.
     */
    public String getId() {
        return id;
    }

    /**
     * Sets the id.
     */
    public void setId(String id) {
        this.id = id;
    }

    public String toString() { return getId(); }

    @Override
    public boolean equals(final Object o) {
        return getId().equals(((Taxon)o).getId());
    }

    @Override
    public int hashCode() {
    	return getId().hashCode();
    }

    // **************************************************************
    // Comparable IMPLEMENTATION
    // **************************************************************

    public int compareTo(Taxon o) {
        return getId().compareTo(o.getId());
    }


    private static void addDateToTimeScale(Date date) {
        if (date != null && (mostRecentDate == null || date.after(mostRecentDate))) {
            mostRecentDate = date;
            timeScale = null;
        }
    }

    public static double getHeightFromDate(Date date) {

        if (timeScale == null) {
            Date mostRecent = mostRecentDate;
            if (mostRecent == null) {
                mostRecent = dr.evolution.util.Date.createRelativeAge(0.0, date.getUnits());
            }

            timeScale = new TimeScale(mostRecent.getUnits(), true, mostRecent.getAbsoluteTimeValue());
        }

        return timeScale.convertTime(date.getTimeValue(), date);
    }

    public static Date getMostRecentDate() {
        return mostRecentDate;
    }

    private static dr.evolution.util.Date mostRecentDate = null;
    private static TimeScale timeScale = null;
}