Merge branch 'develop' into features/JAL-2446NCList

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index fe84012..8a59a4b 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -689,24 +689,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           break;
         }
         case KeyEvent.VK_PAGE_UP:
-          if (viewport.getWrapAlignment())
-          {
-            vpRanges.scrollUp(true);
-          }
-          else
-          {
-            vpRanges.pageUp();
-          }
+          vpRanges.pageUp();
           break;
         case KeyEvent.VK_PAGE_DOWN:
-          if (viewport.getWrapAlignment())
-          {
-            vpRanges.scrollUp(false);
-          }
-          else
-          {
-            vpRanges.pageDown();
-          }
+          vpRanges.pageDown();
           break;
         }
       }
@@ -2456,7 +2442,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.setSelectionGroup(null);
     viewport.getColumnSelection().clear();
     viewport.setSelectionGroup(null);
-    alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
     // JAL-2034 - should delegate to
     // alignPanel to decide if overview needs
@@ -2959,7 +2944,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void showAllColumns_actionPerformed(ActionEvent e)
   {
     viewport.showAllHiddenColumns();
-    repaint();
+    alignPanel.paintAlignment(true);
     viewport.sendSelection();
   }
 
@@ -2967,7 +2952,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void hideSelSequences_actionPerformed(ActionEvent e)
   {
     viewport.hideAllSelectedSeqs();
-    // alignPanel.paintAlignment(true);
   }
 
   /**
@@ -3214,10 +3198,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
     alignPanel.paintAlignment(true);
-    if (alignPanel.getOverviewPanel() != null)
-    {
-      alignPanel.getOverviewPanel().updateOverviewImage();
-    }
   }
 
   /**
@@ -3273,7 +3253,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     JInternalFrame frame = new JInternalFrame();
-    OverviewPanel overview = new OverviewPanel(alignPanel);
+    final OverviewPanel overview = new OverviewPanel(alignPanel);
     frame.setContentPane(overview);
     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
             "label.overview_params", new Object[] { this.getTitle() }),
@@ -3286,6 +3266,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       public void internalFrameClosed(
               javax.swing.event.InternalFrameEvent evt)
       {
+        overview.dispose();
         alignPanel.setOverviewPanel(null);
       };
     });
@@ -3343,7 +3324,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
      * 'User Defined' opens a panel to configure or load a
      * user-defined colour scheme
      */
-    if (ResidueColourScheme.USER_DEFINED.equals(name))
+    if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
     {
       new UserDefinedColours(alignPanel);
       return;