/* * StateChange.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.markovjumps; /** * A class to represent a state-change in a continuous-time Markov chain. * This class is equivalent to ColourChange in terms of parameters, but labels events * more generically as either forward or backwards (instead of just backwards) in time. * <p/> * TODO Remove dr.evolution.tree.ColourChange (wrong package) * * @author Alexei Drummond * @author Marc A. Suchard * <p/> * This work is supported by NSF grant 0856099 */ public class StateChange { // time of the change in colour private double time; // the state associated with this time private int state; private int previousState; public StateChange(StateChange change) { this(change.time, change.state); } public StateChange(double time, int state, int previousState) { this.time = time; this.state = state; this.previousState = previousState; } public StateChange(double time, int state) { this.time = time; this.state = state; this.previousState = -1; } public StateChange clone() { return new StateChange(time, state, previousState); } /** * @return the time of this change in colour */ public final double getTime() { return time; } /** * @return the state associated with the time */ public final int getState() { return state; } public final int getPreviousState() { return previousState; } public final void setPreviousState(int state) { this.previousState = state; } /** * @param state sets the state of this event */ public final void setState(int state) { this.state = state; } public final void setTime(double time) { this.time = time; } public String toString() { StringBuilder sb = new StringBuilder(); sb.append("{").append(getTime()).append(",").append(getState()).append("}"); return sb.toString(); } }