fix the 3rd bug, and review any missing updates in Standard.xml #115

Author: walterxie

beast-fx/src/main/resources/beast.fx/fxtemplates/Standard.xml

@@ -290,8 +290,8 @@ ClusterTree/clusterType/,
             <taxonset id='TaxonSet.$(n)' spec='beast.base.evolution.alignment.TaxonSet' alignment='@$(n)' />
             <plugin spec='beast.base.evolution.tree.Tree' id='Tree.t:$(n)' taxonset='@TaxonSet.$(n)'/>
 
-            <!--plugin spec='beast.base.evolution.tree.coalescent.RandomTree' id='RandomTree.t:$(n)' estimate='false' trait='@datetrait.$(n)' initial='@Tree.t:$(n)'-->
-            <plugin spec='beast.base.evolution.tree.coalescent.RandomTree' id='RandomTree.t:$(n)' estimate='false' initial='@Tree.t:$(n)'>
+            <!--plugin spec='beast.base.spec.evolution.tree.coalescent.RandomTree' id='RandomTree.t:$(n)' estimate='false' trait='@datetrait.$(n)' initial='@Tree.t:$(n)'-->
+            <plugin spec='beast.base.spec.evolution.tree.coalescent.RandomTree' id='RandomTree.t:$(n)' estimate='false' initial='@Tree.t:$(n)'>
                 <taxa idref='data'/>
                 <populationModel id='ConstantPopulation0.t:$(n)' spec='ConstantPopulation'>
             		<popSize id='randomPopSize.t:$(n)' spec='parameter.RealParameter' value='1'/>
@@ -473,7 +473,7 @@ ClusterTree/clusterType/,
 <!-- Tree initialisation -->
 <!-- Random tree -->
 
-        <subtemplate id='RandomTree' class='beast.base.evolution.tree.coalescent.RandomTree' mainid='RandomTree.t:$(n)'>
+        <subtemplate id='RandomTree' class='beast.base.spec.evolution.tree.coalescent.RandomTree' mainid='RandomTree.t:$(n)'>
 <![CDATA[
             <tree spec='beast.base.evolution.tree.coalescent.RandomTree' id='RandomTree.t:$(n)' estimate='false' initial="@Tree.t:$(n)">
                 <taxa idref='data'/>
@@ -486,9 +486,9 @@ ClusterTree/clusterType/,
 
 <!-- Cluster tree (defaults to UPGMA) -->
 
-        <subtemplate id='ClusterTree' class='beast.base.evolution.tree.ClusterTree' mainid='ClusterTree.t:$(n)'>
+        <subtemplate id='ClusterTree' class='beast.base.spec.evolution.tree.ClusterTree' mainid='ClusterTree.t:$(n)'>
 <![CDATA[
-        <tree spec='beast.base.evolution.tree.ClusterTree' id='ClusterTree.t:$(n)' initial="@Tree.t:$(n)" clusterType='upgma' estimate='false' taxa='@$(n)'/>
+        <tree spec='beast.base.spec.evolution.tree.ClusterTree' id='ClusterTree.t:$(n)' initial="@Tree.t:$(n)" clusterType='upgma' estimate='false' taxa='@$(n)'/>
 ]]>
         </subtemplate>