From 97b7598a26cbf6fd38625ae5ba33f14fbbef0975 Mon Sep 17 00:00:00 2001
From: Denise <denise.kuehnert@gmail.com>
Date: Mon, 1 Jun 2015 14:30:01 +0200
Subject: [PATCH] make operator ID's unique

---
 build.xml                  |  8 ++++----
 templates/BDSKY_serial.xml | 20 ++++++++++----------
 2 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/build.xml b/build.xml
index 1b80cf8..a5d5f44 100644
--- a/build.xml
+++ b/build.xml
@@ -17,8 +17,8 @@
 	<property name="libBeast2" location="${beast2path}/lib" />
 	<property name="srcBeast2" location="${beast2path}/src" />
 	<property name="beast2classpath" location="${beast2path}/build" />
-    <property name="beastiiclasspath" location="../beastii/build" />
-    <!--property name="beastclassicclasspath" location="../beast-classic/build" /-->
+    <!--property name="beastlabsclasspath" location="../BEASTLabs/build" /-->
+    <property name="beastclassicclasspath" location="../beast-classic/build" />
 	<property name="Add_on_dir" value="${release_dir}/add-on" />
 
     <import file="${beast2path}/build.xml" />
@@ -32,8 +32,8 @@
 		<fileset dir="${libBeast2}" includes="fest.jar"/>
 		<fileset dir="${libBeast2}" includes="jam.jar"/>
         <pathelement path="${beast2classpath}"/>
-        <pathelement path="${beastiiclasspath}"/>
-        <!--pathelement path="${beastclassicclasspath}"/-->
+        <!--pathelement path="${beastlabsclasspath}"/-->
+        <pathelement path="${beastclassicclasspath}"/>
 	</path>
 
 	<!-- start -->
diff --git a/templates/BDSKY_serial.xml b/templates/BDSKY_serial.xml
index 54bb074..97178ac 100644
--- a/templates/BDSKY_serial.xml
+++ b/templates/BDSKY_serial.xml
@@ -74,16 +74,16 @@ suppressInputs='beast.evolution.speciation.BirthDeathSkylineModel.intervalTimes,
 	<operator id='BDSKY_serialWilsonBalding.t:$(n)' spec='WilsonBalding' weight="3" tree="@Tree.t:$(n)"/>
 
 	<!-- BDSKY operators -->
-	<operator id='becomeUninfectiousRateScaler.t:$(n)' spec='ScaleOperator' scaleFactor=".75" weight="2" parameter="@becomeUninfectiousRate.s.t:$(n)"/>
-	<operator id='samplingScaler.t:$(n)' spec='ScaleOperator' scaleFactor=".75" weight="2" parameter="@samplingProportion.s.t:$(n)"/>
-	<operator id='RScaler.t:$(n)' spec='ScaleOperator' scaleFactor=".75" weight="10" parameter="@R0.s.t:$(n)"/>
+	<operator id='becomeUninfectiousRateScaler.s.t:$(n)' spec='ScaleOperator' scaleFactor=".75" weight="2" parameter="@becomeUninfectiousRate.s.t:$(n)"/>
+	<operator id='samplingScaler.s.t:$(n)' spec='ScaleOperator' scaleFactor=".75" weight="2" parameter="@samplingProportion.s.t:$(n)"/>
+	<operator id='RScaler.s.t:$(n)' spec='ScaleOperator' scaleFactor=".75" weight="10" parameter="@R0.s.t:$(n)"/>
 
-	<operator id="updownBD.t:$(n)" spec="UpDownOperator" scaleFactor=".75" weight="2">
+	<operator id="updownBD.s.t:$(n)" spec="UpDownOperator" scaleFactor=".75" weight="2">
 		<up idref="R0.s.t:$(n)"/>
 		<down idref="becomeUninfectiousRate.s.t:$(n)"/>
 	</operator>
 
-	<operator id='origScaler.t:$(n)' spec='ScaleOperator' scaleFactor=".75" weight="1" parameter="@origin.s.t:$(n)"/>
+	<operator id='origScaler.s.t:$(n)' spec='ScaleOperator' scaleFactor=".75" weight="1" parameter="@origin.s.t:$(n)"/>
 ]]>
             <connect srcID='BirthDeathSkySerial.t:$(n)' targetID='prior' inputName='distribution' if='inposterior(BirthDeathSkySerial.t:$(n)) and inlikelihood(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'/>
             <connect srcID='RandomTree.t:$(n)'                targetID='BirthDeathSkySerial.t:$(n)' inputName='init'   if='inposterior(Tree.t:$(n))'/>
@@ -101,11 +101,11 @@ suppressInputs='beast.evolution.speciation.BirthDeathSkylineModel.intervalTimes,
             <connect srcID='BDSKY_serialwide.t:$(n)'                      targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkySerial.t:$(n)) and inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'>Wide exchange performs global rearrangement of tree t:$(n)</connect>
             <connect srcID='BDSKY_serialWilsonBalding.t:$(n)'             targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkySerial.t:$(n)) and inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'>Performs Wilson-Balding global rearrangement of tree t:$(n)</connect>
 
-            <connect srcID='becomeUninfectiousRateScaler.t:$(n)' targetID='mcmc' inputName='operator'     if='inposterior(BirthDeathSkySerial.t:$(n)) and becomeUninfectiousRate.s.t:$(n)/estimate=true'/>
-            <connect srcID='samplingScaler.t:$(n)' targetID='mcmc' inputName='operator'     if='inposterior(BirthDeathSkySerial.t:$(n)) and samplingProportion.s.t:$(n)/estimate=true'/>
-            <connect srcID='RScaler.t:$(n)' targetID='mcmc' inputName='operator'     if='inposterior(BirthDeathSkySerial.t:$(n)) and R0.s.t:$(n)/estimate=true'/>
-            <connect srcID='updownBD.t:$(n)' targetID='mcmc' inputName='operator'     if='inposterior(BirthDeathSkySerial.t:$(n)) and R0.s.t:$(n)/estimate=true and becomeUninfectiousRate.s.t:$(n)/estimate=true'/>
-            <connect srcID='origScaler.t:$(n)' targetID='mcmc' inputName='operator'     if='inposterior(BirthDeathSkySerial.t:$(n)) and origin.s.t:$(n)/estimate=true'/>
+            <connect srcID='becomeUninfectiousRateScaler.s.t:$(n)' targetID='mcmc' inputName='operator'     if='inposterior(BirthDeathSkySerial.t:$(n)) and becomeUninfectiousRate.s.t:$(n)/estimate=true'/>
+            <connect srcID='samplingScaler.s.t:$(n)' targetID='mcmc' inputName='operator'     if='inposterior(BirthDeathSkySerial.t:$(n)) and samplingProportion.s.t:$(n)/estimate=true'/>
+            <connect srcID='RScaler.s.t:$(n)' targetID='mcmc' inputName='operator'     if='inposterior(BirthDeathSkySerial.t:$(n)) and R0.s.t:$(n)/estimate=true'/>
+            <connect srcID='updownBD.s.t:$(n)' targetID='mcmc' inputName='operator'     if='inposterior(BirthDeathSkySerial.t:$(n)) and R0.s.t:$(n)/estimate=true and becomeUninfectiousRate.s.t:$(n)/estimate=true'/>
+            <connect srcID='origScaler.s.t:$(n)' targetID='mcmc' inputName='operator'     if='inposterior(BirthDeathSkySerial.t:$(n)) and origin.s.t:$(n)/estimate=true'/>