X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=3d3e99f63e36932397444462666b07492bcf87fb;hb=072176426bbe5af5d6588b3a6eb6d5969fe1b01e;hp=d1056bf42f10c30228b746512c49463c406499cc;hpb=53fe06e7ae7a8c00ec902413391cea15362bdbf2;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index d1056bf..3d3e99f 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -73,6 +73,8 @@ import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
 import jalview.io.NewickFile;
 import jalview.io.gff.SequenceOntologyFactory;
+import jalview.jbgui.QuitHandler;
+import jalview.jbgui.QuitHandler.QResponse;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.util.ChannelProperties;
@@ -271,6 +273,25 @@ public class Jalview
     if (!Platform.isJS())
     {
       System.setSecurityManager(null);
+
+      Runtime.getRuntime().addShutdownHook(new Thread()
+      {
+        public void run()
+        {
+          Console.debug("Running shutdown hook");
+          if (QuitHandler.gotQuitResponse() == QResponse.CANCEL_QUIT)
+          {
+            Console.debug("Checking for saving files");
+            QuitHandler.getQuitResponse(false);
+          }
+          else
+          {
+            Console.debug("Nothing more to do");
+          }
+          Console.debug("Exiting, bye!");
+          // shutdownHook cannot be cancelled, JVM will now halt
+        }
+      });
     }
 
     System.out
@@ -279,6 +300,7 @@ public class Jalview
     System.out.println(System.getProperty("os.arch") + " "
             + System.getProperty("os.name") + " "
             + System.getProperty("os.version"));
+
     String val = System.getProperty("sys.install4jVersion");
     if (val != null)
     {
@@ -299,10 +321,12 @@ public class Jalview
     Cache.loadBuildProperties(true);
 
     ArgsParser aparser = new ArgsParser(args);
+
     boolean headless = false;
 
     String usrPropsFile = aparser.getValue("props");
-    Cache.loadProperties(usrPropsFile); // must do this before
+    Cache.loadProperties(usrPropsFile); // must do this
+                                        // before
     if (usrPropsFile != null)
     {
       System.out.println(
@@ -380,7 +404,9 @@ public class Jalview
     try
     {
       Console.initLogger();
-    } catch (NoClassDefFoundError error)
+    } catch (
+
+    NoClassDefFoundError error)
     {
       error.printStackTrace();
       System.out.println("\nEssential logging libraries not found."
@@ -555,8 +581,11 @@ public class Jalview
     }
 
     String file = null, data = null;
+
     FileFormatI format = null;
+
     DataSourceType protocol = null;
+
     FileLoader fileLoader = new FileLoader(!headless);
 
     String groovyscript = null; // script to execute after all loading is
@@ -570,6 +599,7 @@ public class Jalview
       System.out.println("No files to open!");
       System.exit(1);
     }
+
     long progress = -1;
     // Finally, deal with the remaining input data.
     if (file != null)
@@ -829,6 +859,7 @@ public class Jalview
         }
       }
     }
+
     AlignFrame startUpAlframe = null;
     // We'll only open the default file if the desktop is visible.
     // And the user
@@ -1365,19 +1396,12 @@ public class Jalview
   }
 
   /**
-   * Quit method delegates to Desktop.quit - unless running in headless mode
-   * when it just ends the JVM
+   * jalview.bin.Jalview.quit() will just run the non-GUI shutdownHook and exit
    */
   public void quit()
   {
-    if (desktop != null)
-    {
-      desktop.quit();
-    }
-    else
-    {
-      System.exit(0);
-    }
+    // System.exit will run the shutdownHook first
+    System.exit(0);
   }
 
   public static AlignFrame getCurrentAlignFrame()