Merge branch 'bug/JAL-2536' into develop

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index ca37196..a9a970f 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -691,23 +691,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         case KeyEvent.VK_PAGE_UP:
           if (viewport.getWrapAlignment())
           {
-            alignPanel.scrollUp(true);
+            vpRanges.scrollUp(true);
           }
           else
           {
-            alignPanel.setScrollValues(vpRanges.getStartRes(),
-                    2 * vpRanges.getStartSeq() - vpRanges.getEndSeq());
+            vpRanges.pageUp();
           }
           break;
         case KeyEvent.VK_PAGE_DOWN:
           if (viewport.getWrapAlignment())
           {
-            alignPanel.scrollUp(false);
+            vpRanges.scrollUp(false);
           }
           else
           {
-            alignPanel.setScrollValues(vpRanges.getStartRes(),
-                    vpRanges.getEndSeq());
+            vpRanges.pageDown();
           }
           break;
         }
@@ -1325,7 +1323,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     alignmentStartEnd = alignmentToExport
             .getVisibleStartAndEndIndex(viewport.getAlignment()
                     .getHiddenColumns()
-                    .getListOfCols());
+                    .getHiddenRegions());
     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
             omitHidden, alignmentStartEnd, settings);
     return ed;
@@ -1890,7 +1888,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
               .getSelectionGroup().getEndRes();
       for (int[] region : viewport.getAlignment().getHiddenColumns()
-              .getListOfCols())
+              .getHiddenRegions())
       {
         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
         {
@@ -3280,7 +3278,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     frame.setContentPane(overview);
     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
             "label.overview_params", new Object[] { this.getTitle() }),
-            frame.getWidth(), frame.getHeight());
+            true, frame.getWidth(), frame.getHeight(), true, true);
     frame.pack();
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
@@ -3591,19 +3589,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (viewport.getSelectionGroup() != null
             && viewport.getSelectionGroup().getSize() > 0)
     {
-      if (viewport.getSelectionGroup().getSize() < 3)
-      {
-        JvOptionPane
-                .showMessageDialog(
-                        Desktop.desktop,
-                        MessageManager
-                                .getString("label.you_need_more_two_sequences_selected_build_tree"),
-                        MessageManager
-                                .getString("label.not_enough_sequences"),
-                        JvOptionPane.WARNING_MESSAGE);
-        return;
-      }
-
       SequenceGroup sg = viewport.getSelectionGroup();
 
       /* Decide if the selection is a column region */