clean code

beast-dev · Dec 9, 2023 · f3b481c · f3b481c
1 parent c8b32fa
commit f3b481c
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Showing 4 changed files with 18 additions and 52 deletions.
diff --git a/src/dr/evomodel/coalescent/basta/BastaLikelihood.java b/src/dr/evomodel/coalescent/basta/BastaLikelihood.java
@@ -281,7 +281,7 @@ private double calculateLogLikelihood() {
         final List<TransitionMatrixOperation> matrixOperations =
                 treeTraversalDelegate.getMatrixOperations();
         final List<Integer> intervalStarts = treeTraversalDelegate.getIntervalStarts();
-        
+
         if (COUNT_TOTAL_OPERATIONS) {
             totalPropagationCount += branchOperations.size();
             totalMatrixUpdateCount += matrixOperations.size();

diff --git a/src/dr/evomodel/coalescent/basta/BastaLikelihoodDelegate.java b/src/dr/evomodel/coalescent/basta/BastaLikelihoodDelegate.java
@@ -101,15 +101,14 @@ public AbstractBastaLikelihoodDelegate(String name,
         }
 
         private int getMaxNumberOfCoalescentIntervals(Tree tree) {
-//            BigFastTreeIntervals intervals = new BigFastTreeIntervals((TreeModel) tree); // TODO fix BFTI to take a Tree
-//            int zeroLengthSampling = 0;
-//            for (int i = 0; i < intervals.getIntervalCount(); ++i) {
-//                if (intervals.getIntervalType(i) == IntervalType.SAMPLE && intervals.getIntervalTime(i) == 0.0) {
-//                    ++zeroLengthSampling;
-//                }
-//            }
-//            return tree.getNodeCount() - zeroLengthSampling;
-            return tree.getNodeCount();
+            BigFastTreeIntervals intervals = new BigFastTreeIntervals((TreeModel) tree); // TODO fix BFTI to take a Tree
+            int zeroLengthSampling = 0;
+            for (int i = 0; i < intervals.getIntervalCount(); ++i) {
+                if (intervals.getIntervalType(i) == IntervalType.SAMPLE && intervals.getIntervalTime(i) == 0.0) {
+                    ++zeroLengthSampling;
+                }
+            }
+            return tree.getNodeCount() - zeroLengthSampling;
         }
 
         @Override
@@ -147,11 +146,9 @@ enum ParallelizationScheme {
             FULL
         }
 
-        abstract protected void clearAll();
-
-        abstract protected double computeBranchIntervalOperations(List<BranchIntervalOperation> branchIntervalOperations);
+        abstract protected void computeBranchIntervalOperations(List<BranchIntervalOperation> branchIntervalOperations);
 
-        abstract protected double computeTransitionProbabilityOperations(List<TransitionMatrixOperation> matrixOperations);
+        abstract protected void computeTransitionProbabilityOperations(List<TransitionMatrixOperation> matrixOperations);
 
         abstract protected double computeCoalescentIntervalReduction(List<Integer> intervalStarts,
                                                                      List<BranchIntervalOperation> branchIntervalOperations);
@@ -166,11 +163,9 @@ public double calculateLikelihood(List<BranchIntervalOperation> branchOperations
                 System.err.println("Tree = " + tree);
             }
 
-            double logLikelihood = computeTransitionProbabilityOperations(matrixOperation);
-            logLikelihood += computeBranchIntervalOperations(branchOperations);
-            logLikelihood += computeCoalescentIntervalReduction(intervalStarts, branchOperations);
-
-            return logLikelihood;
+            computeTransitionProbabilityOperations(matrixOperation);
+            computeBranchIntervalOperations(branchOperations);
+            return computeCoalescentIntervalReduction(intervalStarts, branchOperations);
         }
 
         @Override

diff --git a/src/dr/evomodel/coalescent/basta/GenericBastaLikelihoodDelegate.java b/src/dr/evomodel/coalescent/basta/GenericBastaLikelihoodDelegate.java
@@ -12,8 +12,6 @@
  */
 public class GenericBastaLikelihoodDelegate extends BastaLikelihoodDelegate.AbstractBastaLikelihoodDelegate {
 
-    private static final boolean PRINT_COMMANDS = true;
-
     private final double[] partials;
     private final double[] matrices;
     private final double[] sizes;
@@ -48,20 +46,7 @@ public GenericBastaLikelihoodDelegate(String name,
     }
 
     @Override
-    protected void clearAll() {
-//        Arrays.fill(partials, tree.getExternalNodeCount() * stateCount, partials.length, 0.0);
-//        Arrays.fill(matrices, 0.0);
-//        Arrays.fill(sizes, 0.0);
-
-//        Arrays.fill(coalescent, 0.0);
-//        Arrays.fill(e, 0.0);
-//        Arrays.fill(f, 0.0);
-//        Arrays.fill(g, 0.0);
-//        Arrays.fill(h, 0.0);
-    }
-
-    @Override
-    protected double computeBranchIntervalOperations(List<BranchIntervalOperation> branchIntervalOperations) {
+    protected void computeBranchIntervalOperations(List<BranchIntervalOperation> branchIntervalOperations) {
 
         Arrays.fill(coalescent, 0.0);
 
@@ -81,12 +66,10 @@ protected double computeBranchIntervalOperations(List<BranchIntervalOperation> b
                         new WrappedVector.Raw(partials, operation.outputBuffer * stateCount, stateCount));
             }
         }
-
-        return 0.0;
     }
 
     @Override
-    protected double computeTransitionProbabilityOperations(List<TransitionMatrixOperation> matrixOperations) {
+    protected void computeTransitionProbabilityOperations(List<TransitionMatrixOperation> matrixOperations) {
 
         for (TransitionMatrixOperation operation : matrixOperations) { // TODO execute in parallel
             computeTransitionProbabilities(
@@ -101,8 +84,6 @@ protected double computeTransitionProbabilityOperations(List<TransitionMatrixOpe
                                 operation.outputBuffer * stateCount * stateCount, stateCount * stateCount));
             }
         }
-
-        return 0.0;
     }
 
     @Override
@@ -142,7 +123,6 @@ protected double computeCoalescentIntervalReduction(List<Integer> intervalStarts
             System.err.println("logL = " + logL + "\n");
         }
 
-//        return 0.0;
         return logL;
     }
 

diff --git a/src/dr/evomodel/coalescent/basta/NativeBastaLikelihoodDelegate.java b/src/dr/evomodel/coalescent/basta/NativeBastaLikelihoodDelegate.java
@@ -22,30 +22,21 @@ public NativeBastaLikelihoodDelegate(String name,
     }
 
     @Override
-    protected  void clearAll() {
-
-    }
-
-    @Override
-    protected double computeBranchIntervalOperations(List<BranchIntervalOperation> branchIntervalOperations) {
+    protected void computeBranchIntervalOperations(List<BranchIntervalOperation> branchIntervalOperations) {
         if (branchIntervalOperations != null) {
             for (BranchIntervalOperation operation : branchIntervalOperations) {
                 System.err.println(operation.toString());
             }
         }
-
-        return 0.0;
     }
 
     @Override
-    protected double computeTransitionProbabilityOperations(List<TransitionMatrixOperation> matrixOperations) {
+    protected void computeTransitionProbabilityOperations(List<TransitionMatrixOperation> matrixOperations) {
         if (matrixOperations != null) {
             for (TransitionMatrixOperation operation : matrixOperations) {
                 System.err.println(operation.toString());
             }
         }
-
-        return 0.0;
     }
 
     @Override