From 58735c979dbb573eb12d57e33ef7d6e3f3a82c8e Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Wed, 11 Oct 2023 12:12:28 +0100
Subject: [PATCH] JAL-3772 Preference to NOT prompt to save remotely loaded
 alignments

---
 src/jalview/io/DataSourceType.java |    5 +++++
 src/jalview/io/FileLoader.java     |   23 +++++++++++++++++------
 2 files changed, 22 insertions(+), 6 deletions(-)

diff --git a/src/jalview/io/DataSourceType.java b/src/jalview/io/DataSourceType.java
index 6d00a7d..c983dfe 100644
--- a/src/jalview/io/DataSourceType.java
+++ b/src/jalview/io/DataSourceType.java
@@ -28,4 +28,9 @@ public enum DataSourceType
   {
     return this != FILE;
   }
+
+  public boolean isUrl()
+  {
+    return this == URL || this == RELATIVE_URL;
+  }
 }
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index dc7adac..de88ce9 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -361,8 +361,9 @@ public class FileLoader implements Runnable
           // We read the data anyway - it might make sense.
         }
         // BH 2018 switch to File object here instead of filename
-        alignFrame = new Jalview2XML(raiseGUI && !Jalview.isBatchMode()).loadJalviewAlign(
-                selectedFile == null ? file : selectedFile);
+        alignFrame = new Jalview2XML(raiseGUI && !Jalview.isBatchMode())
+                .loadJalviewAlign(
+                        selectedFile == null ? file : selectedFile);
       }
       else
       {
@@ -563,7 +564,8 @@ public class FileLoader implements Runnable
 
     } catch (Exception er)
     {
-      jalview.bin.Console.errPrintln("Exception whilst opening file '" + file);
+      jalview.bin.Console
+              .errPrintln("Exception whilst opening file '" + file);
       er.printStackTrace();
       if (raiseGUI && !Jalview.isBatchMode())
       {
@@ -603,7 +605,8 @@ public class FileLoader implements Runnable
           }
         });
       }
-      jalview.bin.Console.errPrintln("Out of memory loading file " + file + "!!");
+      jalview.bin.Console
+              .errPrintln("Out of memory loading file " + file + "!!");
 
     }
     loadtime += System.currentTimeMillis();
@@ -684,10 +687,18 @@ public class FileLoader implements Runnable
     AlignViewport avp = af.getViewport();
     if (avp == null)
       return;
-    avp.setSavedUpToDate(!protocol.isDynamic(),
-            QuitHandler.Message.UNSAVED_ALIGNMENTS);
+    boolean upToDate = !protocol.isDynamic();
+    if (protocol.isUrl()
+            && Cache.getDefault(PROMPT_SAVE_UNCHANGED_URL_ALIGNMENTS, true))
+    {
+      upToDate = true;
+    }
+    avp.setSavedUpToDate(upToDate,
+            upToDate ? null : QuitHandler.Message.UNSAVED_ALIGNMENTS);
   }
 
+  public static final String PROMPT_SAVE_UNCHANGED_URL_ALIGNMENTS = "PROMPT_SAVE_UNCHANGED_URL_ALIGNMENTS";
+
   public static boolean getUseDefaultFileFormat()
   {
     return useDefaultFileFormat;
-- 
1.7.10.2