From bd6b037b9baac08b6fc10f536060525dfe9eceab Mon Sep 17 00:00:00 2001
From: Walter <walterxie@users.noreply.github.com>
Date: Thu, 18 Jan 2024 15:54:18 +1300
Subject: [PATCH] add comment

---
 lphy-studio/src/main/java/lphystudio/app/LinguaPhyloStudio.java | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/lphy-studio/src/main/java/lphystudio/app/LinguaPhyloStudio.java b/lphy-studio/src/main/java/lphystudio/app/LinguaPhyloStudio.java
index 5e05a804..78cf94ea 100644
--- a/lphy-studio/src/main/java/lphystudio/app/LinguaPhyloStudio.java
+++ b/lphy-studio/src/main/java/lphystudio/app/LinguaPhyloStudio.java
@@ -294,6 +294,8 @@ private void buildFileMenu(JMenu fileMenu) {
                     // retrieve all simulated alignments stored in the map
                     Map<Integer, List<Value>> valuesMap = panel.getValuesAllRepsMap();
 
+                    // TODO: Cannot specify to call which formatter in the core, as Nexus formatter is in the base,
+                    // so call ValueFileLoggerListener instead, however the alignment will be simulated again.
                     ValueFileLoggerListener fileLoggerListener = new ValueFileLoggerListener();
                     // set alignment directory
                     fileLoggerListener.setOutputDir(selectedDir.getAbsolutePath());