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

diff --combined src/jalview/gui/AlignFrame.java
index 2a4b6dc,060d7b1..f4dd851
--- 1/src/jalview/gui/AlignFrame.java
--- 2/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@@ -167,7 -167,7 +167,7 @@@ public class AlignFrame extends GAlignF
  
    public AlignViewControllerI avc;
  
 -  List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
 +  List<AlignmentPanel> alignPanels = new ArrayList<>();
  
    /**
     * Last format used to load or save alignments in this window
@@@ -396,8 -396,8 +396,8 @@@
  
      addKeyListener();
  
 -    final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
 -    final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
 +    final List<AlignmentPanel> selviews = new ArrayList<>();
 +    final List<AlignmentPanel> origview = new ArrayList<>();
      final String menuLabel = MessageManager
              .getString("label.copy_format_from");
      ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
@@@ -410,7 -410,7 +410,7 @@@
                  origview.clear();
                  origview.add(alignPanel);
                  // make an array of all alignment panels except for this one
 -                List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
 +                List<AlignmentPanel> aps = new ArrayList<>(
                          Arrays.asList(Desktop.getAlignmentPanels(null)));
                  aps.remove(AlignFrame.this.alignPanel);
                  return aps.toArray(new AlignmentPanel[aps.size()]);
@@@ -689,10 -689,24 +689,10 @@@
            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;
          }
        }
@@@ -1306,8 -1320,10 +1306,8 @@@
      {
        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;
@@@ -1716,7 -1732,7 +1716,7 @@@
  
    synchronized void slideSequences(boolean right, int size)
    {
 -    List<SequenceI> sg = new ArrayList<SequenceI>();
 +    List<SequenceI> sg = new ArrayList<>();
      if (viewport.cursorMode)
      {
        sg.add(viewport.getAlignment().getSequenceAt(
@@@ -1735,7 -1751,7 +1735,7 @@@
        return;
      }
  
 -    List<SequenceI> invertGroup = new ArrayList<SequenceI>();
 +    List<SequenceI> invertGroup = new ArrayList<>();
  
      for (SequenceI seq : viewport.getAlignment().getSequences())
      {
@@@ -1868,12 -1884,11 +1868,12 @@@
      ArrayList<int[]> hiddenColumns = null;
      if (viewport.hasHiddenColumns())
      {
 -      hiddenColumns = new ArrayList<int[]>();
 -      int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
 -              .getSelectionGroup().getEndRes();
 -      for (int[] region : viewport.getAlignment().getHiddenColumns()
 -              .getHiddenRegions())
 +      hiddenColumns = new ArrayList<>();
 +      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)
          {
@@@ -1979,7 -1994,7 +1979,7 @@@
        }
  
        int alwidth = 0;
 -      ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
 +      ArrayList<Integer> newGraphGroups = new ArrayList<>();
        int fgroup = -1;
  
        if (newAlignment)
@@@ -2811,7 -2826,7 +2811,7 @@@
     */
    protected List<String> getExistingViewNames(List<Component> comps)
    {
 -    List<String> existingNames = new ArrayList<String>();
 +    List<String> existingNames = new ArrayList<>();
      for (Component comp : comps)
      {
        if (comp instanceof AlignmentPanel)
@@@ -2945,7 -2960,7 +2945,7 @@@
    public void showAllColumns_actionPerformed(ActionEvent e)
    {
      viewport.showAllHiddenColumns();
 -    repaint();
 +    alignPanel.paintAlignment(true);
      viewport.sendSelection();
    }
  
@@@ -2953,6 -2968,7 +2953,6 @@@
    public void hideSelSequences_actionPerformed(ActionEvent e)
    {
      viewport.hideAllSelectedSeqs();
 -    // alignPanel.paintAlignment(true);
    }
  
    /**
@@@ -3199,6 -3215,10 +3199,6 @@@
    {
      viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
      alignPanel.paintAlignment(true);
 -    if (alignPanel.getOverviewPanel() != null)
 -    {
 -      alignPanel.getOverviewPanel().updateOverviewImage();
 -    }
    }
  
    /**
@@@ -3254,7 -3274,7 +3254,7 @@@
      }
  
      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() }),
@@@ -3267,7 -3287,6 +3267,7 @@@
        public void internalFrameClosed(
                javax.swing.event.InternalFrameEvent evt)
        {
 +        overview.dispose();
          alignPanel.setOverviewPanel(null);
        };
      });
@@@ -3325,7 -3344,7 +3325,7 @@@
       * '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;
@@@ -3741,7 -3760,7 +3741,7 @@@
  
      List<Component> comps = PaintRefresher.components.get(viewport
              .getSequenceSetId());
 -    List<TreePanel> treePanels = new ArrayList<TreePanel>();
 +    List<TreePanel> treePanels = new ArrayList<>();
      for (Component comp : comps)
      {
        if (comp instanceof TreePanel)
@@@ -4001,7 -4020,7 +4001,7 @@@
        @Override
        public void run()
        {
 -        final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
 +        final List<JMenuItem> legacyItems = new ArrayList<>();
          try
          {
            // System.err.println("Building ws menu again "
@@@ -4016,7 -4035,7 +4016,7 @@@
            // TODO: group services by location as well as function and/or
            // introduce
            // object broker mechanism.
 -          final Vector<JMenu> wsmenu = new Vector<JMenu>();
 +          final Vector<JMenu> wsmenu = new Vector<>();
            final IProgressIndicator af = me;
  
            /*
@@@ -4384,8 -4403,8 +4384,8 @@@
      // Java's Transferable for native dnd
      evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
      Transferable t = evt.getTransferable();
 -    List<String> files = new ArrayList<String>();
 -    List<DataSourceType> protocols = new ArrayList<DataSourceType>();
 +    List<String> files = new ArrayList<>();
 +    List<DataSourceType> protocols = new ArrayList<>();
  
      try
      {
@@@ -4405,8 -4424,8 +4405,8 @@@
          /**
           * Object[] { String,SequenceI}
           */
 -        ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
 -        ArrayList<String> filesnotmatched = new ArrayList<String>();
 +        ArrayList<Object[]> filesmatched = new ArrayList<>();
 +        ArrayList<String> filesnotmatched = new ArrayList<>();
          for (int i = 0; i < files.size(); i++)
          {
            String file = files.get(i).toString();
@@@ -5397,7 -5416,7 +5397,7 @@@
      {
        return;
      }
 -    List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
 +    List<SequenceI> cdnaSeqs = new ArrayList<>();
      for (SequenceI aaSeq : alignment.getSequences())
      {
        for (AlignedCodonFrame acf : mappings)