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resolve clone source/target against the list their indices came from #172

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Merged
rbouckaert merged 1 commit into from
Sep 27, 2026
Merged

resolve clone source/target against the list their indices came from #172

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22 changes: 12 additions & 10 deletions beast-fx/src/main/java/beastfx/app/inputeditor/BeautiPanel.java
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,6 @@
import beast.base.evolution.branchratemodel.BranchRateModel;
import beast.base.evolution.sitemodel.SiteModelInterface;
import beast.base.evolution.tree.TreeInterface;
import beast.base.inference.CompoundDistribution;
import beast.base.parser.PartitionContext;
import beast.base.spec.evolution.likelihood.GenericTreeLikelihood;
import beast.base.spec.evolution.sitemodel.SiteModel;
Expand Down Expand Up @@ -410,10 +409,8 @@ public void cloneFrom(String sourceID, String targetID) {
throw new RuntimeException("Programmer error: sourceID and targetID should be in list");
}

CompoundDistribution likelihoods = (CompoundDistribution) doc.pluginmap.get("likelihood");

GenericTreeLikelihood likelihoodSource = (GenericTreeLikelihood) likelihoods.pDistributions.get().get(source);
GenericTreeLikelihood likelihood = (GenericTreeLikelihood) likelihoods.pDistributions.get().get(target);
GenericTreeLikelihood likelihoodSource = (GenericTreeLikelihood) list.get(source);
GenericTreeLikelihood likelihood = (GenericTreeLikelihood) list.get(target);
PartitionContext oldContext = doc.getContextFor(likelihoodSource);
PartitionContext newContext = doc.getContextFor(likelihood);
// this ensures the config.sync does not set any input value
Expand Down Expand Up @@ -471,11 +468,16 @@ public void cloneFrom(String sourceID, String targetID) {
TreeInterface tree = null;
TreeInterface treeSource = likelihoodSource.treeInput.get();
try {
tree = (TreeInterface) BeautiDoc.deepCopyPlugin((BEASTInterface) treeSource, likelihood,
doc.getMCMC(), oldContext, newContext, doc, null);
} catch (Exception e) {
Alert.showMessageDialog(((Pane)this.getContent()), "Could not clone " + sourceID + " to " + targetID + " " + e.getMessage());
return;
tree = (TreeInterface) BeautiDoc.deepCopyPlugin((BEASTInterface) treeSource, likelihood,
doc.getMCMC(), oldContext, newContext, doc, null);
} catch (Exception e) {
Alert.showMessageDialog(((Pane)this.getContent()), "Could not clone " + sourceID + " to " + targetID + " " + e.getMessage());
return;
}
// deepCopyPlugin returns null instead of throwing when nothing was copied
if (tree == null) {
Alert.showMessageDialog(((Pane)this.getContent()), "Could not clone " + sourceID + " to " + targetID + ": no copy of " + treeSource.getID() + " was made");
return;
}
// sanity check: make sure taxon sets are compatible
Taxon.assertSameTaxa(tree.getID(), tree.getTaxonset().getTaxaNames(),
Expand Down
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