release 1.2.5

build.xml

@@ -18,7 +18,7 @@
 	<property name="srcBeast2" location="${beast2path}/src" />
 	<property name="beast2classpath" location="${beast2path}/build" />
 	<property name="Add_on_dir" value="${release_dir}/add-on" />
-	<property name="version" value="1.2.4" />
+	<property name="version" value="1.2.5" />
 
     <import file="${beast2path}/build.xml" />
 
@@ -29,6 +29,7 @@
         <pathelement path="${buildRBS}"/>
 		<fileset dir="${libBeast2}" includes="junit-4.8.2.jar"/>
 		<fileset dir="${libBeast2}" includes="beagle.jar"/>
+                <fileset dir="${libBeast2}" includes="jam.jar"/>
         <pathelement path="${beast2classpath}"/>
 	</path>
 

src/beast/evolution/likelihood/PartitionProvider.java

@@ -238,8 +238,9 @@ public void initStateNodes() throws Exception {
 		tabuList.add(this);
 		for (int i = 1; i < numPartitions.get(); i++) {
 			BeautiDoc doc = new BeautiDoc();
-			PartitionContext context = new PartitionContext(sPartition+i);
-			BEASTInterface plugin = BeautiDoc.deepCopyPlugin(siteModel, this, mcmc, context, doc, tabuList);
+			PartitionContext oldContext = new PartitionContext(sPartition);
+			PartitionContext newContext = new PartitionContext(sPartition+i);
+			BEASTInterface plugin = BeautiDoc.deepCopyPlugin(siteModel, this, mcmc, oldContext, newContext, doc, tabuList);
 			m_pSiteModel.get().add((SiteModel.Base) plugin);
 		}
 		if (siteModel instanceof SiteModel) {

templates/AutoPartition.xml

@@ -211,12 +211,13 @@
             <operator id='allTipDatesRandomWalker.t:$(n)' spec='TipDatesRandomWalker' windowSize="1" weight="0" tree="@Tree.t:$(n)"/>
 			<operator id='PartitionLengthsDeltaExchangeOperator.$(n)' spec='DeltaExchangeOperator' intparameter='@partitionLengths.$(n)' integer='true' delta='1' weight='10'/>
 
-            <operator id='treeScaler.t:$(n)' spec='ScaleOperator' scaleFactor="0.5" weight="1" tree="@Tree.t:$(n)"/>
-            <operator id='UniformOperator.t:$(n)' spec='Uniform' weight="10" tree="@Tree.t:$(n)"/>
-            <operator id='SubtreeSlide.t:$(n)' spec='SubtreeSlide' weight="5" gaussian="true" size="1.0" tree="@Tree.t:$(n)"/>
-            <operator id='narrow.t:$(n)' spec='Exchange' isNarrow='true' weight="1" tree="@Tree.t:$(n)"/>
-            <operator id='wide.t:$(n)' spec='Exchange' isNarrow='false' weight="1" tree="@Tree.t:$(n)"/>
-            <operator id='WilsonBalding.t:$(n)' spec='WilsonBalding' weight="1" tree="@Tree.t:$(n)"/>
+            <operator id='YuleModelTreeScaler.t:$(n)' spec='ScaleOperator' scaleFactor="0.5" weight="3" tree="@Tree.t:$(n)"/>
+            <operator id='YuleModelTreeRootScaler.t:$(n)' spec='ScaleOperator' scaleFactor="0.5" weight="3" tree="@Tree.t:$(n)" rootOnly='true'/>
+            <operator id='YuleModelUniformOperator.t:$(n)' spec='Uniform' weight="30" tree="@Tree.t:$(n)"/>
+            <operator id='YuleModelSubtreeSlide.t:$(n)' spec='SubtreeSlide' weight="15" gaussian="true" size="1.0" tree="@Tree.t:$(n)"/>
+            <operator id='YuleModelNarrow.t:$(n)' spec='Exchange' isNarrow='true' weight="15" tree="@Tree.t:$(n)"/>
+            <operator id='YuleModelWide.t:$(n)' spec='Exchange' isNarrow='false' weight="3" tree="@Tree.t:$(n)"/>
+            <operator id='YuleModelWilsonBalding.t:$(n)' spec='WilsonBalding' weight="3" tree="@Tree.t:$(n)"/>
 
 
             <prior id='YuleBirthRatePrior.t:$(n)' spec='Prior' x='@birthRate.t:$(n)'><distr spec="beast.math.distributions.Uniform" lower='0' /></prior>

version.xml

@@ -1,3 +1,3 @@
-<addon name='RBS' version='1.2.4'>
+<addon name='RBS' version='1.2.5'>
 	<depends on='beast2' atleast='2.3.0'/>
 </addon>