From ddc55cb591947f7e90c01a1362003893a5a22da4 Mon Sep 17 00:00:00 2001
From: rbouckaert <higgs.ml@gmail.com>
Date: Mon, 8 Jan 2024 13:47:19 +1300
Subject: [PATCH] robustify for drag/dropping alignments. fixes #72

---
 .../inputeditor/AlignmentListInputEditor.java   | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

diff --git a/src/beastfx/app/inputeditor/AlignmentListInputEditor.java b/src/beastfx/app/inputeditor/AlignmentListInputEditor.java
index 81f49e7..3c6a8ef 100644
--- a/src/beastfx/app/inputeditor/AlignmentListInputEditor.java
+++ b/src/beastfx/app/inputeditor/AlignmentListInputEditor.java
@@ -1240,7 +1240,22 @@ private void addItem(File[] fileArray) {
 						break;
 					}
 				}
-				alignments.add(likelihood.dataInput.get());
+				if (likelihood != null) {
+					alignments.add(likelihood.dataInput.get());
+				} else {
+					// alignment maybe wrapped in a FilteredAlignment
+					for (BEASTInterface o2 : b.getOutputs()) {
+						if (o2 instanceof FilteredAlignment) {
+							for (BEASTInterface o : ((FilteredAlignment) o2).getOutputs()) {
+								if (o instanceof GenericTreeLikelihood) {
+									likelihood = (GenericTreeLikelihood) o;
+									alignments.add(likelihood.dataInput.get());
+									break;
+								}
+							}
+						}
+					}
+				}
 			}
 			partitionCount = alignments.size();
 			tableData = null;