store useAmbiguities in PreOrderSettings for later getTipStates/Parti…

…als operation in node height diagonal hessian calculation

src/dr/evomodel/treedatalikelihood/PreOrderSettings.java

@@ -8,13 +8,19 @@ public class PreOrderSettings {
     boolean branchRateDerivative;
     boolean branchInfinitesimalDerivative;
 
-    public PreOrderSettings(boolean usePreOrder, boolean branchRateDerivative, boolean branchInfinitesimalDerivative) {
+    boolean useAmbiguities;
+
+    public PreOrderSettings(boolean usePreOrder,
+                            boolean branchRateDerivative,
+                            boolean branchInfinitesimalDerivative,
+                            boolean useAmbiguities) {
         this.usePreOrder = usePreOrder;
         this.branchRateDerivative = branchRateDerivative;
         this.branchInfinitesimalDerivative = branchInfinitesimalDerivative;
+        this.useAmbiguities = useAmbiguities;
     }
 
     public static PreOrderSettings getDefault() {
-        return new PreOrderSettings(false, false, false);
+        return new PreOrderSettings(false, false, false, false);
     }
 }

src/dr/evomodelxml/treedatalikelihood/TreeDataLikelihoodParser.java

@@ -34,14 +34,12 @@
 import dr.evomodel.branchratemodel.BranchRateModel;
 import dr.evomodel.siteratemodel.DiscretizedSiteRateModel;
 import dr.evomodel.siteratemodel.GammaSiteRateModel;
-import dr.evomodel.siteratemodel.HomogeneousRateDelegate;
 import dr.evomodel.siteratemodel.SiteRateModel;
 import dr.evomodel.substmodel.FrequencyModel;
 import dr.evomodel.substmodel.SubstitutionModel;
 import dr.evomodel.tipstatesmodel.TipStatesModel;
 import dr.evomodel.treedatalikelihood.*;
 import dr.evomodel.treelikelihood.PartialsRescalingScheme;
-import dr.evomodelxml.siteratemodel.OldGammaSiteModelParser;
 import dr.inference.model.CompoundLikelihood;
 import dr.inference.model.Likelihood;
 import dr.xml.*;
@@ -240,7 +238,7 @@ public Object parseXMLObject(XMLObject xo) throws XMLParseException {
         if (usePreOrder != (branchRateDerivative || branchInfinitesimalDerivative)) {
             throw new RuntimeException("Need to specify derivative types.");
         }
-        PreOrderSettings settings = new PreOrderSettings(usePreOrder, branchRateDerivative, branchInfinitesimalDerivative);
+        PreOrderSettings settings = new PreOrderSettings(usePreOrder, branchRateDerivative, branchInfinitesimalDerivative, useAmbiguities);
 
         int beagleInstanceCount = xo.getAttribute(INSTANCE_COUNT, 1);
         String bic = System.getProperty(BEAGLE_INSTANCE_COUNT);