Updating code with latest master branch version and (hopefully) resol…

…ved conflicts.
beast-dev · Aug 19, 2024 · 95d319f · 95d319f
1 parent be9cb63
commit 95d319f
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Showing 38 changed files with 7,716 additions and 159 deletions.
diff --git a/src/dr/app/beast/development_parsers.properties b/src/dr/app/beast/development_parsers.properties
@@ -424,4 +424,15 @@ dr.evoxml.ReportSitePatternMapParser
 dr.inferencexml.loggers.TimeLoggerXMLParser
 
 # Attempt
-dr.inferencexml.distribution.WeightsParser
+dr.inferencexml.distribution.WeightsParser
+
+#Partition Models
+dr.evomodelxml.treedatalikelihood.DataSquashingOperatorParser
+dr.evomodelxml.treedatalikelihood.HDPDataSquashingOperatorParser
+dr.evomodelxml.treedatalikelihood.DirichletProcessPolyaUrnParser
+dr.evomodelxml.treedatalikelihood.HMMPolyaUrnParser
+dr.evomodelxml.treedatalikelihood.HDPPolyaUrnParser
+dr.evomodel.treedatalikelihood.HDPDrawsFromCommonBaseOperator
+dr.evomodel.treedatalikelihood.HDPStickPropsOperator
+dr.evomodel.treedatalikelihood.BaseDistPrecisionGibbsOperator
+dr.inferencexml.distribution.DirichletDistributionModelParser
diff --git a/src/dr/evolution/alignment/PatternList.java b/src/dr/evolution/alignment/PatternList.java
@@ -63,6 +63,8 @@ public interface PatternList extends TaxonList, Identifiable {
      */
     int[] getPattern(int patternIndex);
 
+    int getPatternIndex(int siteIndex);
+
     /**
      * Gets the pattern as an array of state frequency vectors (one per sequence)
      *

diff --git a/src/dr/evolution/alignment/Patterns.java b/src/dr/evolution/alignment/Patterns.java
@@ -456,6 +456,11 @@ public int[] getPattern(int patternIndex) {
         return patterns[patternIndex];
     }
 
+    public int getPatternIndex(int siteIndex){
+        // Not implemented yet
+        return -1;
+    }
+
     @Override
     public double[][] getUncertainPattern(int patternIndex) {
         throw new UnsupportedOperationException("uncertain patterns not implemented yet");

diff --git a/src/dr/evolution/alignment/ResamplePatterns.java b/src/dr/evolution/alignment/ResamplePatterns.java
@@ -137,6 +137,10 @@ public double[] getPatternWeights() {
 		return weights;
 	}
 
+	public int getPatternIndex(int siteIndex){
+		// Not implemented yet
+		return -1;
+	}
 	/**
 	 * @return the DataType of this siteList
 	 */

diff --git a/src/dr/evolution/alignment/TaxaFilteredSitePatterns.java b/src/dr/evolution/alignment/TaxaFilteredSitePatterns.java
@@ -128,6 +128,10 @@ public double[] getPatternWeights() {
 
     }
 
+    public int getPatternIndex(int siteIndex){
+        // Not implemented yet
+        return -1;
+    }
     @Override
     public DataType getDataType() {
         return original.getDataType();

diff --git a/src/dr/evomodel/bigfasttree/thorney/ThorneyDataLikelihoodDelegate.java b/src/dr/evomodel/bigfasttree/thorney/ThorneyDataLikelihoodDelegate.java
@@ -32,11 +32,9 @@
 
 import dr.evolution.tree.NodeRef;
 import dr.evolution.tree.Tree;
-import dr.evomodel.treedatalikelihood.DataLikelihoodDelegate;
-import dr.evomodel.treedatalikelihood.RateRescalingScheme;
-import dr.evomodel.treedatalikelihood.TreeDataLikelihood;
-import dr.evomodel.treedatalikelihood.TreeTraversal;
+import dr.evomodel.treedatalikelihood.*;
 import dr.evomodel.treedatalikelihood.TreeTraversal.TraversalType;
+import dr.evomodel.treelikelihood.PartialsRescalingScheme;
 import dr.inference.model.AbstractModel;
 import dr.inference.model.Model;
 import dr.inference.model.Variable;
@@ -222,6 +220,15 @@ public void setComputePostOrderStatisticsOnly(boolean computePostOrderStatistics
     @Override
     public boolean providesPostOrderStatisticsOnly() { return false;    }
 
+    public int getPartitionCat(){
+        // not meaningful right now, need to update
+        return 0;
+    };
+
+    public double[] getSiteLogLikelihoods(){
+        throw new RuntimeException("getSiteLogLikelihoods() not implemented");
+    }
+
     @Override
     protected void handleModelChangedEvent(Model model, Object object, int index) { // substitution model here
         // TODO Auto-generated method stub
@@ -239,6 +246,26 @@ protected void acceptState() {
         // nada
     }
 
+    public PreOrderSettings getPreOrderSettings() {
+        return null;
+    }
+
+    @Override
+    public boolean getPreferGPU() {
+        return true;
+    }
+
+    public boolean getUseAmbiguities() {
+        return true;
+    }
+
+    public PartialsRescalingScheme getRescalingScheme() {
+        return null;
+    }
+
+    public boolean getDelayRescalingUntilUnderflow() {
+        return true;
+    }
     // get the mutation map
     protected MutationBranchMap getMutationMap() {
         return mutationMap;

diff --git a/src/dr/evomodel/branchmodel/lineagespecific/CountableRealizationsParameter.java b/src/dr/evomodel/branchmodel/lineagespecific/CountableRealizationsParameter.java
@@ -107,26 +107,55 @@ protected void adoptValues(Parameter source) {
     }
 
     public double getParameterValue(int index) {
-    	
+
 //    	int whichCategoryIndex = index % dim; // TODO Maybe?
 //    	int whichDimIndex = index - whichCategoryIndex * dim; // TODO Maybe?
 //    	Parameter param = uniquelyRealizedParameters.getParameter((int) categoriesParameter.getParameterValue(whichCategoryIndex));
-//    	return param.getParameterValue(whichDimIndex);     
-    	
-    	int whichCategoryIndex = categoriesParameter.getValue(index).intValue();//
-    	int whichDimIndex = 0;
-    	
-    	Parameter param = uniquelyRealizedParameters.getParameter(whichCategoryIndex);
-    	
-    	return param.getParameterValue(whichDimIndex);     
+//    	return param.getParameterValue(whichDimIndex);
+
+        int whichCategoryIndex = categoriesParameter.getValue(index).intValue();//
+        int whichDimIndex = 0;
+
+        Parameter param = uniquelyRealizedParameters.getParameter(whichCategoryIndex);
+
+        return param.getParameterValue(whichDimIndex);
     }//END: getParameterValue
 
-	public void setParameterValue(int dim, double value) {
+    public double[] getAllParameterValues(int index) {
+
+        int whichCategoryIndex = categoriesParameter.getValue(index).intValue();//
+
+        Parameter param = uniquelyRealizedParameters.getParameter(whichCategoryIndex);
+        double[] returnVal = new double[param.getSize()];
+
+        for(int i = 0; i < param.getSize(); i++){
+            returnVal[i] = param.getParameterValue(i);
+        }
+
+        return returnVal;
+    }
+
+    public void setParameterValue(int dim, double value) {
+
+        int whichCategoryIndex = (int) categoriesParameter.getParameterValue(dim);
+        uniquelyRealizedParameters.setParameterValue(whichCategoryIndex, value);
+
+    }//END: setParameterValue
 
-		int whichCategoryIndex = (int) categoriesParameter.getParameterValue(dim);
-		uniquelyRealizedParameters.setParameterValue(whichCategoryIndex, value);
+    public void setParameterValue(int dim, double[] value) {
+
+        int whichCategoryIndex = (int) categoriesParameter.getParameterValue(dim);
+
+        if(uniquelyRealizedParameters.getParameter(whichCategoryIndex).getSize() != value.length){
+            throw new RuntimeException("parameter and array with parameter values must have same dimension");
+        }
+
+        for(int i = 0; i < value.length; i++){
+            uniquelyRealizedParameters.getParameter(whichCategoryIndex).setParameterValue(i,value[i]);
+        }
+        //uniquelyRealizedParameters.setParameterValue(whichCategoryIndex, value);
 
-	}//END: setParameterValue
+    }//END: setParameterValue
 
     public void setParameterValueQuietly(int dim, double value) {
         throw new RuntimeException("Not implemented");

diff --git a/src/dr/evomodel/continuous/TreeTraitNormalDistributionModel.java b/src/dr/evomodel/continuous/TreeTraitNormalDistributionModel.java
@@ -173,6 +173,9 @@ public double logPdf(Object x) {
         return distribution.logPdf(x);
     }
 
+    public int getDimension(){
+        return dim;
+    }
     // *****************************************************************
     // Interface DensityModel
     // *****************************************************************

diff --git a/src/dr/evomodel/epidemiology/casetocase/CategoryOutbreak.java b/src/dr/evomodel/epidemiology/casetocase/CategoryOutbreak.java
@@ -188,6 +188,10 @@ private void buildDistanceMatrix(){
         }
     }
 
+    public int getPatternIndex(int siteIndex){
+        // Not implemented yet
+        return -1;
+    }
     protected void handleModelChangedEvent(Model model, Object object, int index) {
         if(!(model instanceof AbstractPeriodPriorDistribution)) {
             fireModelChanged(object);

diff --git a/src/dr/evomodel/tree/HiddenLinkageModel.java b/src/dr/evomodel/tree/HiddenLinkageModel.java
@@ -523,6 +523,10 @@ public double[] getPatternWeights() {
 		return data.getAlignment().getPatternWeights();
 	}
 
+	public int getPatternIndex(int siteIndex){
+		// Not implemented yet
+		return -1;
+	}
 	public int getStateCount() {
 		return data.getAlignment().getStateCount();
 	}