Description: Add Class file that is contained in pal source code copy
 used by https://github.com/MesquiteProject/MesquiteCore
 Original location of this file is
   https://github.com/MesquiteProject/MesquiteCore/blob/master/LibrarySource/pal/substmodel/TransitionProbability.java
Author: Andreas Tille <tille@debian.org>
Last-Update: Mon, 23 May 2016 22:30:16 +0200

--- /dev/null
+++ b/src/pal/substmodel/TransitionProbability.java
@@ -0,0 +1,48 @@
+// TransistionProbability.java
+//
+// (c) 1999-2001 PAL Development Core Team
+//
+// This package may be distributed under the
+// terms of the Lesser GNU General Public License (LGPL)
+
+package pal.substmodel;
+
+import pal.math.*;
+
+
+/**
+ * For objects that represent a source of transition probabilities
+ *
+ * TransitionProbability.java,v 1.3 2000/08/08 22:58:29 alexi Exp $
+ *
+ * @author Matthew Goode
+ */
+public interface TransitionProbability extends Cloneable, java.io.Serializable {
+
+	/**
+	 * compute transition probabilities for a expected distance
+	 * using the prespecified rate matrix
+	 *
+	 * @param arc expected distance
+	 */
+	void setDistance(double arc);
+	/**
+	 * compute transition probabilities for a expected time span
+	 * using the prespecified rate matrix
+	 *
+	 * @param start start time
+	 * @param end end time
+	 */
+	void setTime(double start, double end);
+
+	/**
+		* Returns the transition probability for changing from
+		* startState into endState
+		* @param startState - the starting state
+		* @param endState - the resulting state
+		*/
+	double getTransitionProbability(int startState, int endState);
+
+	int getDimension();
+}
+