1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
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@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();
+}
+
|
