move addUpDownOperator to the same class creating all operators #109

LinguaPhylo · Jan 15, 2024 · 8ac4505 · 8ac4505
1 parent dbc1cf6
commit 8ac4505
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Showing 2 changed files with 19 additions and 18 deletions.
diff --git a/lphybeast/src/main/java/lphybeast/tobeast/generators/PhyloCTMCToBEAST.java b/lphybeast/src/main/java/lphybeast/tobeast/generators/PhyloCTMCToBEAST.java
@@ -11,7 +11,6 @@
 import beast.base.evolution.substitutionmodel.SubstitutionModel;
 import beast.base.evolution.tree.Tree;
 import beast.base.inference.distribution.Prior;
-import beast.base.inference.operator.kernel.BactrianUpDownOperator;
 import beast.base.inference.parameter.RealParameter;
 import beastclassic.evolution.alignment.AlignmentFromTrait;
 import beastclassic.evolution.likelihood.AncestralStateTreeLikelihood;
@@ -33,6 +32,7 @@
 import lphybeast.BEASTContext;
 import lphybeast.GeneratorToBEAST;
 import lphybeast.tobeast.loggers.TraitTreeLogger;
+import lphybeast.tobeast.operators.DefaultOperatorStrategy;
 
 import java.util.Map;
 
@@ -215,7 +215,7 @@ public static void constructTreeAndBranchRate(PhyloCTMC phyloCTMC, GenericTreeLi
             treeLikelihood.setInputValue("branchRateModel", clockModel);
 
             if (clockRate instanceof RandomVariable && timeTreeValue instanceof RandomVariable && skipBranchOperators == false) {
-                addUpDownOperator(tree, clockRatePara, context);
+                DefaultOperatorStrategy.addUpDownOperator(tree, clockRatePara, context);
             }
         }
     }
@@ -323,21 +323,6 @@ private static void addRelaxedClockOperators(Tree tree, UCRelaxedClockModel rela
         context.addExtraOperator(smallPulley);
     }
 
-    // when both mu and tree are random var
-    private static void addUpDownOperator(Tree tree, RealParameter clockRate, BEASTContext context) {
-        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();
-            upDownOperator.setID(idStr);
-            upDownOperator.setInputValue("up", clockRate);
-            upDownOperator.setInputValue("down", tree);
-            upDownOperator.setInputValue("scaleFactor", 0.9);
-            upDownOperator.setInputValue("weight", BEASTContext.getOperatorWeight(tree.getInternalNodeCount()+1));
-            context.addExtraOperator(upDownOperator);
-        }
-    }
-
     @Override
     public Class<PhyloCTMC> getGeneratorClass() {
         return PhyloCTMC.class;

diff --git a/lphybeast/src/main/java/lphybeast/tobeast/operators/DefaultOperatorStrategy.java b/lphybeast/src/main/java/lphybeast/tobeast/operators/DefaultOperatorStrategy.java
@@ -10,6 +10,7 @@
 import beast.base.inference.operator.IntRandomWalkOperator;
 import beast.base.inference.operator.kernel.BactrianDeltaExchangeOperator;
 import beast.base.inference.operator.kernel.BactrianRandomWalkOperator;
+import beast.base.inference.operator.kernel.BactrianUpDownOperator;
 import beast.base.inference.parameter.BooleanParameter;
 import beast.base.inference.parameter.IntegerParameter;
 import beast.base.inference.parameter.RealParameter;
@@ -187,5 +188,20 @@ private Operator createBitFlipOperator(BooleanParameter parameter) {
         return operator;
     }
 
-
+    //*** static methods ***//
+
+    // when both mu and tree are random var
+    public static void addUpDownOperator(Tree tree, RealParameter clockRate, BEASTContext context) {
+        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();
+            upDownOperator.setID(idStr);
+            upDownOperator.setInputValue("up", clockRate);
+            upDownOperator.setInputValue("down", tree);
+            upDownOperator.setInputValue("scaleFactor", 0.9);
+            upDownOperator.setInputValue("weight", BEASTContext.getOperatorWeight(tree.getInternalNodeCount()+1));
+            context.addExtraOperator(upDownOperator);
+        }
+    }
 }