JAL-3253 preliminary static fixes for JavaScript

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 27a0f76..594319f 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -392,7 +392,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     });
     buildColourMenu();
 
-    if (Desktop.desktop != null)
+    if (Desktop.getDesktopPane() != null)
     {
       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
       if (!Platform.isJS())
@@ -815,7 +815,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   private void addServiceListeners()
   {
     final java.beans.PropertyChangeListener thisListener;
-    Desktop.instance.addJalviewPropertyChangeListener("services",
+    Desktop.getInstance().addJalviewPropertyChangeListener("services",
             thisListener = new java.beans.PropertyChangeListener()
             {
               @Override
@@ -846,7 +846,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               javax.swing.event.InternalFrameEvent evt)
       {
         // System.out.println("deregistering discoverer listener");
-        Desktop.instance.removeJalviewPropertyChangeListener("services",
+        Desktop.getInstance().removeJalviewPropertyChangeListener("services",
                 thisListener);
         closeMenuItem_actionPerformed(true);
       }
@@ -1027,7 +1027,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void addFromFile_actionPerformed(ActionEvent e)
   {
-    Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
+    Desktop.getInstance().inputLocalFileMenuItem_actionPerformed(viewport);
   }
 
   @Override
@@ -1041,7 +1041,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // file is reloaded.
       if (FileFormat.Jalview.equals(currentFileFormat))
       {
-        JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+        JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
         for (int i = 0; i < frames.length; i++)
         {
           if (frames[i] instanceof AlignFrame && frames[i] != this
@@ -1051,14 +1051,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             try
             {
               frames[i].setSelected(true);
-              Desktop.instance.closeAssociatedWindows();
+              Desktop.getInstance().closeAssociatedWindows();
             } catch (java.beans.PropertyVetoException ex)
             {
             }
           }
 
         }
-        Desktop.instance.closeAssociatedWindows();
+        Desktop.getInstance().closeAssociatedWindows();
 
         FileLoader loader = new FileLoader();
         DataSourceType protocol = fileName.startsWith("http:")
@@ -1116,14 +1116,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void addFromText_actionPerformed(ActionEvent e)
   {
-    Desktop.instance
+    Desktop.getInstance()
             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
   }
 
   @Override
   public void addFromURL_actionPerformed(ActionEvent e)
   {
-    Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
+    Desktop.getInstance().inputURLMenuItem_actionPerformed(viewport);
   }
 
   @Override
@@ -1167,7 +1167,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // todo is this (2005) test now obsolete - value is never null?
     while (currentFileFormat == null)
     {
-      JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+      JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
               MessageManager
                       .getString("label.select_file_format_before_saving"),
               MessageManager.getString("label.file_format_not_specified"),
@@ -1939,7 +1939,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               .setContents(new StringSelection(""), null);
 
       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
-              Desktop.instance);
+              Desktop.getInstance());
     } catch (OutOfMemoryError er)
     {
       new OOMWarning("copying region", er);
@@ -2439,7 +2439,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             + 1) == viewport.getAlignment().getWidth()) ? true : false;
        if (wholeHeight && wholeWidth)
        {
-           JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
+           JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.getDesktopPane());
                dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
            Object[] options = new Object[] { MessageManager.getString("action.ok"),
                    MessageManager.getString("action.cancel") };
@@ -2913,7 +2913,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void gatherViews_actionPerformed(ActionEvent e)
   {
-    Desktop.instance.gatherViews(this);
+    Desktop.getInstance().gatherViews(this);
   }
 
   /**
@@ -3690,7 +3690,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         if (_s.getLength() < sg.getEndRes())
         {
-          JvOptionPane.showMessageDialog(Desktop.desktop,
+          JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
                   MessageManager.getString(
                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
                   MessageManager.getString(
@@ -4012,7 +4012,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
         } catch (Exception ex)
         {
-          JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
+          JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), ex.getMessage(),
                   MessageManager
                           .getString("label.problem_reading_tree_file"),
                   JvOptionPane.WARNING_MESSAGE);
@@ -4020,7 +4020,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         }
         if (fin != null && fin.hasWarningMessage())
         {
-          JvOptionPane.showMessageDialog(Desktop.desktop,
+          JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
                   fin.getWarningMessage(),
                   MessageManager.getString(
                           "label.possible_problem_with_tree_file"),
@@ -4400,7 +4400,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       final String errorTitle = MessageManager
               .getString("label.implementation_error")
               + MessageManager.getString("label.translation_failed");
-      JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
+      JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), msg, errorTitle,
               JvOptionPane.ERROR_MESSAGE);
       return;
     }
@@ -4410,7 +4410,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
       final String errorTitle = MessageManager
               .getString("label.translation_failed");
-      JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
+      JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), msg, errorTitle,
               JvOptionPane.WARNING_MESSAGE);
     }
     else
@@ -4626,7 +4626,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                     PDBEntry pe = new AssociatePdbFileWithSeq()
                             .associatePdbWithSeq(fm[0].toString(),
                                     (DataSourceType) fm[1], toassoc, false,
-                                    Desktop.instance);
+                                    Desktop.getInstance());
                     if (pe != null)
                     {
                       System.err.println("Associated file : "
@@ -4737,7 +4737,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             {
               // some problem - if no warning its probable that the ID matching
               // process didn't work
-              JvOptionPane.showMessageDialog(Desktop.desktop,
+              JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
                       tcf.getWarningMessage() == null
                               ? MessageManager.getString(
                                       "label.check_file_matches_sequence_ids_alignment")
@@ -4830,7 +4830,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                       + (format != null
                               ? "(parsing as '" + format + "' file)"
                               : ""),
-              oom, Desktop.desktop);
+              oom, Desktop.getDesktopPane());
     }
   }
 
@@ -5639,7 +5639,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       } catch (Exception ex)
       {
         System.err.println((ex.toString()));
-        JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+        JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
                 MessageManager.getString("label.couldnt_run_groovy_script"),
                 MessageManager.getString("label.groovy_support_failed"),
                 JvOptionPane.ERROR_MESSAGE);