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

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 0a6fabc..7b310b1 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -980,7 +980,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void setProgressBar(String message, long id)
   {
-    progressBar.setProgressBar(message, id);
+    if (!Platform.isHeadless())
+      progressBar.setProgressBar(message, id);
   }
 
   @Override
@@ -2914,6 +2915,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       viewport.setGatherViewsHere(true);
     }
     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
+
     return newap;
   }
 
@@ -3429,29 +3431,33 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Opens an Overview panel for the alignment, unless one is open already
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   @Override
   public void overviewMenuItem_actionPerformed(ActionEvent e)
   {
+    boolean showHiddenRegions = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START,
+                false);
+    openOverviewPanel(showHiddenRegions);
+  }
+
+  public OverviewPanel openOverviewPanel(boolean showHidden)
+  {
     if (alignPanel.overviewPanel != null)
     {
-      return;
+      return alignPanel.overviewPanel;
     }
-
     JInternalFrame frame = new JInternalFrame();
-    final OverviewPanel overview = new OverviewPanel(alignPanel);
+    final OverviewPanel overview = new OverviewPanel(alignPanel, frame, showHidden);
     frame.setContentPane(overview);
-    Desktop.addInternalFrame(frame, MessageManager
-            .formatMessage("label.overview_params", new Object[]
-            { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
+    Desktop.addInternalFrame(frame, "", true, frame.getWidth(), frame.getHeight(),
             true, true);
     frame.setFrameIcon(null);
     frame.pack();
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
+    final AlignmentPanel thePanel = this.alignPanel; 
     frame.addInternalFrameListener(
             new javax.swing.event.InternalFrameAdapter()
             {
@@ -3460,7 +3466,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                       javax.swing.event.InternalFrameEvent evt)
               {
                 overview.dispose();
-                alignPanel.setOverviewPanel(null);
+                thePanel.setOverviewPanel(null);
               }
             });
     if (getKeyListeners().length > 0)
@@ -3469,6 +3475,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     alignPanel.setOverviewPanel(overview);
+    alignPanel.setOverviewTitle(this);
+    
+    return overview;
   }
 
   @Override
@@ -4960,7 +4969,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     if (index > -1)
     {
+      /*
+       * update current Overview window title (if there is one)
+       * to add view name "Original" if necessary
+       */
+      alignPanel.setOverviewTitle(this);
+      
+      /*
+       * switch panels and set Overview title (if there is one
+       * because it was opened automatically)
+       */
       alignPanel = alignPanels.get(index);
+      alignPanel.setOverviewTitle(this);
+
       viewport = alignPanel.av;
       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
       setMenusFromViewport(viewport);
@@ -5830,6 +5851,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                     | ActionEvent.CTRL_MASK)) != 0);
   }
 
+  @Override
+  protected void copyHighlightedColumns_actionPerformed(
+          ActionEvent actionEvent)
+  {
+    avc.copyHighlightedRegionsToClipboard();
+  }
+
   /**
    * Rebuilds the Colour menu, including any user-defined colours which have
    * been loaded either on startup or during the session