Merge branch 'bug/JAL-2592userDefinedScheme' into develop

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index e79e303..f4dd851 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;
         }
       }
@@ -1320,10 +1306,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       alignmentToExport = viewport.getAlignment();
     }
-    alignmentStartEnd = alignmentToExport
-            .getVisibleStartAndEndIndex(viewport.getAlignment()
-                    .getHiddenColumns()
-                    .getHiddenRegions());
+    alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
+            .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
             omitHidden, alignmentStartEnd, settings);
     return ed;
@@ -1885,9 +1869,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (viewport.hasHiddenColumns())
     {
       hiddenColumns = new ArrayList<>();
-      int hiddenOffset = viewport.getSelectionGroup().getStartRes(),
-              hiddenCutoff = viewport.getSelectionGroup().getEndRes();
-      for (int[] region : viewport.getAlignment().getHiddenColumns())
+      int hiddenOffset = viewport.getSelectionGroup().getStartRes();
+      int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
+      ArrayList<int[]> hiddenRegions = viewport.getAlignment()
+              .getHiddenColumns().getHiddenColumnsCopy();
+      for (int[] region : hiddenRegions)
       {
         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
         {
@@ -2959,7 +2945,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void showAllColumns_actionPerformed(ActionEvent e)
   {
     viewport.showAllHiddenColumns();
-    repaint();
+    alignPanel.paintAlignment(true);
     viewport.sendSelection();
   }
 
@@ -2967,7 +2953,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void hideSelSequences_actionPerformed(ActionEvent e)
   {
     viewport.hideAllSelectedSeqs();
-    // alignPanel.paintAlignment(true);
   }
 
   /**
@@ -3214,10 +3199,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
     alignPanel.paintAlignment(true);
-    if (alignPanel.getOverviewPanel() != null)
-    {
-      alignPanel.getOverviewPanel().updateOverviewImage();
-    }
   }
 
   /**
@@ -3273,7 +3254,7 @@ 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 +3267,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       public void internalFrameClosed(
               javax.swing.event.InternalFrameEvent evt)
       {
+        overview.dispose();
         alignPanel.setOverviewPanel(null);
       };
     });
@@ -3343,7 +3325,7 @@ 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;