JAL-4305 Isolate and unify the Jalview object from all the gubbins in jalview.bin...

[jalview.git] / src / jalview / gui / Desktop.java

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index e785431..b1f9000 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -113,6 +113,9 @@ import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
 import jalview.bin.Jalview.ExitCode;
+import jalview.bin.argparser.Arg;
+import jalview.bin.groovy.JalviewObject;
+import jalview.bin.groovy.JalviewObjectI;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.Sequence;
@@ -157,7 +160,7 @@ import jalview.ws.utils.UrlDownloadClient;
  */
 public class Desktop extends jalview.jbgui.GDesktop
         implements DropTargetListener, ClipboardOwner, IProgressIndicator,
-        jalview.api.StructureSelectionManagerProvider
+        jalview.api.StructureSelectionManagerProvider, JalviewObjectI
 {
   private static final String CITATION;
   static
@@ -498,7 +501,28 @@ public class Desktop extends jalview.jbgui.GDesktop
 
     boolean selmemusage = Cache.getDefault("SHOW_MEMUSAGE", false);
 
-    boolean showjconsole = Cache.getDefault("SHOW_JAVA_CONSOLE", false);
+    boolean showjconsole = Cache.getArgCacheDefault(Arg.JAVACONSOLE,
+            "SHOW_JAVA_CONSOLE", false);
+
+    // start dialogue queue for single dialogues
+    startDialogQueue();
+
+    if (!Platform.isJS())
+    /**
+     * Java only
+     * 
+     * @j2sIgnore
+     */
+    {
+      Desktop.instance.acquireDialogQueue();
+
+      jconsole = new Console(this);
+      jconsole.setHeader(Cache.getVersionDetailsForConsole());
+      showConsole(showjconsole);
+
+      Desktop.instance.releaseDialogQueue();
+    }
+
     desktop = new MyDesktopPane(selmemusage);
 
     showMemusage.setSelected(selmemusage);
@@ -545,9 +569,6 @@ public class Desktop extends jalview.jbgui.GDesktop
       setBounds(xPos, yPos, 900, 650);
     }
 
-    // start dialogue queue for single dialogues
-    startDialogQueue();
-
     if (!Platform.isJS())
     /**
      * Java only
@@ -555,10 +576,6 @@ public class Desktop extends jalview.jbgui.GDesktop
      * @j2sIgnore
      */
     {
-      jconsole = new Console(this, showjconsole);
-      jconsole.setHeader(Cache.getVersionDetailsForConsole());
-      showConsole(showjconsole);
-
       showNews.setVisible(false);
 
       experimentalFeatures.setSelected(showExperimental());
@@ -787,17 +804,17 @@ public class Desktop extends jalview.jbgui.GDesktop
         iw = (int) (iw * sw);
         iy = (int) (iy * sh);
         ih = (int) (ih * sh);
-        while (ix >= screenSize.width)
+        if (ix >= screenSize.width)
         {
           jalview.bin.Console.debug(
                   "Window geometry location recall error: shifting horizontal to within screenbounds.");
-          ix -= screenSize.width;
+          ix = ix % screenSize.width;
         }
-        while (iy >= screenSize.height)
+        if (iy >= screenSize.height)
         {
           jalview.bin.Console.debug(
                   "Window geometry location recall error: shifting vertical to within screenbounds.");
-          iy -= screenSize.height;
+          iy = iy % screenSize.height;
         }
         jalview.bin.Console.debug(
                 "Got last known dimensions for " + windowName + ": x:" + ix
@@ -1041,7 +1058,7 @@ public class Desktop extends jalview.jbgui.GDesktop
         {
           if (itf instanceof AlignFrame)
           {
-            Jalview.setCurrentAlignFrame((AlignFrame) itf);
+            Jalview.getInstance().setCurrentAlignFrame((AlignFrame) itf);
           }
           itf.requestFocus();
         }
@@ -1664,7 +1681,7 @@ public class Desktop extends jalview.jbgui.GDesktop
       {
       }
     }
-    Jalview.setCurrentAlignFrame(null);
+    Jalview.getInstance().setCurrentAlignFrame(null);
     jalview.bin.Console.info("ALL CLOSED");
 
     /*
@@ -2123,7 +2140,7 @@ public class Desktop extends jalview.jbgui.GDesktop
       return null;
     }
     List<AlignmentPanel> aps = new ArrayList<>();
-    AlignFrame[] frames = getAlignFrames();
+    AlignFrame[] frames = Desktop.getDesktopAlignFrames();
     if (frames == null)
     {
       return null;
@@ -2160,7 +2177,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     List<AlignmentViewport> viewp = new ArrayList<>();
     if (desktop != null)
     {
-      AlignFrame[] frames = Desktop.getAlignFrames();
+      AlignFrame[] frames = Desktop.getDesktopAlignFrames();
 
       for (AlignFrame afr : frames)
       {
@@ -2521,12 +2538,12 @@ public class Desktop extends jalview.jbgui.GDesktop
    * 
    * @return an array of AlignFrame, or null if none found
    */
-  public static AlignFrame[] getAlignFrames()
+  @Override
+  public AlignFrame[] getAlignFrames()
   {
-    if (Jalview.isHeadlessMode())
+    if (desktop == null)
     {
-      // Desktop.desktop is null in headless mode
-      return new AlignFrame[] { Jalview.currentAlignFrame };
+      return null;
     }
 
     JInternalFrame[] frames = Desktop.desktop.getAllFrames();
@@ -2568,6 +2585,25 @@ public class Desktop extends jalview.jbgui.GDesktop
   }
 
   /**
+   * static version
+   */
+  public static AlignFrame[] getDesktopAlignFrames()
+  {
+    if (Jalview.isHeadlessMode())
+    {
+      // Desktop.desktop is null in headless mode
+      return Jalview.getInstance().getAlignFrames();
+    }
+
+    if (instance != null && desktop != null)
+    {
+      return instance.getAlignFrames();
+    }
+
+    return null;
+  }
+
+  /**
    * Returns an array of any AppJmol frames in the Desktop (or null if none).
    * 
    * @return
@@ -2609,7 +2645,7 @@ public class Desktop extends jalview.jbgui.GDesktop
       openGroovyConsole();
     } catch (Exception ex)
     {
-      jalview.bin.Console.error("Groovy Shell Creation failed.", ex);
+      jalview.bin.Console.error("Groovy Console creation failed.", ex);
       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
 
               MessageManager.getString("label.couldnt_create_groovy_shell"),
@@ -2625,8 +2661,10 @@ public class Desktop extends jalview.jbgui.GDesktop
   {
     if (groovyConsole == null)
     {
-      groovyConsole = new groovy.ui.Console();
-      groovyConsole.setVariable("Jalview", this);
+      JalviewObjectI j = new JalviewObject(this);
+      groovyConsole = new groovy.console.ui.Console();
+      groovyConsole.setVariable("Jalview", j);
+      groovyConsole.setVariable("currentAlFrame", getCurrentAlignFrame());
       groovyConsole.run();
 
       /*
@@ -2699,7 +2737,7 @@ public class Desktop extends jalview.jbgui.GDesktop
      */
     groovyShell.setEnabled(!enabled);
 
-    AlignFrame[] alignFrames = getAlignFrames();
+    AlignFrame[] alignFrames = getDesktopAlignFrames();
     if (alignFrames != null)
     {
       for (AlignFrame af : alignFrames)
@@ -3108,7 +3146,7 @@ public class Desktop extends jalview.jbgui.GDesktop
    */
   private Semaphore block = new Semaphore(0);
 
-  private static groovy.ui.Console groovyConsole;
+  private static groovy.console.ui.Console groovyConsole;
 
   /**
    * add another dialog thread to the queue
@@ -3370,7 +3408,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     myTopFrame.setDisplayedView(myTopFrame.alignPanel);
   }
 
-  public static groovy.ui.Console getGroovyConsole()
+  public static groovy.console.ui.Console getGroovyConsole()
   {
     return groovyConsole;
   }
@@ -3747,13 +3785,21 @@ public class Desktop extends jalview.jbgui.GDesktop
   public void nonBlockingDialog(String title, String message, String button,
           int type, boolean scrollable, boolean modal)
   {
-    nonBlockingDialog(32, 2, title, message, null, button, type, scrollable,
-            false, modal);
+    nonBlockingDialog(title, message, null, button, type, scrollable, false,
+            modal, -1);
+  }
+
+  public void nonBlockingDialog(String title, String message,
+          String boxtext, String button, int type, boolean scrollable,
+          boolean html, boolean modal, int timeout)
+  {
+    nonBlockingDialog(32, 2, title, message, boxtext, button, type,
+            scrollable, html, modal, timeout);
   }
 
   public void nonBlockingDialog(int width, int height, String title,
           String message, String boxtext, String button, int type,
-          boolean scrollable, boolean html, boolean modal)
+          boolean scrollable, boolean html, boolean modal, int timeout)
   {
     if (type < 0)
     {
@@ -3815,9 +3861,16 @@ public class Desktop extends jalview.jbgui.GDesktop
 
     jvp.setResponseHandler(JOptionPane.YES_OPTION, () -> {
     });
+    jvp.setTimeout(timeout);
+    JButton jb = new JButton(button);
     jvp.showDialogOnTopAsync(this, jp, title, JOptionPane.YES_OPTION, type,
             null, new Object[]
-            { button }, button, modal, null, false);
+            { button }, button, modal, new JButton[] { jb }, false);
   }
 
+  @Override
+  public AlignFrame getCurrentAlignFrame()
+  {
+    return Jalview.getInstance().getCurrentAlignFrame();
+  }
 }