[med-svn] [libpal-java] 01/03: Add Class file that is contained in pal source code copy used by https://github.com/MesquiteProject/MesquiteCore

[Andreas Tille]

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tille pushed a commit to branch master
in repository libpal-java.

commit 4bfa00434a7c3b8a52ebb94d9a16c201c4b4d3f6
Author: Andreas Tille <tille at debian.org>
Date:   Mon May 23 22:34:23 2016 +0200

    Add Class file that is contained in pal source code copy used by https://github.com/MesquiteProject/MesquiteCore
---
 debian/changelog                           |  7 ++++
 debian/patches/TransitionProbability.patch | 58 ++++++++++++++++++++++++++++++
 debian/patches/series                      |  1 +
 3 files changed, 66 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 6bbc848..79cc94e 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+libpal-java (1.5.1+dfsg-2) UNRELEASED; urgency=medium
+
+  * Add Class file that is contained in pal source code copy
+    used by https://github.com/MesquiteProject/MesquiteCore
+
+ -- Andreas Tille <tille at debian.org>  Mon, 23 May 2016 22:30:16 +0200
+
 libpal-java (1.5.1+dfsg-1) unstable; urgency=low
 
   * debian/copyright:
diff --git a/debian/patches/TransitionProbability.patch b/debian/patches/TransitionProbability.patch
new file mode 100644
index 0000000..3140a8c
--- /dev/null
+++ b/debian/patches/TransitionProbability.patch
@@ -0,0 +1,58 @@
+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 at 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();
++}
++
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..2b26127
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+TransitionProbability.patch

-- 
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