Merge pull request #65 from bioDS/svs_lphybeast

Merge Stochastic Variable Selection lphybeast

phylonco-lphybeast/src/main/java/phylonco/lphybeast/tobeast/values/SVSPopulationFunctionToBEAST.java

@@ -0,0 +1,63 @@
+package phylonco.lphybeast.tobeast.values;
+
+import beast.base.inference.parameter.RealParameter;
+import lphy.base.evolution.coalescent.PopulationFunction;
+import lphy.base.evolution.coalescent.populationmodel.SVSFunction;
+import lphy.base.evolution.coalescent.populationmodel.SVSPopulationFunction;
+import lphy.core.model.GraphicalModelNode;
+import lphy.core.model.Value;
+import lphybeast.BEASTContext;
+import lphybeast.ValueToBEAST;
+import lphybeast.tobeast.values.ValueToParameter;
+import phylonco.beast.evolution.populationmodel.StochasticVariableSelection;
+
+public class SVSPopulationFunctionToBEAST implements ValueToBEAST<SVSPopulationFunction, StochasticVariableSelection> {
+
+    @Override
+    public StochasticVariableSelection valueToBEAST(Value<SVSPopulationFunction> lphyPopFuncVal, BEASTContext context) {
+
+        StochasticVariableSelection beastPopFunc = new StochasticVariableSelection();
+
+        SVSFunction gen = (SVSFunction) lphyPopFuncVal.getGenerator();
+
+
+        RealParameter indicatorParam = context.getAsRealParameter(gen.getIndicator());
+        Value<PopulationFunction[]> modelsValue = gen.getModels();
+        Object[] modelsObjArray = modelsValue.value();
+
+        PopulationFunction[] modelsArray = new PopulationFunction[modelsObjArray.length];
+        for (int i = 0; i < modelsArray.length; i++) {
+            modelsArray[i] = (PopulationFunction) modelsObjArray[i];
+        }
+
+        beast.base.evolution.tree.coalescent.PopulationFunction[] modelFuncs = new beast.base.evolution.tree.coalescent.PopulationFunction[modelsArray.length];
+
+        for (int i = 0; i < modelsArray.length; i++) {
+            String modelName = gen.MODELS_PARAM_NAME;
+            GraphicalModelNode node = (GraphicalModelNode) (gen.getParams().get(modelName).getInputs().get(0));
+            Object contextObj = context.getBEASTObject((Value) node.getInputs().get(i));
+            beast.base.evolution.tree.coalescent.PopulationFunction beastPopFunction;
+            beastPopFunction = (beast.base.evolution.tree.coalescent.PopulationFunction) contextObj;
+            modelFuncs[i] = beastPopFunction;
+        }
+
+
+        beastPopFunc.setInputValue("indicator", indicatorParam);
+        beastPopFunc.setInputValue("models", modelFuncs);
+        beastPopFunc.initAndValidate();
+
+        ValueToParameter.setID(beastPopFunc, lphyPopFuncVal);
+
+        return beastPopFunc;
+    }
+
+    @Override
+    public Class getValueClass() {
+        return SVSPopulationFunction.class;
+    }
+
+    @Override
+    public Class<StochasticVariableSelection> getBEASTClass() {
+        return StochasticVariableSelection.class;
+    }
+}

phylonco-lphybeast/src/main/java/phylonco/lphybeast/tobeast/values/SVSToBEAST.java

@@ -23,7 +23,7 @@ public StochasticVariableSelection valueToBEAST(Value<SVSFunction> lphyPopFuncVa
         beast.base.evolution.tree.coalescent.PopulationFunction[] modelFuncs = new beast.base.evolution.tree.coalescent.PopulationFunction[modelsArray.length];
 
         for (int i = 0; i < modelsArray.length; i++) {
-            modelFuncs[i] = (beast.base.evolution.tree.coalescent.PopulationFunction) context.getBEASTObject(new Value<>(modelsArray[i], gen));
+            modelFuncs[i] = (beast.base.evolution.tree.coalescent.PopulationFunction) context.getBEASTObject(new Value<>(null, modelsArray[i]));
         }
 
         // Create and return the StochasticVariableSelection instance with the converted models

phylonco-lphybeast/version.xml

@@ -35,6 +35,8 @@
         <provider classname="phylonco.beast.evolution.populationmodel.LogisticGrowth"/>
         <provider classname="phylonco.beast.evolution.populationmodel.GompertzGrowth_t50"/>
         <provider classname="phylonco.beast.evolution.populationmodel.ConstantGrowth"/>
+        <provider classname="phylonco.beast.evolution.populationmodel.StochasticVariableSelection"/>
+
 
     </service>