clean code

beast-dev · Oct 7, 2023 · 52331dc · 52331dc
1 parent 8e07963
commit 52331dc
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Showing 3 changed files with 4 additions and 14 deletions.
diff --git a/src/dr/evomodel/substmodel/DifferentiableSubstitutionModelUtil.java b/src/dr/evomodel/substmodel/DifferentiableSubstitutionModelUtil.java
@@ -108,11 +108,9 @@ static double[] getAffineDifferentialMassMatrix(double time,
         multiply(tmp, oneMinusQPlusQ, differentials, 1.0, stateCount);
         multiply(correction, tmp, qQPlus, 1.0, stateCount);
 
-//        System.err.println("corr: " + new WrappedVector.Raw(correction));
-
-            for (int i = 0; i < differentials.length; ++i) {
-                differentials[i] -= correction[i];
-            }
+        for (int i = 0; i < differentials.length; ++i) {
+            differentials[i] -= correction[i];
+        }
 
         return differentials;
     }

diff --git a/src/dr/evomodel/substmodel/DifferentialMassProvider.java b/src/dr/evomodel/substmodel/DifferentialMassProvider.java
@@ -72,9 +72,6 @@ public double[] dispatch(double time,
                                      DifferentiableSubstitutionModel model,
                                      WrappedMatrix infinitesimalDifferentialMatrix) {
 
-                double[] q = new double[16];
-                model.getInfinitesimalMatrix(q);
-
                 return DifferentiableSubstitutionModelUtil.getAffineDifferentialMassMatrix(
                         time, infinitesimalDifferentialMatrix, model.getEigenDecomposition());
             }

diff --git a/src/dr/evomodel/treedatalikelihood/discrete/HomogeneousSubstitutionParameterGradient.java b/src/dr/evomodel/treedatalikelihood/discrete/HomogeneousSubstitutionParameterGradient.java
@@ -1,7 +1,7 @@
 /*
  * HomogeneousSubstitutionParameterGradient.java
  *
- * Copyright (c) 2002-2017 Alexei Drummond, Andrew Rambaut and Marc Suchard
+ * Copyright (c) 2002-2023 Alexei Drummond, Andrew Rambaut and Marc Suchard
  *
  * This file is part of BEAST.
  * See the NOTICE file distributed with this work for additional
@@ -55,11 +55,6 @@ public class HomogeneousSubstitutionParameterGradient implements GradientWrtPara
     private final TreeDataLikelihood treeDataLikelihood;
     private final TreeTrait treeTraitProvider;
     private final Tree tree;
-
-//    private final Mode mode = Mode.EXACT;
-//    private final Mode mode = Mode.FIRST_ORDER;
-//    private final Mode mode = Mode.AFFINE;
-
     private final Mode mode;
 
     public HomogeneousSubstitutionParameterGradient(String traitName,