From 71df1286f1b200d85d6a1d40080f2fc4285a2549 Mon Sep 17 00:00:00 2001
From: jordandouglas <jordandouglas@windowslive.com>
Date: Mon, 5 Sep 2022 17:05:10 +1200
Subject: [PATCH] template clock model reversion

---
 fxtemplates/StarBeast3.xml                         |  2 ++
 .../evolution/branchratemodel/StarBeast3Clock.java | 14 +++++++-------
 2 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/fxtemplates/StarBeast3.xml b/fxtemplates/StarBeast3.xml
index 507a2ba..cde331b 100644
--- a/fxtemplates/StarBeast3.xml
+++ b/fxtemplates/StarBeast3.xml
@@ -234,10 +234,12 @@ ClusterTree/clusterType//'>
 		<panel spec="beastfx.app.inputeditor.BeautiPanelConfig" panelname="Site Model" tiptext="Site model and substitution model specifications" path="siteModel" hasPartitions="SiteModel" icon="3.pngx" forceExpansion="TRUE"/>
 		<mergepoint id="aux-sb3-sitemodel-panels"/>
 
+		<!--
 		<panel spec='beastfx.app.inputeditor.BeautiPanelConfig' panelname="Gene Clock Model" tiptext="Clock model"
             path='branchRateModel' type="starbeast3.evolution.branchratemodel.StarBeast3Clock"
             hasPartitions="ClockModel" forceExpansion='TRUE'
         />
+    -->
 		<mergepoint id='aux-sb3-clockmodel-panels'/>
 
 		<panel spec="beastfx.app.inputeditor.BeautiPanelConfig" panelname="Species Clock Model" icon='4.png.x' tiptext="Species Clock model" path="init/sharedRateModel/branchRateModel" forceExpansion="TRUE"/>
diff --git a/src/starbeast3/evolution/branchratemodel/StarBeast3Clock.java b/src/starbeast3/evolution/branchratemodel/StarBeast3Clock.java
index aae3608..3897bf0 100644
--- a/src/starbeast3/evolution/branchratemodel/StarBeast3Clock.java
+++ b/src/starbeast3/evolution/branchratemodel/StarBeast3Clock.java
@@ -209,8 +209,7 @@ public double getRateForBranch(Node node) {
     private static Boolean initialValueOfAutoSet = null;
     public static void estimateGeneClockRates(BeautiDoc doc) {
     	
-    	if (true) return;
-    	
+    	/*
     	if (initialValueOfAutoSet == null) initialValueOfAutoSet = doc.beauti.get_autoSetClockRate().isSelected();
     	
     	// Loaded in an old file. Do not overwrite
@@ -225,7 +224,7 @@ public static void estimateGeneClockRates(BeautiDoc doc) {
     		beautiClocksChecked.clear();
     		return;
     	}
-    	
+    	*/
     	for (String str : doc.pluginmap.keySet()) {
     		
     		// Find the StarBeast3Clocks
@@ -234,18 +233,19 @@ public static void estimateGeneClockRates(BeautiDoc doc) {
     			
     			StarBeast3Clock clock = (StarBeast3Clock)obj;
     			
+    			/*
     			// Do not revisit this clock or the users wishes will be overridden
 				if (beautiClocksChecked.containsKey(clock) && beautiClocksChecked.get(clock) > 0) {
 					Log.warning("StarBeast3Clock Skipping " + clock.getID());
 					continue;
 				}
-    			
+    			*/
     			
     			if (clock.meanRateInput.get() != null && clock.meanRateInput.get() instanceof StateNode) {
 					
     				StateNode rp = (StateNode)clock.meanRateInput.get();
-    				
-    				
+    				rp.isEstimatedInput.set(true);
+    				/*
     				// The first clock is not estimated
         			if (firstBeautiClock == null || firstBeautiClock == clock) {
         				firstBeautiClock = clock;
@@ -260,7 +260,7 @@ public static void estimateGeneClockRates(BeautiDoc doc) {
         				val += beautiClocksChecked.get(clock);
         			}
         			beautiClocksChecked.put(clock, val);
-    				
+    				*/
 				}
     			
     		}