JAL-3783 Updated groovy jars. Requires javaparser-core library to run too

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

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index ee24c25..0ebc58b 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -95,6 +95,7 @@ import javax.swing.JProgressBar;
 import javax.swing.JScrollPane;
 import javax.swing.JTextArea;
 import javax.swing.JTextField;
+import javax.swing.JTextPane;
 import javax.swing.KeyStroke;
 import javax.swing.SwingUtilities;
 import javax.swing.WindowConstants;
@@ -102,6 +103,7 @@ import javax.swing.event.HyperlinkEvent;
 import javax.swing.event.HyperlinkEvent.EventType;
 import javax.swing.event.InternalFrameAdapter;
 import javax.swing.event.InternalFrameEvent;
+import javax.swing.text.JTextComponent;
 
 import org.stackoverflowusers.file.WindowsShortcut;
 
@@ -111,6 +113,7 @@ 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.datamodel.Alignment;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.Sequence;
@@ -496,7 +499,28 @@ 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);
@@ -543,9 +567,6 @@ public class Desktop extends jalview.jbgui.GDesktop
       setBounds(xPos, yPos, 900, 650);
     }
 
-    // start dialogue queue for single dialogues
-    startDialogQueue();
-
     if (!Platform.isJS())
     /**
      * Java only
@@ -553,10 +574,6 @@ 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());
@@ -785,17 +802,17 @@ 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
@@ -2607,7 +2624,7 @@ 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"),
@@ -2623,7 +2640,7 @@ public class Desktop extends jalview.jbgui.GDesktop
   {
     if (groovyConsole == null)
     {
-      groovyConsole = new groovy.ui.Console();
+      groovyConsole = new groovy.console.ui.Console();
       groovyConsole.setVariable("Jalview", this);
       groovyConsole.run();
 
@@ -3106,7 +3123,7 @@ 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
@@ -3368,7 +3385,7 @@ 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;
   }
@@ -3745,13 +3762,21 @@ 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,
-            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 modal)
+          boolean scrollable, boolean html, boolean modal, int timeout)
   {
     if (type < 0)
     {
@@ -3759,15 +3784,31 @@ public class Desktop extends jalview.jbgui.GDesktop
     }
     JLabel jl = new JLabel(message);
 
-    JTextArea jta = new JTextArea(height, width);
-    // jta.setLineWrap(true);
-    jta.setEditable(false);
-    jta.setWrapStyleWord(true);
-    jta.setAutoscrolls(true);
-    jta.setText(boxtext);
+    JTextComponent jtc = null;
+    if (html)
+    {
+      JTextPane jtp = new JTextPane();
+      jtp.setContentType("text/html");
+      jtp.setEditable(false);
+      jtp.setAutoscrolls(true);
+      jtp.setText(boxtext);
+
+      jtc = jtp;
+    }
+    else
+    {
+      JTextArea jta = new JTextArea(height, width);
+      // jta.setLineWrap(true);
+      jta.setEditable(false);
+      jta.setWrapStyleWord(true);
+      jta.setAutoscrolls(true);
+      jta.setText(boxtext);
+
+      jtc = jta;
+    }
 
     JScrollPane jsp = scrollable
-            ? new JScrollPane(jta, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
+            ? new JScrollPane(jtc, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
                     JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED)
             : null;
 
@@ -3790,16 +3831,18 @@ public class Desktop extends jalview.jbgui.GDesktop
       }
       else
       {
-        jta.setAlignmentX(Component.LEFT_ALIGNMENT);
-        jp.add(jta);
+        jtc.setAlignmentX(Component.LEFT_ALIGNMENT);
+        jp.add(jtc);
       }
     }
 
     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);
   }
 
 }