From 3bf2b5ea57b1d77d6e2e7adc11a50387e5376dc0 Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Thu, 15 Jun 2023 13:15:26 +0100
Subject: [PATCH] JAL-4206 Use All Known Alignment Files as default until a
 file is loaded

---
 src/jalview/gui/Desktop.java           |   11 +++++++----
 src/jalview/io/FileLoader.java         |    9 +++++++++
 src/jalview/io/JalviewFileChooser.java |    5 +++++
 3 files changed, 21 insertions(+), 4 deletions(-)

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 2dfe820..6fd70a9 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -569,15 +569,16 @@ public class Desktop extends jalview.jbgui.GDesktop
       }
 
       // Thread off a new instance of the file chooser - this reduces the time
-      // it
-      // takes to open it later on.
+      // it takes to open it later on.
       new Thread(new Runnable()
       {
         @Override
         public void run()
         {
           jalview.bin.Console.debug("Filechooser init thread started.");
-          String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
+          String fileFormat = FileLoader.getUseDefaultFileFormat()
+                  ? Cache.getProperty("DEFAULT_FILE_FORMAT")
+                  : null;
           JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"),
                   fileFormat);
           jalview.bin.Console.debug("Filechooser init thread finished.");
@@ -1235,7 +1236,9 @@ public class Desktop extends jalview.jbgui.GDesktop
   @Override
   public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
   {
-    String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
+    String fileFormat = FileLoader.getUseDefaultFileFormat()
+            ? Cache.getProperty("DEFAULT_FILE_FORMAT")
+            : null;
     JalviewFileChooser chooser = JalviewFileChooser.forRead(
             Cache.getProperty("LAST_DIRECTORY"), fileFormat,
             BackupFiles.getEnabled());
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index a2585b3..9ede0f5 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -74,6 +74,8 @@ public class FileLoader implements Runnable
 
   private File selectedFile;
 
+  private static boolean useDefaultFileFormat = false;
+
   /**
    * default constructor always raised errors in GUI dialog boxes
    */
@@ -642,6 +644,8 @@ public class FileLoader implements Runnable
     }
 
     this.setShouldBeSaved();
+    // after first file loaded we revert to assuming a default file format
+    useDefaultFileFormat = true;
   }
 
   /**
@@ -684,4 +688,9 @@ public class FileLoader implements Runnable
             QuitHandler.Message.UNSAVED_ALIGNMENTS);
   }
 
+  public static boolean getUseDefaultFileFormat()
+  {
+    return useDefaultFileFormat;
+  }
+
 }
diff --git a/src/jalview/io/JalviewFileChooser.java b/src/jalview/io/JalviewFileChooser.java
index 1a4326c..b01536e 100755
--- a/src/jalview/io/JalviewFileChooser.java
+++ b/src/jalview/io/JalviewFileChooser.java
@@ -286,6 +286,11 @@ public class JalviewFileChooser extends JFileChooser
     alljvf.setExtensionListInDescription(false);
     addChoosableFileFilter(alljvf);
 
+    if (selected == null)
+    {
+      chosen = alljvf;
+    }
+
     for (String[] format : formats)
     {
       JalviewFileFilter jvf = new JalviewFileFilter(format[0], format[1]);
-- 
1.7.10.2