X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=5aa9499c209c59089820124a63ad09bb02811498;hb=5757f3c3ee60e52a2446ab111f35452cf4435ab2;hp=1dbc9b81d699513a7c2fe203f9784ce7d09de385;hpb=14b1b2a878190d5fffda298c4b9a901c72c74ad3;p=jalview.git

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 1dbc9b8..5aa9499 100644
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -20,31 +20,35 @@
  */
 package jalview.gui;
 
+import jalview.api.AlignViewportI;
 import jalview.api.FeatureColourI;
 import jalview.api.FeatureSettingsControllerI;
+import jalview.api.ViewStyleI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureMatcher;
 import jalview.datamodel.features.FeatureMatcherI;
 import jalview.datamodel.features.FeatureMatcherSet;
 import jalview.datamodel.features.FeatureMatcherSetI;
 import jalview.gui.Help.HelpId;
+import jalview.gui.JalviewColourChooser.ColourChooserListener;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
-import jalview.schemabinding.version2.Filter;
-import jalview.schemabinding.version2.JalviewUserColours;
-import jalview.schemabinding.version2.MatcherSet;
 import jalview.schemes.FeatureColour;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
-import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
-import jalview.ws.DasSequenceFeatureFetcher;
-import jalview.ws.dbsources.das.api.jalviewSourceI;
+import jalview.viewmodel.styles.ViewStyle;
+import jalview.xml.binding.jalview.JalviewUserColours;
+import jalview.xml.binding.jalview.JalviewUserColours.Colour;
+import jalview.xml.binding.jalview.JalviewUserColours.Filter;
+import jalview.xml.binding.jalview.ObjectFactory;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Component;
 import java.awt.Dimension;
+import java.awt.FlowLayout;
 import java.awt.Font;
 import java.awt.Graphics;
 import java.awt.GridLayout;
@@ -74,7 +78,6 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
-import java.util.Vector;
 
 import javax.help.HelpSetException;
 import javax.swing.AbstractCellEditor;
@@ -83,8 +86,6 @@ import javax.swing.Icon;
 import javax.swing.JButton;
 import javax.swing.JCheckBox;
 import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JColorChooser;
-import javax.swing.JDialog;
 import javax.swing.JInternalFrame;
 import javax.swing.JLabel;
 import javax.swing.JLayeredPane;
@@ -96,13 +97,20 @@ import javax.swing.JSlider;
 import javax.swing.JTable;
 import javax.swing.ListSelectionModel;
 import javax.swing.SwingConstants;
-import javax.swing.SwingUtilities;
+import javax.swing.ToolTipManager;
+import javax.swing.border.Border;
 import javax.swing.event.ChangeEvent;
 import javax.swing.event.ChangeListener;
 import javax.swing.table.AbstractTableModel;
+import javax.swing.table.JTableHeader;
 import javax.swing.table.TableCellEditor;
 import javax.swing.table.TableCellRenderer;
 import javax.swing.table.TableColumn;
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.Marshaller;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamReader;
 
 public class FeatureSettings extends JPanel
         implements FeatureSettingsControllerI
@@ -127,11 +135,8 @@ public class FeatureSettings extends JPanel
 
   private static final int MIN_HEIGHT = 400;
 
-  DasSourceBrowser dassourceBrowser;
-
-  DasSequenceFeatureFetcher dasFeatureFetcher;
-
-  JPanel dasSettingsPane = new JPanel();
+  private final static String BASE_TOOLTIP = MessageManager
+          .getString("label.click_to_edit");
 
   final FeatureRenderer fr;
 
@@ -142,7 +147,9 @@ public class FeatureSettings extends JPanel
    */
   Object[][] originalData;
 
-  private float originalTransparency;
+  float originalTransparency;
+
+  private ViewStyleI originalViewStyle;
 
   private Map<String, FeatureMatcherSetI> originalFilters;
 
@@ -163,18 +170,12 @@ public class FeatureSettings extends JPanel
 
   int selectedRow = -1;
 
-  JButton fetchDAS = new JButton();
-
-  JButton saveDAS = new JButton();
-
-  JButton cancelDAS = new JButton();
-
   boolean resettingTable = false;
 
   /*
    * true when Feature Settings are updating from feature renderer
    */
-  private boolean handlingUpdate = false;
+  boolean handlingUpdate = false;
 
   /*
    * holds {featureCount, totalExtent} for each feature type
@@ -197,6 +198,7 @@ public class FeatureSettings extends JPanel
     transparency.setMaximum(100 - originalTransparencyAsPercent);
 
     originalFilters = new HashMap<>(fr.getFeatureFilters()); // shallow copy
+    originalViewStyle = new ViewStyle(af.viewport.getViewStyle());
 
     try
     {
@@ -213,44 +215,66 @@ public class FeatureSettings extends JPanel
       {
         String tip = null;
         int column = table.columnAtPoint(e.getPoint());
+        int row = table.rowAtPoint(e.getPoint());
+
         switch (column)
         {
         case TYPE_COLUMN:
           tip = JvSwingUtils.wrapTooltip(true, MessageManager
                   .getString("label.feature_settings_click_drag"));
           break;
+        case COLOUR_COLUMN:
+          FeatureColourI colour = (FeatureColourI) table.getValueAt(row,
+                  column);
+          tip = getColorTooltip(colour, true);
+          break;
         case FILTER_COLUMN:
-          int row = table.rowAtPoint(e.getPoint());
           FeatureMatcherSet o = (FeatureMatcherSet) table.getValueAt(row,
                   column);
           tip = o.isEmpty()
-                  ? MessageManager.getString("label.filters_tooltip")
+                  ? MessageManager
+                          .getString("label.configure_feature_tooltip")
                   : o.toString();
           break;
         default:
           break;
         }
+
         return tip;
       }
+
+      /**
+       * Position the tooltip near the bottom edge of, and half way across, the
+       * current cell
+       */
+      @Override
+      public Point getToolTipLocation(MouseEvent e)
+      {
+        Point point = e.getPoint();
+        int column = table.columnAtPoint(point);
+        int row = table.rowAtPoint(point);
+        Rectangle r = getCellRect(row, column, false);
+        Point loc = new Point(r.x + r.width / 2, r.y + r.height - 3);
+        return loc;
+      }
     };
-    table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));
+    JTableHeader tableHeader = table.getTableHeader();
+    tableHeader.setFont(new Font("Verdana", Font.PLAIN, 12));
+    tableHeader.setReorderingAllowed(false);
     table.setFont(new Font("Verdana", Font.PLAIN, 12));
-
-    // table.setDefaultRenderer(Color.class, new ColorRenderer());
-    // table.setDefaultEditor(Color.class, new ColorEditor(this));
-    //
-    table.setDefaultEditor(FeatureColour.class, new ColorEditor(this));
+    ToolTipManager.sharedInstance().registerComponent(table);
+    table.setDefaultEditor(FeatureColour.class, new ColorEditor());
     table.setDefaultRenderer(FeatureColour.class, new ColorRenderer());
 
-    table.setDefaultEditor(FeatureMatcherSet.class, new FilterEditor(this));
+    table.setDefaultEditor(FeatureMatcherSet.class, new FilterEditor());
     table.setDefaultRenderer(FeatureMatcherSet.class, new FilterRenderer());
 
     TableColumn colourColumn = new TableColumn(COLOUR_COLUMN, 75,
-            new ColorRenderer(), new ColorEditor(this));
+            new ColorRenderer(), new ColorEditor());
     table.addColumn(colourColumn);
 
     TableColumn filterColumn = new TableColumn(FILTER_COLUMN, 75,
-            new FilterRenderer(), new FilterEditor(this));
+            new FilterRenderer(), new FilterEditor());
     table.addColumn(filterColumn);
 
     table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
@@ -260,21 +284,23 @@ public class FeatureSettings extends JPanel
       @Override
       public void mousePressed(MouseEvent evt)
       {
-        selectedRow = table.rowAtPoint(evt.getPoint());
+        Point pt = evt.getPoint();
+        selectedRow = table.rowAtPoint(pt);
         String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN);
         if (evt.isPopupTrigger())
         {
           Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN);
-          popupSort(selectedRow, type, colour, fr.getMinMax(), evt.getX(),
-                  evt.getY());
+          showPopupMenu(selectedRow, type, colour, evt.getPoint());
         }
-        else if (evt.getClickCount() == 2)
+        else if (evt.getClickCount() == 2
+                && table.columnAtPoint(pt) == TYPE_COLUMN)
         {
           boolean invertSelection = evt.isAltDown();
           boolean toggleSelection = Platform.isControlDown(evt);
           boolean extendSelection = evt.isShiftDown();
           fr.ap.alignFrame.avc.markColumnsContainingFeatures(
                   invertSelection, extendSelection, toggleSelection, type);
+          fr.ap.av.sendSelection();
         }
       }
 
@@ -287,8 +313,7 @@ public class FeatureSettings extends JPanel
         {
           String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN);
           Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN);
-          popupSort(selectedRow, type, colour, fr.getMinMax(), evt.getX(),
-                  evt.getY());
+          showPopupMenu(selectedRow, type, colour, evt.getPoint());
         }
       }
     });
@@ -325,9 +350,6 @@ public class FeatureSettings extends JPanel
     // MessageManager.getString("label.feature_settings_click_drag")));
     scrollPane.setViewportView(table);
 
-    dassourceBrowser = new DasSourceBrowser(this);
-    dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER);
-
     if (af.getViewport().isShowSequenceFeatures() || !fr.hasRenderOrder())
     {
       fr.findAllFeatures(true); // display everything!
@@ -354,18 +376,9 @@ public class FeatureSettings extends JPanel
 
     frame = new JInternalFrame();
     frame.setContentPane(this);
-    if (Platform.isAMac())
-    {
-      Desktop.addInternalFrame(frame,
-              MessageManager.getString("label.sequence_feature_settings"),
-              600, 480);
-    }
-    else
-    {
-      Desktop.addInternalFrame(frame,
-              MessageManager.getString("label.sequence_feature_settings"),
-              600, 450);
-    }
+    Desktop.addInternalFrame(frame,
+            MessageManager.getString("label.sequence_feature_settings"),
+            600, Platform.isAMacAndNotJS() ? 480 : 450);
     frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
 
     frame.addInternalFrameListener(
@@ -376,88 +389,82 @@ public class FeatureSettings extends JPanel
                       javax.swing.event.InternalFrameEvent evt)
               {
                 fr.removePropertyChangeListener(change);
-                dassourceBrowser.fs = null;
-              };
+              }
             });
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
     inConstruction = false;
   }
 
-  protected void popupSort(final int rowSelected, final String type,
-          final Object typeCol, final Map<String, float[][]> minmax, int x,
-          int y)
+  /**
+   * Constructs and shows a popup menu of possible actions on the selected row
+   * and feature type
+   * 
+   * @param rowSelected
+   * @param type
+   * @param typeCol
+   * @param pt
+   */
+  protected void showPopupMenu(final int rowSelected, final String type,
+          final Object typeCol, final Point pt)
   {
-    final FeatureColourI featureColour = (FeatureColourI) typeCol;
-
     JPopupMenu men = new JPopupMenu(MessageManager
             .formatMessage("label.settings_for_param", new String[]
             { type }));
-    JMenuItem scr = new JMenuItem(
-            MessageManager.getString("label.sort_by_score"));
-    men.add(scr);
-    final FeatureSettings me = this;
-    scr.addActionListener(new ActionListener()
-    {
-
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        me.af.avc
-                .sortAlignmentByFeatureScore(Arrays.asList(new String[]
-                { type }));
-      }
-
-    });
-    JMenuItem dens = new JMenuItem(
-            MessageManager.getString("label.sort_by_density"));
-    dens.addActionListener(new ActionListener()
-    {
-
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        me.af.avc
-                .sortAlignmentByFeatureDensity(Arrays.asList(new String[]
-                { type }));
-      }
-
-    });
-    men.add(dens);
+    final FeatureColourI featureColour = (FeatureColourI) typeCol;
 
     /*
-     * variable colour options include colour by label, by score,
-     * by selected attribute text, or attribute value
+     * menu option to select (or deselect) variable colour
      */
-    final JCheckBoxMenuItem mxcol = new JCheckBoxMenuItem(
+    final JCheckBoxMenuItem variableColourCB = new JCheckBoxMenuItem(
             MessageManager.getString("label.variable_colour"));
-    mxcol.setSelected(!featureColour.isSimpleColour());
-    men.add(mxcol);
-    mxcol.addActionListener(new ActionListener()
-    {
-      JColorChooser colorChooser;
+    variableColourCB.setSelected(!featureColour.isSimpleColour());
+    men.add(variableColourCB);
 
+    /*
+     * checkbox action listener doubles up as listener to OK
+     * from the variable colour / filters dialog
+     */
+    variableColourCB.addActionListener(new ActionListener()
+    {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        if (e.getSource() == mxcol)
+        if (e.getSource() == variableColourCB)
         {
+          men.setVisible(true); // BH 2018 for JavaScript because this is a
+                                // checkbox
+          men.setVisible(false); // BH 2018 for JavaScript because this is a
+                                 // checkbox
           if (featureColour.isSimpleColour())
           {
-            FeatureTypeSettings fc = new FeatureTypeSettings(me.fr, type);
+            /*
+             * toggle simple colour to variable colour - show dialog
+             */
+            FeatureTypeSettings fc = new FeatureTypeSettings(fr, type);
             fc.addActionListener(this);
           }
           else
           {
-            // bring up simple color chooser
-            colorChooser = new JColorChooser();
+            /*
+             * toggle variable to simple colour - show colour chooser
+             */
             String title = MessageManager
-                    .getString("label.select_colour");
-            JDialog dialog = JColorChooser.createDialog(me,
-                    title, true, // modal
-                    colorChooser, this, // OK button handler
-                    null); // no CANCEL button handler
-            colorChooser.setColor(featureColour.getMaxColour());
-            dialog.setVisible(true);
+                    .formatMessage("label.select_colour_for", type);
+            ColourChooserListener listener = new ColourChooserListener()
+            {
+              @Override
+              public void colourSelected(Color c)
+              {
+                table.setValueAt(new FeatureColour(c), rowSelected,
+                        COLOUR_COLUMN);
+                table.validate();
+                updateFeatureRenderer(
+                        ((FeatureTableModel) table.getModel()).getData(),
+                        false);
+              }
+            };
+            JalviewColourChooser.showColourChooser(FeatureSettings.this,
+                    title, featureColour.getMaxColour(), listener);
           }
         }
         else
@@ -469,23 +476,43 @@ public class FeatureSettings extends JPanel
              * colour will have already been set in the FeatureRenderer
              */
             FeatureColourI fci = fr.getFeatureColours().get(type);
-            table.setValueAt(fci, rowSelected, 1);
-            table.validate();
-          }
-          else
-          {
-            // probably the color chooser!
-            table.setValueAt(new FeatureColour(colorChooser.getColor()),
-                    rowSelected, 1);
-            table.validate();
-            me.updateFeatureRenderer(
-                    ((FeatureTableModel) table.getModel()).getData(),
-                    false);
+            table.setValueAt(fci, rowSelected, COLOUR_COLUMN);
+            // BH 2018 setting a table value does not invalidate it.
+            // System.out.println("FeatureSettings is valied" +
+            // table.validate();
           }
         }
       }
+    });
+
+    men.addSeparator();
+
+    JMenuItem scr = new JMenuItem(
+            MessageManager.getString("label.sort_by_score"));
+    men.add(scr);
+    scr.addActionListener(new ActionListener()
+    {
+
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        af.avc.sortAlignmentByFeatureScore(Arrays.asList(new String[]
+                { type }));
+      }
+    });
+    JMenuItem dens = new JMenuItem(
+            MessageManager.getString("label.sort_by_density"));
+    dens.addActionListener(new ActionListener()
+    {
 
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        af.avc.sortAlignmentByFeatureDensity(Arrays.asList(new String[]
+                { type }));
+      }
     });
+    men.add(dens);
 
     JMenuItem selCols = new JMenuItem(
             MessageManager.getString("label.select_columns_containing"));
@@ -496,6 +523,7 @@ public class FeatureSettings extends JPanel
       {
         fr.ap.alignFrame.avc.markColumnsContainingFeatures(false, false,
                 false, type);
+        fr.ap.av.sendSelection();
       }
     });
     JMenuItem clearCols = new JMenuItem(MessageManager
@@ -507,6 +535,7 @@ public class FeatureSettings extends JPanel
       {
         fr.ap.alignFrame.avc.markColumnsContainingFeatures(true, false,
                 false, type);
+        fr.ap.av.sendSelection();
       }
     });
     JMenuItem hideCols = new JMenuItem(
@@ -517,6 +546,7 @@ public class FeatureSettings extends JPanel
       public void actionPerformed(ActionEvent arg0)
       {
         fr.ap.alignFrame.hideFeatureColumns(type, true);
+        fr.ap.av.sendSelection();
       }
     });
     JMenuItem hideOtherCols = new JMenuItem(
@@ -527,13 +557,14 @@ public class FeatureSettings extends JPanel
       public void actionPerformed(ActionEvent arg0)
       {
         fr.ap.alignFrame.hideFeatureColumns(type, false);
+        fr.ap.av.sendSelection();
       }
     });
     men.add(selCols);
     men.add(clearCols);
     men.add(hideCols);
     men.add(hideOtherCols);
-    men.show(table, x, y);
+    men.show(table, pt.x, pt.y);
   }
 
   @Override
@@ -590,7 +621,7 @@ public class FeatureSettings extends JPanel
       {
         fr.setGroupVisibility(check.getText(), check.isSelected());
         resetTable(new String[] { grp });
-        af.alignPanel.paintAlignment(true, true);
+        refreshDisplay();
       }
     });
     groupPanel.add(check);
@@ -688,7 +719,7 @@ public class FeatureSettings extends JPanel
         data[dataIndex][FILTER_COLUMN] = featureFilter == null
                 ? new FeatureMatcherSet()
                 : featureFilter;
-        data[dataIndex][SHOW_COLUMN] = new Boolean(
+        data[dataIndex][SHOW_COLUMN] = Boolean.valueOf(
                 af.getViewport().getFeaturesDisplayed().isVisible(type));
         dataIndex++;
         displayableTypes.remove(type);
@@ -715,7 +746,7 @@ public class FeatureSettings extends JPanel
       data[dataIndex][FILTER_COLUMN] = featureFilter == null
               ? new FeatureMatcherSet()
               : featureFilter;
-      data[dataIndex][SHOW_COLUMN] = new Boolean(true);
+      data[dataIndex][SHOW_COLUMN] = Boolean.valueOf(true);
       dataIndex++;
       displayableTypes.remove(type);
     }
@@ -746,8 +777,8 @@ public class FeatureSettings extends JPanel
   }
 
   /**
-   * Updates 'originalData' (used for restore on Cancel) if we detect that changes
-   * have been made outwith this dialog
+   * Updates 'originalData' (used for restore on Cancel) if we detect that
+   * changes have been made outwith this dialog
    * <ul>
    * <li>a new feature type added (and made visible)</li>
    * <li>a feature colour changed (in the Amend Features dialog)</li>
@@ -811,8 +842,8 @@ public class FeatureSettings extends JPanel
 
   /**
    * Remove from the groups panel any checkboxes for groups that are not in the
-   * foundGroups set. This enables removing a group from the display when the last
-   * feature in that group is deleted.
+   * foundGroups set. This enables removing a group from the display when the
+   * last feature in that group is deleted.
    * 
    * @param foundGroups
    */
@@ -867,14 +898,16 @@ public class FeatureSettings extends JPanel
     chooser.setDialogTitle(
             MessageManager.getString("label.load_feature_colours"));
     chooser.setToolTipText(MessageManager.getString("action.load"));
-
-    int value = chooser.showOpenDialog(this);
-
-    if (value == JalviewFileChooser.APPROVE_OPTION)
+    chooser.setResponseHandler(0, new Runnable()
     {
-      File file = chooser.getSelectedFile();
-      load(file);
-    }
+      @Override
+      public void run()
+      {
+        File file = chooser.getSelectedFile();
+        load(file);
+      }
+    });
+    chooser.showOpenDialog(this);
   }
 
   /**
@@ -889,30 +922,39 @@ public class FeatureSettings extends JPanel
       InputStreamReader in = new InputStreamReader(
               new FileInputStream(file), "UTF-8");
 
-      JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
+      JAXBContext jc = JAXBContext
+              .newInstance("jalview.xml.binding.jalview");
+      javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
+      XMLStreamReader streamReader = XMLInputFactory.newInstance()
+              .createXMLStreamReader(in);
+      JAXBElement<JalviewUserColours> jbe = um.unmarshal(streamReader,
+              JalviewUserColours.class);
+      JalviewUserColours jucs = jbe.getValue();
+
+      // JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
 
       /*
        * load feature colours
        */
-      for (int i = jucs.getColourCount() - 1; i >= 0; i--)
+      for (int i = jucs.getColour().size() - 1; i >= 0; i--)
       {
-        jalview.schemabinding.version2.Colour newcol = jucs.getColour(i);
-        FeatureColourI colour = Jalview2XML.unmarshalColour(newcol);
+        Colour newcol = jucs.getColour().get(i);
+        FeatureColourI colour = jalview.project.Jalview2XML
+                .parseColour(newcol);
         fr.setColour(newcol.getName(), colour);
-        fr.setOrder(newcol.getName(), i / (float) jucs.getColourCount());
+        fr.setOrder(newcol.getName(), i / (float) jucs.getColour().size());
       }
 
       /*
        * load feature filters; loaded filters will replace any that are
        * currently defined, other defined filters are left unchanged 
        */
-      for (int i = 0; i < jucs.getFilterCount(); i++)
+      for (int i = 0; i < jucs.getFilter().size(); i++)
       {
-        jalview.schemabinding.version2.Filter filterModel = jucs
-                .getFilter(i);
+        Filter filterModel = jucs.getFilter().get(i);
         String featureType = filterModel.getFeatureType();
-        FeatureMatcherSetI filter = Jalview2XML.unmarshalFilter(featureType,
-                filterModel.getMatcherSet());
+        FeatureMatcherSetI filter = jalview.project.Jalview2XML
+                .parseFilter(featureType, filterModel.getMatcherSet());
         if (!filter.isEmpty())
         {
           fr.setFeatureFilter(featureType, filter);
@@ -925,8 +967,7 @@ public class FeatureSettings extends JPanel
       if (table != null)
       {
         resetTable(null);
-        Object[][] data = ((FeatureTableModel) table.getModel())
-                .getData();
+        Object[][] data = ((FeatureTableModel) table.getModel()).getData();
         ensureOrder(data);
         updateFeatureRenderer(data, false);
         table.repaint();
@@ -949,12 +990,11 @@ public class FeatureSettings extends JPanel
     chooser.setDialogTitle(
             MessageManager.getString("label.save_feature_colours"));
     chooser.setToolTipText(MessageManager.getString("action.save"));
-
-    int value = chooser.showSaveDialog(this);
-
-    if (value == JalviewFileChooser.APPROVE_OPTION)
+    int option = chooser.showSaveDialog(this);
+    if (option == JalviewFileChooser.APPROVE_OPTION)
     {
-      save(chooser.getSelectedFile());
+      File file = chooser.getSelectedFile();
+      save(file);
     }
   }
 
@@ -969,8 +1009,8 @@ public class FeatureSettings extends JPanel
     ucs.setSchemeName("Sequence Features");
     try
     {
-      PrintWriter out = new PrintWriter(new OutputStreamWriter(
-              new FileOutputStream(file), "UTF-8"));
+      PrintWriter out = new PrintWriter(
+              new OutputStreamWriter(new FileOutputStream(file), "UTF-8"));
 
       /*
        * sort feature types by colour order, from 0 (highest)
@@ -994,9 +1034,9 @@ public class FeatureSettings extends JPanel
       for (String featureType : sortedTypes)
       {
         FeatureColourI fcol = fr.getFeatureStyle(featureType);
-        jalview.schemabinding.version2.Colour col = Jalview2XML.marshalColour(
-                featureType, fcol);
-        ucs.addColour(col);
+        Colour col = jalview.project.Jalview2XML.marshalColour(featureType,
+                fcol);
+        ucs.getColour().add(col);
       }
 
       /*
@@ -1007,18 +1047,28 @@ public class FeatureSettings extends JPanel
         FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
         if (filter != null && !filter.isEmpty())
         {
-          Iterator<FeatureMatcherI> iterator = filter.getMatchers().iterator();
+          Iterator<FeatureMatcherI> iterator = filter.getMatchers()
+                  .iterator();
           FeatureMatcherI firstMatcher = iterator.next();
-          MatcherSet ms = Jalview2XML.marshalFilter(firstMatcher, iterator,
-                  filter.isAnded());
+          jalview.xml.binding.jalview.FeatureMatcherSet ms = jalview.project.Jalview2XML
+                  .marshalFilter(firstMatcher, iterator, filter.isAnded());
           Filter filterModel = new Filter();
           filterModel.setFeatureType(featureType);
           filterModel.setMatcherSet(ms);
-          ucs.addFilter(filterModel);
+          ucs.getFilter().add(filterModel);
         }
       }
+      JAXBContext jaxbContext = JAXBContext
+              .newInstance(JalviewUserColours.class);
+      Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
+      jaxbMarshaller.marshal(
+              new ObjectFactory().createJalviewUserColours(ucs), out);
 
-      ucs.marshal(out);
+      // jaxbMarshaller.marshal(object, pout);
+      // marshaller.marshal(object);
+      out.flush();
+
+      // ucs.marshal(out);
       out.close();
     } catch (Exception ex)
     {
@@ -1028,12 +1078,13 @@ public class FeatureSettings extends JPanel
 
   public void invertSelection()
   {
-    for (int i = 0; i < table.getRowCount(); i++)
+    Object[][] data = ((FeatureTableModel) table.getModel()).getData();
+    for (int i = 0; i < data.length; i++)
     {
-      Boolean value = (Boolean) table.getValueAt(i, SHOW_COLUMN);
-
-      table.setValueAt(new Boolean(!value.booleanValue()), i, SHOW_COLUMN);
+      data[i][SHOW_COLUMN] = !(Boolean) data[i][SHOW_COLUMN];
     }
+    updateFeatureRenderer(data, true);
+    table.repaint();
   }
 
   public void orderByAvWidth()
@@ -1082,7 +1133,8 @@ public class FeatureSettings extends JPanel
       else
       {
         width[i] /= max; // normalize
-        fr.setOrder(data[i][TYPE_COLUMN].toString(), width[i]); // store for later
+        fr.setOrder(data[i][TYPE_COLUMN].toString(), width[i]); // store for
+                                                                // later
       }
       if (i > 0)
       {
@@ -1116,19 +1168,19 @@ public class FeatureSettings extends JPanel
   }
 
   /**
-   * Update the priority order of features; only repaint if this changed the order
-   * of visible features
+   * Update the priority order of features; only repaint if this changed the
+   * order of visible features
    * 
    * @param data
    * @param visibleNew
    */
-  private void updateFeatureRenderer(Object[][] data, boolean visibleNew)
+  void updateFeatureRenderer(Object[][] data, boolean visibleNew)
   {
     FeatureSettingsBean[] rowData = getTableAsBeans(data);
 
     if (fr.setFeaturePriority(rowData, visibleNew))
     {
-      af.alignPanel.paintAlignment(true, true);
+      refreshDisplay();
     }
   }
 
@@ -1157,8 +1209,6 @@ public class FeatureSettings extends JPanel
     JPanel settingsPane = new JPanel();
     settingsPane.setLayout(new BorderLayout());
 
-    dasSettingsPane.setLayout(new BorderLayout());
-
     JPanel bigPanel = new JPanel();
     bigPanel.setLayout(new BorderLayout());
 
@@ -1228,22 +1278,6 @@ public class FeatureSettings extends JPanel
         }
       }
     });
-    help.setFont(JvSwingUtils.getLabelFont());
-    help.setText(MessageManager.getString("action.help"));
-    help.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        try
-        {
-          Help.showHelpWindow(HelpId.SequenceFeatureSettings);
-        } catch (HelpSetException e1)
-        {
-          e1.printStackTrace();
-        }
-      }
-    });
 
     JButton cancel = new JButton(MessageManager.getString("action.cancel"));
     cancel.setFont(JvSwingUtils.getLabelFont());
@@ -1255,6 +1289,7 @@ public class FeatureSettings extends JPanel
         fr.setTransparency(originalTransparency);
         fr.setFeatureFilters(originalFilters);
         updateFeatureRenderer(originalData);
+        af.getViewport().setViewStyle(originalViewStyle);
         close();
       }
     });
@@ -1305,7 +1340,7 @@ public class FeatureSettings extends JPanel
         if (!inConstruction)
         {
           fr.setTransparency((100 - transparency.getValue()) / 100f);
-          af.alignPanel.paintAlignment(true, true);
+          refreshDisplay();
         }
       }
     });
@@ -1313,41 +1348,43 @@ public class FeatureSettings extends JPanel
     transparency.setMaximum(70);
     transparency.setToolTipText(
             MessageManager.getString("label.transparency_tip"));
-    fetchDAS.setText(MessageManager.getString("label.fetch_das_features"));
-    fetchDAS.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        fetchDAS_actionPerformed(e);
-      }
-    });
-    saveDAS.setText(MessageManager.getString("action.save_as_default"));
-    saveDAS.addActionListener(new ActionListener()
+
+    boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
+    String text = MessageManager.formatMessage("label.show_linked_features",
+            nucleotide
+                    ? MessageManager.getString("label.protein")
+                            .toLowerCase()
+                    : "CDS");
+    JCheckBox showComplement = new JCheckBox(text);
+    showComplement.setSelected(af.getViewport().isShowComplementFeatures());
+    showComplement.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        saveDAS_actionPerformed(e);
+        af.getViewport()
+                .setShowComplementFeatures(showComplement.isSelected());
+        refreshDisplay();
       }
     });
 
-    JPanel dasButtonPanel = new JPanel();
-    dasButtonPanel.setBorder(BorderFactory.createEtchedBorder());
-    dasSettingsPane.setBorder(null);
-    cancelDAS.setEnabled(false);
-    cancelDAS.setText(MessageManager.getString("action.cancel_fetch"));
-    cancelDAS.addActionListener(new ActionListener()
+    JCheckBox showComplementOnTop = new JCheckBox(
+            MessageManager.getString("label.on_top"));
+    showComplementOnTop
+            .setSelected(af.getViewport().isShowComplementFeaturesOnTop());
+    showComplementOnTop.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        cancelDAS_actionPerformed(e);
+        af.getViewport().setShowComplementFeaturesOnTop(
+                showComplementOnTop.isSelected());
+        refreshDisplay();
       }
     });
 
-    JPanel transPanel = new JPanel(new GridLayout(1, 2));
-    bigPanel.add(transPanel, BorderLayout.SOUTH);
+    JPanel lowerPanel = new JPanel(new GridLayout(1, 2));
+    bigPanel.add(lowerPanel, BorderLayout.SOUTH);
 
     JPanel transbuttons = new JPanel(new GridLayout(5, 1));
     transbuttons.add(optimizeOrder);
@@ -1355,8 +1392,21 @@ public class FeatureSettings extends JPanel
     transbuttons.add(sortByScore);
     transbuttons.add(sortByDens);
     transbuttons.add(help);
-    transPanel.add(transparency);
-    transPanel.add(transbuttons);
+
+    boolean hasComplement = af.getViewport().getCodingComplement() != null;
+    JPanel transPanelLeft = new JPanel(
+            new GridLayout(hasComplement ? 3 : 2, 1));
+    transPanelLeft.add(new JLabel(" Colour transparency" + ":"));
+    transPanelLeft.add(transparency);
+    if (hasComplement)
+    {
+      JPanel cp = new JPanel(new FlowLayout(FlowLayout.LEFT));
+      cp.add(showComplement);
+      cp.add(showComplementOnTop);
+      transPanelLeft.add(cp);
+    }
+    lowerPanel.add(transPanelLeft);
+    lowerPanel.add(transbuttons);
 
     JPanel buttonPanel = new JPanel();
     buttonPanel.add(ok);
@@ -1364,170 +1414,109 @@ public class FeatureSettings extends JPanel
     buttonPanel.add(loadColours);
     buttonPanel.add(saveColours);
     bigPanel.add(scrollPane, BorderLayout.CENTER);
-    dasSettingsPane.add(dasButtonPanel, BorderLayout.SOUTH);
-    dasButtonPanel.add(fetchDAS);
-    dasButtonPanel.add(cancelDAS);
-    dasButtonPanel.add(saveDAS);
     settingsPane.add(bigPanel, BorderLayout.CENTER);
     settingsPane.add(buttonPanel, BorderLayout.SOUTH);
     this.add(settingsPane);
   }
 
-  public void fetchDAS_actionPerformed(ActionEvent e)
+  /**
+   * Repaints alignment, structure and overview (if shown). If there is a
+   * complementary view which is showing this view's features, then also
+   * repaints that.
+   */
+  void refreshDisplay()
   {
-    fetchDAS.setEnabled(false);
-    cancelDAS.setEnabled(true);
-    dassourceBrowser.setGuiEnabled(false);
-    Vector<jalviewSourceI> selectedSources = dassourceBrowser
-            .getSelectedSources();
-    doDasFeatureFetch(selectedSources, true, true);
+    af.alignPanel.paintAlignment(true, true);
+    AlignViewportI complement = af.getViewport().getCodingComplement();
+    if (complement != null && complement.isShowComplementFeatures())
+    {
+      AlignFrame af2 = Desktop.getAlignFrameFor(complement);
+      af2.alignPanel.paintAlignment(true, true);
+    }
   }
 
   /**
-   * get the features from selectedSources for all or the current selection
+   * Answers a suitable tooltip to show on the colour cell of the table
    * 
-   * @param selectedSources
-   * @param checkDbRefs
-   * @param promptFetchDbRefs
+   * @param fcol
+   * @param withHint
+   *                   if true include 'click to edit' and similar text
+   * @return
    */
-  private void doDasFeatureFetch(List<jalviewSourceI> selectedSources,
-          boolean checkDbRefs, boolean promptFetchDbRefs)
+  public static String getColorTooltip(FeatureColourI fcol,
+          boolean withHint)
   {
-    SequenceI[] dataset, seqs;
-    int iSize;
-    AlignmentViewport vp = af.getViewport();
-    if (vp.getSelectionGroup() != null
-            && vp.getSelectionGroup().getSize() > 0)
+    if (fcol == null)
     {
-      iSize = vp.getSelectionGroup().getSize();
-      dataset = new SequenceI[iSize];
-      seqs = vp.getSelectionGroup().getSequencesInOrder(vp.getAlignment());
+      return null;
     }
-    else
+    if (fcol.isSimpleColour())
     {
-      iSize = vp.getAlignment().getHeight();
-      seqs = vp.getAlignment().getSequencesArray();
+      return withHint ? BASE_TOOLTIP : null;
     }
-
-    dataset = new SequenceI[iSize];
-    for (int i = 0; i < iSize; i++)
+    String description = fcol.getDescription();
+    description = description.replaceAll("<", "&lt;");
+    description = description.replaceAll(">", "&gt;");
+    StringBuilder tt = new StringBuilder(description);
+    if (withHint)
     {
-      dataset[i] = seqs[i].getDatasetSequence();
+      tt.append("<br>").append(BASE_TOOLTIP).append("</br>");
     }
-
-    cancelDAS.setEnabled(true);
-    dasFeatureFetcher = new jalview.ws.DasSequenceFeatureFetcher(dataset,
-            this, selectedSources, checkDbRefs, promptFetchDbRefs);
-    af.getViewport().setShowSequenceFeatures(true);
-    af.showSeqFeatures.setSelected(true);
+    return JvSwingUtils.wrapTooltip(true, tt.toString());
   }
 
-  /**
-   * blocking call to initialise the das source browser
-   */
-  public void initDasSources()
-  {
-    dassourceBrowser.initDasSources();
-  }
-
-  /**
-   * examine the current list of das sources and return any matching the given
-   * nicknames in sources
-   * 
-   * @param sources
-   *          Vector of Strings to resolve to DAS source nicknames.
-   * @return sources that are present in source list.
-   */
-  public List<jalviewSourceI> resolveSourceNicknames(Vector<String> sources)
-  {
-    return dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources);
-  }
-
-  /**
-   * get currently selected das sources. ensure you have called initDasSources
-   * before calling this.
-   * 
-   * @return vector of selected das source nicknames
-   */
-  public Vector<jalviewSourceI> getSelectedSources()
+  public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol,
+          int w, int h)
   {
-    return dassourceBrowser.getSelectedSources();
-  }
+    boolean thr = false;
+    StringBuilder tx = new StringBuilder();
 
-  /**
-   * properly initialise DAS fetcher and then initiate a new thread to fetch
-   * features from the named sources (rather than any turned on by default)
-   * 
-   * @param sources
-   * @param block
-   *          if true then runs in same thread, otherwise passes to the Swing
-   *          executor
-   */
-  public void fetchDasFeatures(Vector<String> sources, boolean block)
-  {
-    initDasSources();
-    List<jalviewSourceI> resolved = dassourceBrowser.sourceRegistry
-            .resolveSourceNicknames(sources);
-    if (resolved.size() == 0)
+    if (gcol.isColourByAttribute())
     {
-      resolved = dassourceBrowser.getSelectedSources();
+      tx.append(FeatureMatcher
+              .toAttributeDisplayName(gcol.getAttributeName()));
     }
-    if (resolved.size() > 0)
+    else if (!gcol.isColourByLabel())
     {
-      final List<jalviewSourceI> dassources = resolved;
-      fetchDAS.setEnabled(false);
-      // cancelDAS.setEnabled(true); doDasFetch does this.
-      Runnable fetcher = new Runnable()
-      {
-
-        @Override
-        public void run()
-        {
-          doDasFeatureFetch(dassources, true, false);
-
-        }
-      };
-      if (block)
+      tx.append(MessageManager.getString("label.score"));
+    }
+    tx.append(" ");
+    if (gcol.isAboveThreshold())
+    {
+      thr = true;
+      tx.append(">");
+    }
+    if (gcol.isBelowThreshold())
+    {
+      thr = true;
+      tx.append("<");
+    }
+    if (gcol.isColourByLabel())
+    {
+      if (thr)
       {
-        fetcher.run();
+        tx.append(" ");
       }
-      else
+      if (!gcol.isColourByAttribute())
       {
-        SwingUtilities.invokeLater(fetcher);
+        tx.append("Label");
       }
+      comp.setIcon(null);
     }
-  }
-
-  public void saveDAS_actionPerformed(ActionEvent e)
-  {
-    dassourceBrowser
-            .saveProperties(jalview.bin.Cache.applicationProperties);
-  }
-
-  public void complete()
-  {
-    fetchDAS.setEnabled(true);
-    cancelDAS.setEnabled(false);
-    dassourceBrowser.setGuiEnabled(true);
-
-  }
-
-  public void cancelDAS_actionPerformed(ActionEvent e)
-  {
-    if (dasFeatureFetcher != null)
+    else
     {
-      dasFeatureFetcher.cancel();
+      Color newColor = gcol.getMaxColour();
+      comp.setBackground(newColor);
+      // System.err.println("Width is " + w / 2);
+      Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr);
+      comp.setIcon(ficon);
+      // tt+="RGB value: Max (" + newColor.getRed() + ", "
+      // + newColor.getGreen() + ", " + newColor.getBlue()
+      // + ")\nMin (" + minCol.getRed() + ", " + minCol.getGreen()
+      // + ", " + minCol.getBlue() + ")");
     }
-    complete();
-  }
-
-  public void noDasSourceActive()
-  {
-    complete();
-    JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
-            MessageManager.getString("label.no_das_sources_selected_warn"),
-            MessageManager.getString("label.no_das_sources_selected_title"),
-            JvOptionPane.DEFAULT_OPTION, JvOptionPane.INFORMATION_MESSAGE);
+    comp.setHorizontalAlignment(SwingConstants.CENTER);
+    comp.setText(tx.toString());
   }
 
   // ///////////////////////////////////////////////////////////////////////
@@ -1538,7 +1527,7 @@ public class FeatureSettings extends JPanel
     private String[] columnNames = {
         MessageManager.getString("label.feature_type"),
         MessageManager.getString("action.colour"),
-        MessageManager.getString("label.filter"),
+        MessageManager.getString("label.configuration"),
         MessageManager.getString("label.show") };
 
     private Object[][] data;
@@ -1588,13 +1577,22 @@ public class FeatureSettings extends JPanel
     }
 
     /**
-     * Answers the class of the object in column c of the first row of the table
+     * Answers the class of column c of the table
      */
     @Override
     public Class<?> getColumnClass(int c)
     {
-      Object v = getValueAt(0, c);
-      return v == null ? null : v.getClass();
+      switch (c)
+      {
+      case TYPE_COLUMN:
+        return String.class;
+      case COLOUR_COLUMN:
+        return FeatureColour.class;
+      case FILTER_COLUMN:
+        return FeatureMatcherSet.class;
+      default:
+        return Boolean.class;
+      }
     }
 
     @Override
@@ -1615,11 +1613,9 @@ public class FeatureSettings extends JPanel
 
   class ColorRenderer extends JLabel implements TableCellRenderer
   {
-    javax.swing.border.Border unselectedBorder = null;
-
-    javax.swing.border.Border selectedBorder = null;
+    Border unselectedBorder = null;
 
-    final String baseTT = "Click to edit, right/apple click for menu.";
+    Border selectedBorder = null;
 
     public ColorRenderer()
     {
@@ -1634,7 +1630,6 @@ public class FeatureSettings extends JPanel
     {
       FeatureColourI cellColour = (FeatureColourI) color;
       setOpaque(true);
-      setToolTipText(baseTT);
       setBackground(tbl.getBackground());
       if (!cellColour.isSimpleColour())
       {
@@ -1741,82 +1736,10 @@ public class FeatureSettings extends JPanel
     renderGraduatedColor(comp, gcol, w, h);
   }
 
-  public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol,
-          int w, int h)
-  {
-    boolean thr = false;
-    StringBuilder tt = new StringBuilder();
-    StringBuilder tx = new StringBuilder();
-
-    if (gcol.isColourByAttribute())
-    {
-      tx.append(String.join(":", gcol.getAttributeName()));
-    }
-    else if (!gcol.isColourByLabel())
-    {
-      tx.append(MessageManager.getString("label.score"));
-    }
-    tx.append(" ");
-    if (gcol.isAboveThreshold())
-    {
-      thr = true;
-      tx.append(">");
-      tt.append("Thresholded (Above ").append(gcol.getThreshold())
-              .append(") ");
-    }
-    if (gcol.isBelowThreshold())
-    {
-      thr = true;
-      tx.append("<");
-      tt.append("Thresholded (Below ").append(gcol.getThreshold())
-              .append(") ");
-    }
-    if (gcol.isColourByLabel())
-    {
-      tt.append("Coloured by label text. ").append(tt);
-      if (thr)
-      {
-        tx.append(" ");
-      }
-      if (!gcol.isColourByAttribute())
-      {
-        tx.append("Label");
-      }
-      comp.setIcon(null);
-    }
-    else
-    {
-      Color newColor = gcol.getMaxColour();
-      comp.setBackground(newColor);
-      // System.err.println("Width is " + w / 2);
-      Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr);
-      comp.setIcon(ficon);
-      // tt+="RGB value: Max (" + newColor.getRed() + ", "
-      // + newColor.getGreen() + ", " + newColor.getBlue()
-      // + ")\nMin (" + minCol.getRed() + ", " + minCol.getGreen()
-      // + ", " + minCol.getBlue() + ")");
-    }
-    comp.setHorizontalAlignment(SwingConstants.CENTER);
-    comp.setText(tx.toString());
-    if (tt.length() > 0)
-    {
-      if (comp.getToolTipText() == null)
-      {
-        comp.setToolTipText(tt.toString());
-      }
-      else
-      {
-        comp.setToolTipText(
-                tt.append(" ").append(comp.getToolTipText()).toString());
-      }
-    }
-  }
-
+  @SuppressWarnings("serial")
   class ColorEditor extends AbstractCellEditor
           implements TableCellEditor, ActionListener
   {
-    FeatureSettings me;
-
     FeatureColourI currentColor;
 
     FeatureTypeSettings chooser;
@@ -1825,17 +1748,12 @@ public class FeatureSettings extends JPanel
 
     JButton button;
 
-    JColorChooser colorChooser;
-
-    JDialog dialog;
-
     protected static final String EDIT = "edit";
 
     int rowSelected = 0;
 
-    public ColorEditor(FeatureSettings me)
+    public ColorEditor()
     {
-      this.me = me;
       // Set up the editor (from the table's point of view),
       // which is a button.
       // This button brings up the color chooser dialog,
@@ -1844,78 +1762,99 @@ public class FeatureSettings extends JPanel
       button.setActionCommand(EDIT);
       button.addActionListener(this);
       button.setBorderPainted(false);
-      // Set up the dialog that the button brings up.
-      colorChooser = new JColorChooser();
-      dialog = JColorChooser.createDialog(button,
-              MessageManager.getString("label.select_colour"), true, // modal
-              colorChooser, this, // OK button handler
-              null); // no CANCEL button handler
     }
 
     /**
-     * Handles events from the editor button and from the dialog's OK button.
+     * Handles events from the editor button, and from the colour/filters
+     * dialog's OK button
      */
     @Override
     public void actionPerformed(ActionEvent e)
     {
-      // todo test e.getSource() instead here
-      if (EDIT.equals(e.getActionCommand()))
-      {
-        // The user has clicked the cell, so
-        // bring up the dialog.
-        if (currentColor.isSimpleColour())
-        {
-          // bring up simple color chooser
-          button.setBackground(currentColor.getColour());
-          colorChooser.setColor(currentColor.getColour());
-          dialog.setVisible(true);
-        }
-        else
-        {
-          // bring up graduated chooser.
-          chooser = new FeatureTypeSettings(me.fr, type);
-          chooser.setRequestFocusEnabled(true);
-          chooser.requestFocus();
-          chooser.addActionListener(this);
-          chooser.showTab(true);
-        }
-        // Make the renderer reappear.
-        fireEditingStopped();
-
-      }
-      else
+      if (button == e.getSource())
       {
         if (currentColor.isSimpleColour())
         {
           /*
-           * read off colour picked in colour chooser after OK pressed
+           * simple colour chooser
            */
-          currentColor = new FeatureColour(colorChooser.getColor());
-          me.table.setValueAt(currentColor, rowSelected, COLOUR_COLUMN);
+          String ttl = MessageManager
+                  .formatMessage("label.select_colour_for", type);
+          ColourChooserListener listener = new ColourChooserListener()
+          {
+            @Override
+            public void colourSelected(Color c)
+            {
+              currentColor = new FeatureColour(c);
+              table.setValueAt(currentColor, rowSelected, COLOUR_COLUMN);
+              fireEditingStopped();
+            }
+
+            @Override
+            public void cancel()
+            {
+              fireEditingStopped();
+            }
+          };
+          JalviewColourChooser.showColourChooser(button, ttl,
+                  currentColor.getColour(), listener);
         }
         else
         {
           /*
-           * after OK in variable colour dialog, any changes to colour 
-           * (or filters!) are already set in FeatureRenderer, so just
-           * update table data without triggering updateFeatureRenderer
+           * variable colour and filters dialog
+           */
+          chooser = new FeatureTypeSettings(fr, type);
+          if (!Platform.isJS())
+          /**
+           * Java only
+           * 
+           * @j2sIgnore
            */
-          currentColor = fr.getFeatureColours().get(type);
-          FeatureMatcherSetI currentFilter = me.fr.getFeatureFilter(type);
-          if (currentFilter == null)
           {
-            currentFilter = new FeatureMatcherSet();
+            chooser.setRequestFocusEnabled(true);
+            chooser.requestFocus();
           }
-          Object[] data = ((FeatureTableModel) table.getModel())
-                  .getData()[rowSelected];
-          data[COLOUR_COLUMN] = currentColor;
-          data[FILTER_COLUMN] = currentFilter;
+          chooser.addActionListener(this);
+          fireEditingStopped();
         }
+      }
+      else
+      {
+        /*
+         * after OK in variable colour dialog, any changes to colour 
+         * (or filters!) are already set in FeatureRenderer, so just
+         * update table data without triggering updateFeatureRenderer
+         */
+        currentColor = fr.getFeatureColours().get(type);
+        FeatureMatcherSetI currentFilter = fr.getFeatureFilter(type);
+        if (currentFilter == null)
+        {
+          currentFilter = new FeatureMatcherSet();
+        }
+        Object[] data = ((FeatureTableModel) table.getModel())
+                .getData()[rowSelected];
+        data[COLOUR_COLUMN] = currentColor;
+        data[FILTER_COLUMN] = currentFilter;
         fireEditingStopped();
-        me.table.validate();
+        // SwingJS needs an explicit repaint() here,
+        // rather than relying upon no validation having
+        // occurred since the stopEditing call was made.
+        // Its laying out has not been stopped by the modal frame
+        table.validate();
+        table.repaint();
       }
     }
 
+    /**
+     * Override allows access to this method from anonymous inner classes
+     */
+    @Override
+    protected void fireEditingStopped()
+    {
+      super.fireEditingStopped();
+    }
+
     // Implement the one CellEditor method that AbstractCellEditor doesn't.
     @Override
     public Object getCellEditorValue()
@@ -1925,14 +1864,14 @@ public class FeatureSettings extends JPanel
 
     // Implement the one method defined by TableCellEditor.
     @Override
-    public Component getTableCellEditorComponent(JTable theTable, Object value,
-            boolean isSelected, int row, int column)
+    public Component getTableCellEditorComponent(JTable theTable,
+            Object value, boolean isSelected, int row, int column)
     {
       currentColor = (FeatureColourI) value;
       this.rowSelected = row;
-      type = me.table.getValueAt(row, TYPE_COLUMN).toString();
+      type = table.getValueAt(row, TYPE_COLUMN).toString();
       button.setOpaque(true);
-      button.setBackground(me.getBackground());
+      button.setBackground(FeatureSettings.this.getBackground());
       if (!currentColor.isSimpleColour())
       {
         JLabel btn = new JLabel();
@@ -1954,14 +1893,14 @@ public class FeatureSettings extends JPanel
 
   /**
    * The cell editor for the Filter column. It displays the text of any filters
-   * for the feature type in that row (in full as a tooltip, possible abbreviated
-   * as display text). On click in the cell, opens the Feature Display Settings
-   * dialog at the Filters tab.
+   * for the feature type in that row (in full as a tooltip, possible
+   * abbreviated as display text). On click in the cell, opens the Feature
+   * Display Settings dialog at the Filters tab.
    */
+  @SuppressWarnings("serial")
   class FilterEditor extends AbstractCellEditor
           implements TableCellEditor, ActionListener
   {
-    FeatureSettings me;
 
     FeatureMatcherSetI currentFilter;
 
@@ -1975,9 +1914,8 @@ public class FeatureSettings extends JPanel
 
     int rowSelected = 0;
 
-    public FilterEditor(FeatureSettings me)
+    public FilterEditor()
     {
-      this.me = me;
       button = new JButton();
       button.setActionCommand(EDIT);
       button.addActionListener(this);
@@ -1992,7 +1930,7 @@ public class FeatureSettings extends JPanel
     {
       if (button == e.getSource())
       {
-        FeatureTypeSettings chooser = new FeatureTypeSettings(me.fr, type);
+        FeatureTypeSettings chooser = new FeatureTypeSettings(fr, type);
         chooser.addActionListener(this);
         chooser.setRequestFocusEnabled(true);
         chooser.requestFocus();
@@ -2003,7 +1941,6 @@ public class FeatureSettings extends JPanel
                   chooser.getWidth(), chooser.getHeight());
           chooser.validate();
         }
-        chooser.showTab(false);
         fireEditingStopped();
       }
       else if (e.getSource() instanceof Component)
@@ -2015,17 +1952,23 @@ public class FeatureSettings extends JPanel
          * update table data without triggering updateFeatureRenderer
          */
         FeatureColourI currentColor = fr.getFeatureColours().get(type);
-        currentFilter = me.fr.getFeatureFilter(type);
+        currentFilter = fr.getFeatureFilter(type);
         if (currentFilter == null)
         {
           currentFilter = new FeatureMatcherSet();
         }
+
         Object[] data = ((FeatureTableModel) table.getModel())
                 .getData()[rowSelected];
         data[COLOUR_COLUMN] = currentColor;
         data[FILTER_COLUMN] = currentFilter;
         fireEditingStopped();
-        me.table.validate();
+        // SwingJS needs an explicit repaint() here,
+        // rather than relying upon no validation having
+        // occurred since the stopEditing call was made.
+        // Its laying out has not been stopped by the modal frame
+        table.validate();
+        table.repaint();
       }
     }
 
@@ -2036,16 +1979,15 @@ public class FeatureSettings extends JPanel
     }
 
     @Override
-    public Component getTableCellEditorComponent(JTable theTable, Object value,
-            boolean isSelected, int row, int column)
+    public Component getTableCellEditorComponent(JTable theTable,
+            Object value, boolean isSelected, int row, int column)
     {
       currentFilter = (FeatureMatcherSetI) value;
       this.rowSelected = row;
-      type = me.table.getValueAt(row, TYPE_COLUMN).toString();
+      type = table.getValueAt(row, TYPE_COLUMN).toString();
       button.setOpaque(true);
-      button.setBackground(me.getBackground());
+      button.setBackground(FeatureSettings.this.getBackground());
       button.setText(currentFilter.toString());
-      button.setToolTipText(currentFilter.toString());
       button.setIcon(null);
       return button;
     }
@@ -2129,7 +2071,8 @@ class FeatureIcon implements Icon
         g.fillRect(s1, 0, e1 - s1, height);
       }
       g.setColor(gcol.getMaxColour());
-      g.fillRect(0, e1, width - e1, height);
+      // g.fillRect(0, e1, width - e1, height); // BH 2018
+      g.fillRect(e1, 0, width - e1, height);
     }
   }
 }