Merge branch 'features/r2_11_2_alphafold/JAL-629' into features/JAL-3858_PAEsInProjects

[jalview.git] / src / jalview / bin / Jalview.java

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index e259cc2..a988a09 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -49,6 +49,7 @@ import javax.swing.JOptionPane;
 import javax.swing.SwingUtilities;
 import javax.swing.UIManager;
 import javax.swing.UIManager.LookAndFeelInfo;
+import javax.swing.UnsupportedLookAndFeelException;
 
 import com.formdev.flatlaf.FlatLightLaf;
 import com.formdev.flatlaf.util.SystemInfo;
@@ -62,6 +63,8 @@ import jalview.ext.so.SequenceOntology;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.gui.PromptUserConfig;
+import jalview.gui.QuitHandler;
+import jalview.gui.QuitHandler.QResponse;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.BioJsHTMLOutput;
 import jalview.io.DataSourceType;
@@ -272,6 +275,28 @@ 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)
+          {
+            // Got to here by a SIGTERM signal.
+            // Note we will not actually cancel the quit from here -- it's too
+            // late -- but we can wait for saving files.
+            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
@@ -280,6 +305,7 @@ 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)
     {
@@ -301,6 +327,7 @@ public class Jalview
 
     // old ArgsParser
     ArgsParser aparser = new ArgsParser(args);
+
     boolean headless = false;
 
     try
@@ -315,7 +342,8 @@ public class Jalview
     }
 
     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(
@@ -587,8 +615,11 @@ 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
@@ -602,6 +633,7 @@ 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)
@@ -861,6 +893,7 @@ public class Jalview
         }
       }
     }
+
     AlignFrame startUpAlframe = null;
     // We'll only open the default file if the desktop is visible.
     // And the user
@@ -1030,7 +1063,7 @@ public class Jalview
       setSystemLookAndFeel();
       if (Platform.isLinux())
       {
-        setMetalLookAndFeel();
+        setLinuxLookAndFeel();
       }
       if (Platform.isMac())
       {
@@ -1121,8 +1154,29 @@ public class Jalview
 
   private static boolean setFlatLookAndFeel()
   {
-    boolean set = setSpecificLookAndFeel("flatlaf light",
-            "com.formdev.flatlaf.FlatLightLaf", false);
+    boolean set = false;
+    if (Platform.isMac()) {
+      try
+      {
+        UIManager.setLookAndFeel("com.formdev.flatlaf.themes.FlatMacLightLaf");
+        set = true;
+      } catch (ClassNotFoundException | InstantiationException
+              | IllegalAccessException | UnsupportedLookAndFeelException e)
+      {
+        Console.debug("Exception loading FlatMacLightLaf", e);
+      }
+    }
+    if (!set) {
+      try
+      {
+        UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
+        set = true;
+      } catch (ClassNotFoundException | InstantiationException
+              | IllegalAccessException | UnsupportedLookAndFeelException e)
+      {
+        Console.debug("Exception loading FlatLightLaf", e);
+      }
+    }
     if (set)
     {
       if (Platform.isMac())
@@ -1155,6 +1209,8 @@ public class Jalview
       UIManager.put("TabbedPane.tabWidthMode", "compact");
       UIManager.put("TabbedPane.selectedBackground", Color.white);
     }
+
+    Desktop.setLiveDragMode(Cache.getDefault("FLAT_LIVE_DRAG_MODE", true));
     return set;
   }
 
@@ -1191,6 +1247,18 @@ public class Jalview
     return set;
   }
 
+  private static boolean setLinuxLookAndFeel()
+  {
+    boolean set = false;
+    set = setFlatLookAndFeel();
+    if (!set)
+      set = setMetalLookAndFeel();
+    // avoid GtkLookAndFeel -- not good results especially on HiDPI
+    if (!set)
+      set = setNimbusLookAndFeel();
+    return set;
+  }
+
   private static void showUsage()
   {
     System.out.println(
@@ -1401,19 +1469,12 @@ 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()