make MultiPartitionTreeLikelihood work with ThreadedTreeLikelihoods

BEAST2-Dev · Oct 16, 2024 · f431489 · f431489
1 parent 8b32cb9
commit f431489
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Showing 3 changed files with 16 additions and 5 deletions.
diff --git a/examples/testMultiParitionTreeLikelihood.xml b/examples/testMultiParitionTreeLikelihood.xml
@@ -104,7 +104,7 @@ spec="Alignment">
             </distribution>
             <distribution id="likelihood" spec="CompoundDistribution" useThreads="true">
 	          <distribution id="MultiPartitionTreeLikelihood0" spec="CompoundDistribution" useThreads="true">
-                <distribution id="treeLikelihood.firsthalf" spec="TreeLikelihood" data="@firsthalf" tree="@Tree.t:tree">
+                <distribution id="treeLikelihood.firsthalf" spec="ThreadedTreeLikelihood" data="@firsthalf" tree="@Tree.t:tree">
                     <siteModel id="SiteModel.s:firsthalf" spec="SiteModel" gammaCategoryCount="4" shape="@gammaShape.s:firsthalf">
                         <mutationRate idref="mutationRate.s:firsthalf"/>
                         <parameter id="proportionInvariant.s:firsthalf" spec="parameter.RealParameter" estimate="false" lower="0.0" name="proportionInvariant" upper="1.0">0.0</parameter>

diff --git a/src/beastlabs/evolution/likelihood/BeagleDebugger.java b/src/beastlabs/evolution/likelihood/BeagleDebugger.java
@@ -59,11 +59,19 @@ private void print(String str, double v) {
 	}
 
 	private void print(String str, int[] v) {
-		out.println(" /*" + str + " = */" + (v == null ? "null" : "new int[] {" + Arrays.toString(v).replaceAll("[\\[\\]]","") + "},"));
+		String values = v == null ? "null" : Arrays.toString(v).replaceAll("[\\[\\]]","");
+		if (values.length() > 100) {
+			values = values.substring(0, 100) + "...";
+		}
+		out.println(" /*" + str + " = */" + (v == null ? "null" : "new int[] {" + values + "},"));
 	}
 
 	private void print(String str, double[] v) {
-		out.println(" /*" + str + " = */" + (v == null ? "null" : "new double[] {" + Arrays.toString(v).replaceAll("[\\[\\]]","") + "},"));
+		String values = v == null ? "null" : Arrays.toString(v).replaceAll("[\\[\\]]","");
+		if (values.length() > 100) {
+			values = values.substring(0, 100) + "...";
+		}
+		out.println(" /*" + str + " = */" + (v == null ? "null" : "new double[] {" + values + "},"));
 	}
 
 	public void setCPUThreadCount(int threadCount) {

diff --git a/src/beastlabs/evolution/likelihood/MultiPartitionTreeLikelihood.java b/src/beastlabs/evolution/likelihood/MultiPartitionTreeLikelihood.java
@@ -40,6 +40,7 @@
 import beast.base.evolution.likelihood.BeagleTreeLikelihood.PartialsRescalingScheme;
 import beast.base.evolution.likelihood.TreeLikelihood.Scaling;
 import beast.base.evolution.likelihood.GenericTreeLikelihood;
+import beast.base.evolution.likelihood.ThreadedTreeLikelihood;
 import beast.base.evolution.sitemodel.SiteModel;
 import beast.base.evolution.substitutionmodel.EigenDecomposition;
 import beast.base.evolution.substitutionmodel.SubstitutionModel;
@@ -205,7 +206,7 @@ public void initAndValidate() {
         tree = tl0.treeInput.get();
         branchRateModel = tl0.branchRateModelInput.get();
         boolean useAmbiguities = (boolean) tl0.getInput("useAmbiguities").get();
-        boolean useTipLikelihoods = (boolean) tl0.getInput("useTipLikelihoods").get();
+        boolean useTipLikelihoods = tl0 instanceof ThreadedTreeLikelihood ? false : (boolean) tl0.getInput("useTipLikelihoods").get();
         rescalingScheme = getRescalingScheme(tl0);
 
         for (GenericTreeLikelihood tl : likelihoodsInput.get()) {
@@ -223,7 +224,9 @@ public void initAndValidate() {
         		throw new IllegalArgumentException("All partitions must use ambiguities, or ignore ambiguities, but found a difference between " +
         				tl.getID() + " and " + likelihoodsInput.get().get(0).getID());
         	}
-        	if (useTipLikelihoods != (boolean)tl.getInput("useTipLikelihoods").get()) {
+
+        	boolean b = tl instanceof ThreadedTreeLikelihood ? false : (boolean)tl.getInput("useTipLikelihoods").get();
+        	if (useTipLikelihoods != b) {
         		throw new IllegalArgumentException("All partitions must use tip likelihoods, or ignore tip likelihoods, but found a difference between " +
         				tl.getID() + " and " + likelihoodsInput.get().get(0).getID());
         	}