Fixed parsers to work properly

beast-dev · Jul 14, 2023 · 39bafa4 · 39bafa4
1 parent f2eda54
commit 39bafa4
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Showing 2 changed files with 12 additions and 4 deletions.
diff --git a/src/dr/evomodelxml/siteratemodel/GammaSiteRateModelParser.java b/src/dr/evomodelxml/siteratemodel/GammaSiteRateModelParser.java
@@ -60,7 +60,7 @@ public String getParserName() {
     public Object parseXMLObject(XMLObject xo) throws XMLParseException {
 
         String msg = "";
-        SubstitutionModel substitutionModel;
+        SubstitutionModel substitutionModel = null;
 
         double muWeight = 1.0;
 
@@ -82,6 +82,10 @@ public Object parseXMLObject(XMLObject xo) throws XMLParseException {
                 msg += " with weight: " + muWeight;
             }
         }
+
+        if(xo.hasChildNamed(SUBSTITUTION_MODEL)){
+            substitutionModel = (SubstitutionModel)xo.getElementFirstChild(SUBSTITUTION_MODEL);
+        }
 
         int catCount = 4;
         catCount = xo.getIntegerAttribute(CATEGORIES);
@@ -124,7 +128,11 @@ public Object parseXMLObject(XMLObject xo) throws XMLParseException {
 
         GammaSiteRateDelegate delegate = new GammaSiteRateDelegate("GammaSiteRateDelegate", shapeParam, catCount, type, invarParam);
 
-        return new DiscretizedSiteRateModel(SiteModel.SITE_MODEL, muParam, muWeight, delegate);
+        DiscretizedSiteRateModel siteRateModel = new DiscretizedSiteRateModel(SiteModel.SITE_MODEL, muParam, muWeight, delegate);
+
+        siteRateModel.setSubstitutionModel(substitutionModel);
+
+        return siteRateModel;
     }
 
     //************************************************************************

diff --git a/src/dr/evomodelxml/treedatalikelihood/TreeDataLikelihoodParser.java b/src/dr/evomodelxml/treedatalikelihood/TreeDataLikelihoodParser.java
@@ -278,9 +278,9 @@ public Object parseXMLObject(XMLObject xo) throws XMLParseException {
                 BranchModel branchModel = (BranchModel) cxo.getChild(BranchModel.class);
                 if (branchModel == null) {
                     SubstitutionModel substitutionModel = (SubstitutionModel) cxo.getChild(SubstitutionModel.class);
-                    if (substitutionModel == null && siteRateModel instanceof GammaSiteRateModel) {
+                    if (substitutionModel == null && siteRateModel instanceof DiscretizedSiteRateModel) {
                         // for backwards compatibility the old GammaSiteRateModelParser can provide the substitution model...
-                        substitutionModel = ((GammaSiteRateModel)siteRateModel).getSubstitutionModel();
+                        substitutionModel = ((DiscretizedSiteRateModel)siteRateModel).getSubstitutionModel();
                     }
                     if (substitutionModel == null) {
                         throw new XMLParseException("No substitution model available for partition " + k + " in DataTreeLikelihood: "+xo.getId());