added Platform settings separating mouse use of win/mac difference
[jalview.git] / src / jalview / gui / FeatureSettings.java
index 90d7c35..26cb104 100644 (file)
@@ -22,12 +22,15 @@ package jalview.gui;
 
 import jalview.api.FeatureColourI;
 import jalview.api.FeatureSettingsControllerI;
+import jalview.bin.Jalview;
 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.schemes.FeatureColour;
@@ -80,8 +83,6 @@ 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;
@@ -93,6 +94,8 @@ import javax.swing.JSlider;
 import javax.swing.JTable;
 import javax.swing.ListSelectionModel;
 import javax.swing.SwingConstants;
+import javax.swing.ToolTipManager;
+import javax.swing.border.Border;
 import javax.swing.event.ChangeEvent;
 import javax.swing.event.ChangeListener;
 import javax.swing.table.AbstractTableModel;
@@ -128,6 +131,8 @@ public class FeatureSettings extends JPanel
 
   private static final int MIN_HEIGHT = 400;
 
+  private final static String BASE_TOOLTIP = MessageManager.getString("label.click_to_edit");
+
   final FeatureRenderer fr;
 
   public final AlignFrame af;
@@ -137,9 +142,9 @@ public class FeatureSettings extends JPanel
    */
   Object[][] originalData;
 
-  private float originalTransparency;
+  float originalTransparency;
 
-  private Map<String, FeatureMatcherSetI> originalFilters;
+  Map<String, FeatureMatcherSetI> originalFilters;
 
   final JInternalFrame frame;
 
@@ -169,7 +174,7 @@ public class FeatureSettings extends JPanel
   /*
    * true when Feature Settings are updating from feature renderer
    */
-  private boolean handlingUpdate = false;
+  boolean handlingUpdate = false;
 
   /*
    * holds {featureCount, totalExtent} for each feature type
@@ -203,49 +208,103 @@ public class FeatureSettings extends JPanel
 
     table = new JTable()
     {
+       
+//     @Override
+//     public void repaint() {
+//       System.out.println("FS repaint");
+//       super.repaint();
+//       
+//     }
+//     
+//     @Override
+//        public void repaint(long tm, int x, int y, int width, int height) {
+//       System.out.println("FS repaint " + x  + " " + y + " " + width + " " + height);
+//       super.repaint(tm, x, y, width, height);
+//       
+//     }
+//     @Override
+//     public void invalidate() {
+//             if (isValid())
+//               System.out.println("FS invalidating ");
+//            super.invalidate();
+//     }
+//     
+//     @Override
+//     public void validate() {
+//            System.out.println("FS validating "  + isValid());
+//            super.validate();
+//     }
+
       @Override
       public String getToolTipText(MouseEvent e)
       {
         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;
+      }
     };
+    
+    // next line is needed to avoid (quiet) exceptions thrown
+    // when column ordering changes so that the above constants
+    // no longer apply.
+    table.getTableHeader().setReorderingAllowed(false); // BH 2018
+    
     table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));
-    table.setFont(new Font("Verdana", Font.PLAIN, 12));
+    ToolTipManager.sharedInstance().registerComponent(table);
 
-    // table.setDefaultRenderer(Color.class, new ColorRenderer());
-    // table.setDefaultEditor(Color.class, new ColorEditor(this));
-    //
-    table.setDefaultEditor(FeatureColour.class, new ColorEditor(this));
+    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);
@@ -260,8 +319,7 @@ public class FeatureSettings extends JPanel
         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)
         {
@@ -282,8 +340,7 @@ 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());
         }
       }
     });
@@ -346,18 +403,9 @@ 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(
@@ -374,84 +422,76 @@ public class FeatureSettings extends JPanel
     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()
+    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()
     {
-      JColorChooser colorChooser;
-
       @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();
-            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);
+            /*
+             * toggle variable to simple colour - show colour chooser
+             */
+            String title = MessageManager.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
+        else    
         {
           if (e.getSource() instanceof FeatureTypeSettings)
           {
@@ -460,23 +500,43 @@ 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.isValid());
+//                 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"));
@@ -524,7 +584,7 @@ public class FeatureSettings extends JPanel
     men.add(clearCols);
     men.add(hideCols);
     men.add(hideOtherCols);
-    men.show(table, x, y);
+    men.show(table, pt.x, pt.y);
   }
 
   @Override
@@ -858,14 +918,16 @@ 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)
-    {
-      File file = chooser.getSelectedFile();
-      load(file);
-    }
+    chooser.setResponseHandler(0, new Runnable()
+    {
+         @Override
+         public void run() 
+         {
+           File file = chooser.getSelectedFile();
+               load(file);
+         }
+       });
+    chooser.showOpenDialog(this);
   }
 
   /**
@@ -949,13 +1011,12 @@ 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)
-    {
-      save(chooser.getSelectedFile());
-    }
+    int option = chooser.showSaveDialog(this);
+       if (option == JalviewFileChooser.APPROVE_OPTION) 
+       {
+         File file = chooser.getSelectedFile();
+         save(file);
+       }
   }
 
   /**
@@ -1133,7 +1194,7 @@ public class FeatureSettings extends JPanel
    * @param data
    * @param visibleNew
    */
-  private void updateFeatureRenderer(Object[][] data, boolean visibleNew)
+  void updateFeatureRenderer(Object[][] data, boolean visibleNew)
   {
     FeatureSettingsBean[] rowData = getTableAsBeans(data);
 
@@ -1346,6 +1407,90 @@ public class FeatureSettings extends JPanel
     this.add(settingsPane);
   }
 
+  /**
+   * Answers a suitable tooltip to show on the colour cell of the table
+   * 
+   * @param fcol
+   * @param withHint
+   *          if true include 'click to edit' and similar text
+   * @return
+   */
+  public static String getColorTooltip(FeatureColourI fcol,
+          boolean withHint)
+  {
+    if (fcol == null)
+    {
+      return null;
+    }
+    if (fcol.isSimpleColour())
+    {
+      return withHint ? BASE_TOOLTIP : null;
+    }
+    String description = fcol.getDescription();
+    description = description.replaceAll("<", "&lt;");
+    description = description.replaceAll(">", "&gt;");
+    StringBuilder tt = new StringBuilder(description);
+    if (withHint)
+    {
+      tt.append("<br>").append(BASE_TOOLTIP).append("</br>");
+    }
+    return JvSwingUtils.wrapTooltip(true, tt.toString());
+  }
+
+  public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol,
+          int w, int h)
+  {
+    boolean thr = false;
+    StringBuilder tx = new StringBuilder();
+  
+    if (gcol.isColourByAttribute())
+    {
+      tx.append(FeatureMatcher
+              .toAttributeDisplayName(gcol.getAttributeName()));
+    }
+    else if (!gcol.isColourByLabel())
+    {
+      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)
+      {
+        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());
+  }
+
   // ///////////////////////////////////////////////////////////////////////
   // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html
   // ///////////////////////////////////////////////////////////////////////
@@ -1354,7 +1499,7 @@ 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;
@@ -1431,11 +1576,9 @@ 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()
     {
@@ -1450,7 +1593,6 @@ public class FeatureSettings extends JPanel
     {
       FeatureColourI cellColour = (FeatureColourI) color;
       setOpaque(true);
-      setToolTipText(baseTT);
       setBackground(tbl.getBackground());
       if (!cellColour.isSimpleColour())
       {
@@ -1557,82 +1699,10 @@ 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());
-      }
-    }
-  }
-
-  class ColorEditor extends AbstractCellEditor
+  @SuppressWarnings("serial")
+class ColorEditor extends AbstractCellEditor
           implements TableCellEditor, ActionListener
   {
-    FeatureSettings me;
-
     FeatureColourI currentColor;
 
     FeatureTypeSettings chooser;
@@ -1641,17 +1711,12 @@ 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,
@@ -1660,79 +1725,92 @@ 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
            */
-          currentColor = fr.getFeatureColours().get(type);
-          FeatureMatcherSetI currentFilter = me.fr.getFeatureFilter(type);
-          if (currentFilter == null)
+          chooser = new FeatureTypeSettings(fr, type);
+          if (!Jalview.isJS())
           {
-            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();
       }
     }
 
-    // Implement the one CellEditor method that AbstractCellEditor doesn't.
+    /**
+     * 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()
     {
@@ -1746,9 +1824,9 @@ public class FeatureSettings extends JPanel
     {
       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();
@@ -1774,10 +1852,10 @@ public class FeatureSettings extends JPanel
    * as display text). On click in the cell, opens the Feature Display Settings
    * dialog at the Filters tab.
    */
-  class FilterEditor extends AbstractCellEditor
+  @SuppressWarnings("serial")
+class FilterEditor extends AbstractCellEditor
           implements TableCellEditor, ActionListener
   {
-    FeatureSettings me;
 
     FeatureMatcherSetI currentFilter;
 
@@ -1791,9 +1869,8 @@ 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);
@@ -1808,7 +1885,7 @@ 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();
@@ -1819,7 +1896,6 @@ public class FeatureSettings extends JPanel
                   chooser.getWidth(), chooser.getHeight());
           chooser.validate();
         }
-        chooser.showTab(false);
         fireEditingStopped();
       }
       else if (e.getSource() instanceof Component)
@@ -1831,17 +1907,23 @@ 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();
       }
     }
 
@@ -1857,11 +1939,10 @@ public class FeatureSettings extends JPanel
     {
       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;
     }
@@ -1945,7 +2026,8 @@ 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);
     }
   }
 }