From 547b42d4ee89ab842eed663907be11f4b3ba6b05 Mon Sep 17 00:00:00 2001
From: Remco Bouckaert <higgs.ml@gmail.com>
Date: Wed, 12 Jun 2024 13:24:55 +1200
Subject: [PATCH] add fix for alignments correctly saving as XML in BEAUti
 #1150

---
 src/beast/base/evolution/alignment/Alignment.java | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/src/beast/base/evolution/alignment/Alignment.java b/src/beast/base/evolution/alignment/Alignment.java
index af94cbb7..3acd0b65 100644
--- a/src/beast/base/evolution/alignment/Alignment.java
+++ b/src/beast/base/evolution/alignment/Alignment.java
@@ -279,6 +279,20 @@ public void initAndValidate() {
         Log.info.println(toString(false));
     }
 
+    
+    /** hack to suppress empty TaxonSets in XML output
+     * this was no problem when Alignments was a CalculationNode,
+     * but became an issue changing it to a StateNode  
+     * TODO: fix this**/
+    @Override
+    public List<Input<?>> listInputs() {
+    	List<Input<?>> inputs = super.listInputs();
+        if (taxonSetInput.get() != null && taxonSetInput.get().getTaxonCount() == 0) {
+        	inputs.remove(taxonSetInput);
+        }
+        return inputs;
+    }
+    
     /**
      * Initializes data types using
      * {@link PackageManager#find(Class, String[]) PackageManager.find}