towards fixing CompEvol/BeastFX#50

BEAST2-Dev · May 17, 2023 · 4f5b496 · 4f5b496
1 parent 5ceb4a5
commit 4f5b496
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Showing 3 changed files with 21 additions and 1 deletion.
diff --git a/fxtemplates/SNAPP.xml b/fxtemplates/SNAPP.xml
@@ -138,6 +138,7 @@
 	          <parameter name='kappa' id='kappa' value='1.0' lower='0.0' estimate='false'/>
 		      <tree spec='beast.base.evolution.tree.ClusterTree' id='Tree.$(n)' nodetype='snap.NodeData' clusterType='upgma' clock.rate="1.0">
 		            <input name='taxa' idref='snap.$(n)'/>
+                    <taxonset spec="TaxonSet" alignment="@snap.$(n)"/>
 		      </tree>
 		      <parameter name='coalescenceRate' id='coalescenceRate' value='10'/>
         </distribution>

diff --git a/src/snap/Data.java b/src/snap/Data.java
@@ -34,6 +34,7 @@
 
 import beast.base.core.Description;
 import beast.base.core.Input;
+import beast.base.core.ProgramStatus;
 import beast.base.core.Input.Validate;
 import beast.base.evolution.alignment.Sequence;
 import beast.base.evolution.alignment.Taxon;
@@ -42,7 +43,7 @@
 import beast.base.evolution.datatype.DataType;
 import beast.base.evolution.datatype.IntegerData;
 import beast.base.evolution.datatype.Nucleotide;
-import beast.base.evolution.datatype.StandardData;
+import beast.base.evolution.datatype.StandardData;import beastfx.app.beauti.Beauti;
 
 
 
@@ -172,6 +173,22 @@ public void initAndValidate() {
 		}
 	} // initAndValidate
 
+	@Override
+	public List<String> getTaxaNames() {
+		if (ProgramStatus.name.equals("BEAUti")) {
+			if (taxaNames == null) {
+				taxaNames = new ArrayList<>();
+			} else {
+				taxaNames.clear();
+			}
+			for (Taxon s : m_taxonsets.get()) {
+				taxaNames.add(s.getID());
+			}
+		}
+		return super.getTaxaNames();
+	}
+
+
 	private void determineTotalCount(Sequence sequence, DataType dataType) {
 		if (sequence.totalCountInput.get() > 0) {
 			return;

diff --git a/src/snap/app/inputeditor/DataInputEditor.java b/src/snap/app/inputeditor/DataInputEditor.java
@@ -288,6 +288,8 @@ private HBox createButtonBox() {
                 taxonMapping.get(rows.get(i)).setTaxon2(taxon);
             }
 			modelToTaxonset();
+			// refresh
+			taxonSetToModel();
 		});
 
 		Button guessButton = new Button("Guess");