From e6b7ccea70632a7ae2d2bbb669a90415bb37c635 Mon Sep 17 00:00:00 2001
From: walterxie <walter@cs.auckland.ac.nz>
Date: Wed, 17 Jan 2024 17:47:57 +1300
Subject: [PATCH] move addDeltaExchangeOperator to the same class creating all
 operators #109

---
 .../operators/DefaultOperatorStrategy.java    | 19 ++++++++++++++++++-
 .../values/DoubleArrayValueToBEAST.java       | 19 ++-----------------
 2 files changed, 20 insertions(+), 18 deletions(-)

diff --git a/lphybeast/src/main/java/lphybeast/tobeast/operators/DefaultOperatorStrategy.java b/lphybeast/src/main/java/lphybeast/tobeast/operators/DefaultOperatorStrategy.java
index 81b56be..9d05d46 100644
--- a/lphybeast/src/main/java/lphybeast/tobeast/operators/DefaultOperatorStrategy.java
+++ b/lphybeast/src/main/java/lphybeast/tobeast/operators/DefaultOperatorStrategy.java
@@ -2,6 +2,7 @@
 
 import beast.base.core.BEASTInterface;
 import beast.base.core.BEASTObject;
+import beast.base.core.Function;
 import beast.base.evolution.operator.kernel.BactrianScaleOperator;
 import beast.base.evolution.tree.Tree;
 import beast.base.inference.Operator;
@@ -17,10 +18,12 @@
 import com.google.common.collect.Multimap;
 import lphy.base.distribution.Dirichlet;
 import lphy.base.distribution.RandomComposition;
+import lphy.base.distribution.WeightedDirichlet;
 import lphy.core.logger.LoggerUtils;
 import lphy.core.model.GenerativeDistribution;
 import lphy.core.model.GraphicalModelNode;
 import lphy.core.model.RandomVariable;
+import lphy.core.model.Value;
 import lphy.core.vectorization.IID;
 import lphybeast.BEASTContext;
 
@@ -195,7 +198,7 @@ public static void addUpDownOperator(Tree tree, RealParameter clockRate, BEASTCo
         String idStr = clockRate.getID() + "Up" + tree.getID() + "DownOperator";
         // avoid to duplicate updown ops from the same pair of rate and tree
         if (!context.hasExtraOperator(idStr)) {
-            BactrianUpDownOperator upDownOperator = new BactrianUpDownOperator();
+            Operator upDownOperator = new BactrianUpDownOperator();
             upDownOperator.setID(idStr);
             upDownOperator.setInputValue("up", clockRate);
             upDownOperator.setInputValue("down", tree);
@@ -204,4 +207,18 @@ public static void addUpDownOperator(Tree tree, RealParameter clockRate, BEASTCo
             context.addExtraOperator(upDownOperator);
         }
     }
+
+    public static void addDeltaExchangeOperator(Value<Double[]> value, List<Function> args, BEASTContext context) {
+        WeightedDirichlet weightedDirichlet = (WeightedDirichlet) value.getGenerator();
+        IntegerParameter weightIntParam = context.getAsIntegerParameter(weightedDirichlet.getWeights());
+
+        Operator operator = new BactrianDeltaExchangeOperator();
+        operator.setInputValue("parameter", args);
+        operator.setInputValue("weight", BEASTContext.getOperatorWeight(args.size() - 1));
+        operator.setInputValue("weightvector", weightIntParam);
+        operator.setInputValue("delta", 1.0 / value.value().length);
+        operator.initAndValidate();
+        operator.setID(value.getCanonicalId() + ".deltaExchange");
+        context.addExtraOperator(operator);
+    }
 }
diff --git a/lphybeast/src/main/java/lphybeast/tobeast/values/DoubleArrayValueToBEAST.java b/lphybeast/src/main/java/lphybeast/tobeast/values/DoubleArrayValueToBEAST.java
index 5a7750b..bff9d31 100644
--- a/lphybeast/src/main/java/lphybeast/tobeast/values/DoubleArrayValueToBEAST.java
+++ b/lphybeast/src/main/java/lphybeast/tobeast/values/DoubleArrayValueToBEAST.java
@@ -2,9 +2,6 @@
 
 import beast.base.core.BEASTInterface;
 import beast.base.core.Function;
-import beast.base.inference.Operator;
-import beast.base.inference.operator.DeltaExchangeOperator;
-import beast.base.inference.parameter.IntegerParameter;
 import beast.base.inference.parameter.Parameter;
 import beast.base.inference.parameter.RealParameter;
 import feast.function.Concatenate;
@@ -14,6 +11,7 @@
 import lphy.core.vectorization.VectorUtils;
 import lphybeast.BEASTContext;
 import lphybeast.ValueToBEAST;
+import lphybeast.tobeast.operators.DefaultOperatorStrategy;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -39,7 +37,7 @@ public BEASTInterface valueToBEAST(Value<Double[]> value, BEASTContext context)
 
             ValueToParameter.setID(concatenatedParameters, value);
 
-            addDeltaExchangeOperator(value, args, context);
+            DefaultOperatorStrategy.addDeltaExchangeOperator(value, args, context);
 
             return concatenatedParameters;
         }
@@ -74,17 +72,4 @@ public Class<BEASTInterface> getBEASTClass() {
         return BEASTInterface.class;
     }
 
-    private void addDeltaExchangeOperator(Value<Double[]> value, List<Function> args, BEASTContext context) {
-        WeightedDirichlet weightedDirichlet = (WeightedDirichlet) value.getGenerator();
-        IntegerParameter weightIntParam = context.getAsIntegerParameter(weightedDirichlet.getWeights());
-
-        Operator operator = new DeltaExchangeOperator();
-        operator.setInputValue("parameter", args);
-        operator.setInputValue("weight", BEASTContext.getOperatorWeight(args.size() - 1));
-        operator.setInputValue("weightvector", weightIntParam);
-        operator.setInputValue("delta", 1.0 / value.value().length);
-        operator.initAndValidate();
-        operator.setID(value.getCanonicalId() + ".deltaExchange");
-        context.addExtraOperator(operator);
-    }
 }