resolving AR conversations

beast-dev · Nov 19, 2024 · e6d89aa · e6d89aa
1 parent f9bb47c
commit e6d89aa
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Showing 5 changed files with 4 additions and 21 deletions.
diff --git a/src/dr/app/beast/development_parsers.properties b/src/dr/app/beast/development_parsers.properties
@@ -1,7 +1,7 @@
 #
 # development_parsers.properties
 #
-# Copyright � 2002-2024 the BEAST Development Team
+# Copyright © 2002-2024 the BEAST Development Team
 # http://beast.community/about
 #
 # This file is part of BEAST.

diff --git a/src/dr/app/beauti/options/PartitionClockModel.java b/src/dr/app/beauti/options/PartitionClockModel.java
@@ -557,7 +557,7 @@ public List<Operator> selectOperators(List<Operator> operators) {
         List<Operator> ops = new ArrayList<Operator>();
 
         if (options.hasData()) {
-            // if (getDataType().getType() != DataType.TREE) {
+            if (getDataType().getType() != DataType.TREE || getPartitionTreeModel().isUsingThorneyBEAST()) {
                 Operator rateOperator = getOperator("clock.rate");
 
                 switch (clockType) {
@@ -670,13 +670,11 @@ public List<Operator> selectOperators(List<Operator> operators) {
 
                     case AUTOCORRELATED:
                         throw new UnsupportedOperationException("Autocorrelated clock not implemented yet");
-//                        break;
-
                     default:
                         throw new IllegalArgumentException("Unknown clock model");
                 }
 
-            // }
+            }
         }
 
         Parameter allMuNus = getParameter(options.useNuRelativeRates() ? "allNus" : "allMus");

diff --git a/src/dr/app/beauti/options/PartitionTreeModel.java b/src/dr/app/beauti/options/PartitionTreeModel.java
@@ -27,7 +27,6 @@
 
 package dr.app.beauti.options;
 
-import dr.app.beauti.mcmcpanel.MCMCPanel;
 import dr.app.beauti.types.*;
 import dr.evolution.tree.Tree;
 
@@ -194,9 +193,6 @@ public List<Parameter> selectParameters(List<Parameter> parameters) {
         // get parameter so their id prefix can be set.
 
         getParameter("tree");
-        if(isUsingEmpiricalTrees()){
-            return parameters;
-        }
         getParameter("treeModel.internalNodeHeights");
         getParameter("treeModel.allInternalNodeHeights");
 

diff --git a/src/dr/app/beauti/sitemodelspanel/PartitionModelPanel.java b/src/dr/app/beauti/sitemodelspanel/PartitionModelPanel.java
@@ -40,7 +40,6 @@
 import dr.app.beauti.types.FrequencyPolicyType;
 import dr.app.beauti.util.PanelUtils;
 import dr.app.gui.components.RealNumberField;
-import dr.app.gui.components.WholeNumberField;
 import dr.app.util.OSType;
 import dr.evolution.datatype.DataType;
 import jam.panels.OptionsPanel;

diff --git a/src/dr/evomodelxml/operators/NodeHeightOperatorParser.java b/src/dr/evomodelxml/operators/NodeHeightOperatorParser.java
@@ -48,9 +48,7 @@ public enum OperatorType {
         RANDOMWALK("random walk"),
         SCALEROOT("scale root"),
         SCALEALL("scale all internal");
-//        MULTIMOVEUNIFORM("multiMoveUniform");
-        // -JT the order in which nodes are picked matters but there is more than
-        // one way to pick the nodes I don't trust the multimove operator
+
 
         OperatorType(String name) {
             this.name = name;
@@ -107,12 +105,6 @@ public Object parseXMLObject(XMLObject xo) throws XMLParseException {
                     throw new XMLParseException("The UniformNodeHeightOperator scaleFactor attribute must be between 0 and 1.");
                 }
             }
-            // if (xo.hasAttribute(MEAN_COUNT)) {
-            //     tuningParameter = xo.getDoubleAttribute(MEAN_COUNT);
-            //     if (tuningParameter <= 0.0) {
-            //         throw new XMLParseException("The UniformNodeHeightOperator nonshifted mean attribute must be positive and non-zero.");
-            //     }
-            // }
 
             final double targetAcceptance = xo.getAttribute(TARGET_ACCEPTANCE, 0.234);
 
@@ -126,8 +118,6 @@ public Object parseXMLObject(XMLObject xo) throws XMLParseException {
                 case SCALEROOT:
                 case SCALEALL:
                     return new ScaleNodeHeightOperator(treeModel, weight, tuningParameter, operatorType, mode, targetAcceptance);
-//                case MULTIMOVEUNIFORM:
-//                    return new MultiMoveUniformNodeHeightOperator(treeModel, weight, tuningParameter,mode,targetAcceptance);
                 default:
                     throw new IllegalArgumentException("Unknown operator type");
             }