From 8f8f511d85fa3ed614c54d0d59f256de30f7701e Mon Sep 17 00:00:00 2001
From: Denise <denise.kuehnert@gmail.com>
Date: Mon, 21 Mar 2016 15:28:44 +0100
Subject: [PATCH] update addon

---
 build.xml                                       |  4 ++--
 .../tree/coalescent/BirthDeathSkylineTest.java  | 17 ++++++++++++++++-
 version.xml                                     |  2 +-
 3 files changed, 19 insertions(+), 4 deletions(-)

diff --git a/build.xml b/build.xml
index a5d5f44..1c88ff3 100644
--- a/build.xml
+++ b/build.xml
@@ -17,7 +17,7 @@
 	<property name="libBeast2" location="${beast2path}/lib" />
 	<property name="srcBeast2" location="${beast2path}/src" />
 	<property name="beast2classpath" location="${beast2path}/build" />
-    <!--property name="beastlabsclasspath" location="../BEASTLabs/build" /-->
+    <property name="beastlabsclasspath" location="../BEASTLabs/build" />
     <property name="beastclassicclasspath" location="../beast-classic/build" />
 	<property name="Add_on_dir" value="${release_dir}/add-on" />
 
@@ -32,7 +32,7 @@
 		<fileset dir="${libBeast2}" includes="fest.jar"/>
 		<fileset dir="${libBeast2}" includes="jam.jar"/>
         <pathelement path="${beast2classpath}"/>
-        <!--pathelement path="${beastlabsclasspath}"/-->
+        <pathelement path="${beastlabsclasspath}"/>
         <pathelement path="${beastclassicclasspath}"/>
 	</path>
 
diff --git a/src/test/beast/evolution/tree/coalescent/BirthDeathSkylineTest.java b/src/test/beast/evolution/tree/coalescent/BirthDeathSkylineTest.java
index 038868b..d6627f3 100644
--- a/src/test/beast/evolution/tree/coalescent/BirthDeathSkylineTest.java
+++ b/src/test/beast/evolution/tree/coalescent/BirthDeathSkylineTest.java
@@ -158,6 +158,21 @@ public void test3intsmitRho() throws Exception {
                     bdssm.initAndValidate();
                     assertEquals(-106.06555718977357, bdssm.calculateTreeLogLikelihood(tree), 1e-4);
                 }
+                case 3:{
+                    BirthDeathSkylineModel bdssm =  new BirthDeathSkylineModel();
+                    bdssm.setInputValue("tree", tree);
+                    bdssm.setInputValue("origin", new RealParameter("2"));
+                    bdssm.setInputValue("conditionOnSurvival", false);
+
+                    bdssm.setInputValue("birthRate", new RealParameter("3. 2. 4. 4."));
+                    bdssm.setInputValue("deathRate", new RealParameter("2.5 1. .5 0.5"));
+                    bdssm.setInputValue("samplingRate", new RealParameter("2. 0.5 1. 2.0"));
+                    bdssm.setInputValue("rho", new RealParameter("0.05 0.01"));
+                    bdssm.setInputValue("rhoSamplingTimes","0. 1.");
+                    bdssm.setInputValue("intervalTimes", new RealParameter("0. 0.5 1. 1.1"));
+                    bdssm.initAndValidate();
+                    assertEquals(-109.6105592003162, bdssm.calculateTreeLogLikelihood(tree), 1e-4);
+                }
             }
         }
     }
@@ -700,7 +715,7 @@ public void testLikelihoodCalculation5reverseAll() throws Exception {
     public void testTreeParser() throws Exception {
 
         TreeParser tree = new TreeParser();
-        String newick = "(((1[&state='1']:1, (2[&state='0']:.5)[&state='1']:1.5)[&state='1']:2)[&state='0']:1, (3[&state='0']:1.5, (4[&state='1']:1.5)[&state='0']:1 )[&state='0']:2)[&state='0']:1;";
+        String newick = "(((1[&state='1']:1, (2[&state='0']:0.5)[&state='1']:1.5)[&state='1']:2)[&state='0']:1, (3[&state='0']:1.5, (4[&state='1']:1.5)[&state='0']:1 )[&state='0']:2)[&state='0']:1;";
         tree.initByName("adjustTipHeights",false, "singlechild", true, "newick", newick);
 
         printNodeState(tree.getRoot());
diff --git a/version.xml b/version.xml
index ad10ba1..2e6ca60 100644
--- a/version.xml
+++ b/version.xml
@@ -1,3 +1,3 @@
-<addon name='BDSKY' version='1.2.2'>
+<addon name='BDSKY' version='1.3.0'>
 	<depends on='beast2' atleast='2.4.0'/>
 </addon>