JAL-2543 identify as JSON before HTML
[jalview.git] / src / jalview / gui / FeatureSettings.java
index 40635c0..419cb34 100644 (file)
  */
 package jalview.gui;
 
+import jalview.api.FeatureColourI;
 import jalview.api.FeatureSettingsControllerI;
 import jalview.bin.Cache;
-import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 import jalview.gui.Help.HelpId;
 import jalview.io.JalviewFileChooser;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.GraduatedColor;
+import jalview.io.JalviewFileView;
+import jalview.schemabinding.version2.JalviewUserColours;
+import jalview.schemes.FeatureColour;
+import jalview.util.Format;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.util.QuickSort;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.ws.dbsources.das.api.jalviewSourceI;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Component;
+import java.awt.Dimension;
 import java.awt.Font;
 import java.awt.Graphics;
 import java.awt.GridLayout;
@@ -55,6 +61,7 @@ import java.io.InputStreamReader;
 import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
 import java.util.Arrays;
+import java.util.HashSet;
 import java.util.Hashtable;
 import java.util.Iterator;
 import java.util.List;
@@ -75,7 +82,6 @@ import javax.swing.JInternalFrame;
 import javax.swing.JLabel;
 import javax.swing.JLayeredPane;
 import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JPopupMenu;
 import javax.swing.JScrollPane;
@@ -122,6 +128,10 @@ public class FeatureSettings extends JPanel implements
 
   JPanel transPanel = new JPanel(new GridLayout(1, 2));
 
+  private static final int MIN_WIDTH = 400;
+
+  private static final int MIN_HEIGHT = 400;
+
   public FeatureSettings(AlignFrame af)
   {
     this.af = af;
@@ -160,8 +170,8 @@ public class FeatureSettings extends JPanel implements
 
     table.setDefaultEditor(Color.class, new ColorEditor(this));
 
-    table.setDefaultEditor(GraduatedColor.class, new ColorEditor(this));
-    table.setDefaultRenderer(GraduatedColor.class, new ColorRenderer());
+    table.setDefaultEditor(FeatureColour.class, new ColorEditor(this));
+    table.setDefaultRenderer(FeatureColour.class, new ColorRenderer());
     table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 
     table.addMouseListener(new MouseAdapter()
@@ -178,14 +188,16 @@ public class FeatureSettings extends JPanel implements
         }
         else if (evt.getClickCount() == 2)
         {
+          boolean invertSelection = evt.isAltDown();
+          boolean toggleSelection = Platform.isControlDown(evt);
+          boolean extendSelection = evt.isShiftDown();
           fr.ap.alignFrame.avc.markColumnsContainingFeatures(
-                  evt.isAltDown(), evt.isShiftDown() || evt.isMetaDown(),
-                  evt.isMetaDown(),
+                  invertSelection, extendSelection, toggleSelection,
                   (String) table.getValueAt(selectedRow, 0));
         }
       }
 
-      // isPopupTrigger fires on mouseReleased on Mac
+      // isPopupTrigger fires on mouseReleased on Windows
       @Override
       public void mouseReleased(MouseEvent evt)
       {
@@ -207,11 +219,20 @@ public class FeatureSettings extends JPanel implements
         int newRow = table.rowAtPoint(evt.getPoint());
         if (newRow != selectedRow && selectedRow != -1 && newRow != -1)
         {
+          /*
+           * reposition 'selectedRow' to 'newRow' (the dragged to location)
+           * this could be more than one row away for a very fast drag action
+           * so just swap it with adjacent rows until we get it there
+           */
           Object[][] data = ((FeatureTableModel) table.getModel())
                   .getData();
-          Object[] temp = data[selectedRow];
-          data[selectedRow] = data[newRow];
-          data[newRow] = temp;
+          int direction = newRow < selectedRow ? -1 : 1;
+          for (int i = selectedRow; i != newRow; i += direction)
+          {
+            Object[] temp = data[i];
+            data[i] = data[i + direction];
+            data[i + direction] = temp;
+          }
           updateFeatureRenderer(data);
           table.repaint();
           selectedRow = newRow;
@@ -251,7 +272,7 @@ public class FeatureSettings extends JPanel implements
 
     frame = new JInternalFrame();
     frame.setContentPane(this);
-    if (new jalview.util.Platform().isAMac())
+    if (Platform.isAMac())
     {
       Desktop.addInternalFrame(frame,
               MessageManager.getString("label.sequence_feature_settings"),
@@ -263,6 +284,7 @@ public class FeatureSettings extends JPanel implements
               MessageManager.getString("label.sequence_feature_settings"),
               400, 450);
     }
+    frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
 
     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
     {
@@ -281,6 +303,8 @@ public class FeatureSettings extends JPanel implements
           final Object typeCol, final Map<String, float[][]> minmax, int x,
           int y)
   {
+    final FeatureColourI featureColour = (FeatureColourI) typeCol;
+
     JPopupMenu men = new JPopupMenu(MessageManager.formatMessage(
             "label.settings_for_param", new String[] { type }));
     JMenuItem scr = new JMenuItem(
@@ -336,7 +360,7 @@ public class FeatureSettings extends JPanel implements
         // positional features
         final JCheckBoxMenuItem mxcol = new JCheckBoxMenuItem(
                 "Graduated Colour");
-        mxcol.setSelected(!(typeCol instanceof Color));
+        mxcol.setSelected(!featureColour.isSimpleColour());
         men.add(mxcol);
         mxcol.addActionListener(new ActionListener()
         {
@@ -347,7 +371,7 @@ public class FeatureSettings extends JPanel implements
           {
             if (e.getSource() == mxcol)
             {
-              if (typeCol instanceof Color)
+              if (featureColour.isSimpleColour())
               {
                 FeatureColourChooser fc = new FeatureColourChooser(me.fr,
                         type);
@@ -361,8 +385,7 @@ public class FeatureSettings extends JPanel implements
                         "Select new Colour", true, // modal
                         colorChooser, this, // OK button handler
                         null); // no CANCEL button handler
-                colorChooser.setColor(((GraduatedColor) typeCol)
-                        .getMaxColor());
+                colorChooser.setColor(featureColour.getMaxColour());
                 dialog.setVisible(true);
               }
             }
@@ -378,7 +401,9 @@ public class FeatureSettings extends JPanel implements
               else
               {
                 // probably the color chooser!
-                table.setValueAt(colorChooser.getColor(), selectedRow, 1);
+                table.setValueAt(
+                        new FeatureColour(colorChooser.getColor()),
+                        selectedRow, 1);
                 table.validate();
                 me.updateFeatureRenderer(
                         ((FeatureTableModel) table.getModel()).getData(),
@@ -445,50 +470,26 @@ public class FeatureSettings extends JPanel implements
   private boolean handlingUpdate = false;
 
   /**
-   * contains a float[3] for each feature type string. created by setTableData
+   * holds {featureCount, totalExtent} for each feature type
    */
-  Hashtable typeWidth = null;
+  Map<String, float[]> typeWidth = null;
 
   @Override
   synchronized public void discoverAllFeatureData()
   {
-    Vector allFeatures = new Vector();
-    Vector allGroups = new Vector();
-    SequenceFeature[] tmpfeatures;
-    String group;
-    for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
-    {
-      tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
-              .getSequenceFeatures();
-      if (tmpfeatures == null)
-      {
-        continue;
-      }
+    Set<String> allGroups = new HashSet<String>();
+    AlignmentI alignment = af.getViewport().getAlignment();
 
-      int index = 0;
-      while (index < tmpfeatures.length)
+    for (int i = 0; i < alignment.getHeight(); i++)
+    {
+      SequenceI seq = alignment.getSequenceAt(i);
+      for (String group : seq.getFeatures().getFeatureGroups(true))
       {
-        if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0)
-        {
-          index++;
-          continue;
-        }
-
-        if (tmpfeatures[index].getFeatureGroup() != null)
-        {
-          group = tmpfeatures[index].featureGroup;
-          if (!allGroups.contains(group))
-          {
-            allGroups.addElement(group);
-            checkGroupState(group);
-          }
-        }
-
-        if (!allFeatures.contains(tmpfeatures[index].getType()))
+        if (group != null && !allGroups.contains(group))
         {
-          allFeatures.addElement(tmpfeatures[index].getType());
+          allGroups.add(group);
+          checkGroupState(group);
         }
-        index++;
       }
     }
 
@@ -554,77 +555,65 @@ public class FeatureSettings extends JPanel implements
 
   synchronized void resetTable(String[] groupChanged)
   {
-    if (resettingTable == true)
+    if (resettingTable)
     {
       return;
     }
     resettingTable = true;
-    typeWidth = new Hashtable();
+    typeWidth = new Hashtable<String, float[]>();
     // TODO: change avWidth calculation to 'per-sequence' average and use long
     // rather than float
-    float[] avWidth = null;
-    SequenceFeature[] tmpfeatures;
-    String group = null, type;
-    Vector visibleChecks = new Vector();
-
-    // Find out which features should be visible depending on which groups
-    // are selected / deselected
-    // and recompute average width ordering
+
+    Set<String> displayableTypes = new HashSet<String>();
+
+    /*
+     * determine which feature types may be visible depending on 
+     * which groups are selected, and recompute average width data
+     */
     for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
     {
 
-      tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
-              .getSequenceFeatures();
-      if (tmpfeatures == null)
-      {
-        continue;
-      }
+      SequenceI seq = af.getViewport().getAlignment().getSequenceAt(i);
 
-      int index = 0;
-      while (index < tmpfeatures.length)
+      /*
+       * get the sequence's groups for positional features
+       * and keep track of which groups are visible
+       */
+      Set<String> groups = seq.getFeatures().getFeatureGroups(true);
+      Set<String> visibleGroups = new HashSet<String>();
+      for (String group : groups)
       {
-        group = tmpfeatures[index].featureGroup;
-
-        if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0)
-        {
-          index++;
-          continue;
-        }
-
         if (group == null || checkGroupState(group))
         {
-          type = tmpfeatures[index].getType();
-          if (!visibleChecks.contains(type))
-          {
-            visibleChecks.addElement(type);
-          }
-        }
-        if (!typeWidth.containsKey(tmpfeatures[index].getType()))
-        {
-          typeWidth.put(tmpfeatures[index].getType(),
-                  avWidth = new float[3]);
-        }
-        else
-        {
-          avWidth = (float[]) typeWidth.get(tmpfeatures[index].getType());
+          visibleGroups.add(group);
         }
-        avWidth[0]++;
-        if (tmpfeatures[index].getBegin() > tmpfeatures[index].getEnd())
-        {
-          avWidth[1] += 1 + tmpfeatures[index].getBegin()
-                  - tmpfeatures[index].getEnd();
-        }
-        else
+      }
+
+      /*
+       * get distinct feature types for visible groups
+       * record distinct visible types, and their count and total length
+       */
+      Set<String> types = seq.getFeatures().getFeatureTypesForGroups(true,
+              visibleGroups.toArray(new String[visibleGroups.size()]));
+      for (String type : types)
+      {
+        displayableTypes.add(type);
+        float[] avWidth = typeWidth.get(type);
+        if (avWidth == null)
         {
-          avWidth[1] += 1 + tmpfeatures[index].getEnd()
-                  - tmpfeatures[index].getBegin();
+          avWidth = new float[2];
+          typeWidth.put(type, avWidth);
         }
-        index++;
+        // todo this could include features with a non-visible group
+        // - do we greatly care?
+        // todo should we include non-displayable features here, and only
+        // update when features are added?
+        avWidth[0] += seq.getFeatures().getFeatureCount(true, type);
+        avWidth[1] += seq.getFeatures().getTotalFeatureLength(type);
       }
     }
 
-    int fSize = visibleChecks.size();
-    Object[][] data = new Object[fSize][3];
+    Object[][] data = new Object[displayableTypes.size()][3];
     int dataIndex = 0;
 
     if (fr.hasRenderOrder())
@@ -640,9 +629,9 @@ public class FeatureSettings extends JPanel implements
       List<String> frl = fr.getRenderOrder();
       for (int ro = frl.size() - 1; ro > -1; ro--)
       {
-        type = frl.get(ro);
+        String type = frl.get(ro);
 
-        if (!visibleChecks.contains(type))
+        if (!displayableTypes.contains(type))
         {
           continue;
         }
@@ -652,16 +641,17 @@ public class FeatureSettings extends JPanel implements
         data[dataIndex][2] = new Boolean(af.getViewport()
                 .getFeaturesDisplayed().isVisible(type));
         dataIndex++;
-        visibleChecks.removeElement(type);
+        displayableTypes.remove(type);
       }
     }
 
-    fSize = visibleChecks.size();
-    for (int i = 0; i < fSize; i++)
+    /*
+     * process any extra features belonging only to 
+     * a group which was just selected
+     */
+    while (!displayableTypes.isEmpty())
     {
-      // These must be extra features belonging to the group
-      // which was just selected
-      type = visibleChecks.elementAt(i).toString();
+      String type = displayableTypes.iterator().next();
       data[dataIndex][0] = type;
 
       data[dataIndex][1] = fr.getFeatureStyle(type);
@@ -674,6 +664,7 @@ public class FeatureSettings extends JPanel implements
 
       data[dataIndex][2] = new Boolean(true);
       dataIndex++;
+      displayableTypes.remove(type);
     }
 
     if (originalData == null)
@@ -730,12 +721,9 @@ public class FeatureSettings extends JPanel implements
 
   void load()
   {
-    JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
-            new String[] { "fc" },
-            new String[] { "Sequence Feature Colours" },
+    JalviewFileChooser chooser = new JalviewFileChooser("fc",
             "Sequence Feature Colours");
-    chooser.setFileView(new jalview.io.JalviewFileView());
+    chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager
             .getString("label.load_feature_colours"));
     chooser.setToolTipText(MessageManager.getString("action.load"));
@@ -751,8 +739,7 @@ public class FeatureSettings extends JPanel implements
         InputStreamReader in = new InputStreamReader(new FileInputStream(
                 file), "UTF-8");
 
-        jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
-        jucs = jucs.unmarshal(in);
+        JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
 
         for (int i = jucs.getColourCount() - 1; i >= 0; i--)
         {
@@ -771,7 +758,7 @@ public class FeatureSettings extends JPanel implements
               Cache.log.warn("Couldn't parse out graduated feature color.",
                       e);
             }
-            GraduatedColor gcol = new GraduatedColor(mincol, maxcol,
+            FeatureColourI gcol = new FeatureColour(mincol, maxcol,
                     newcol.getMin(), newcol.getMax());
             if (newcol.hasAutoScale())
             {
@@ -783,31 +770,28 @@ public class FeatureSettings extends JPanel implements
             }
             if (newcol.hasThreshold())
             {
-              gcol.setThresh(newcol.getThreshold());
-              gcol.setThreshType(AnnotationColourGradient.NO_THRESHOLD); // default
+              gcol.setThreshold(newcol.getThreshold());
             }
             if (newcol.getThreshType().length() > 0)
             {
               String ttyp = newcol.getThreshType();
-              if (ttyp.equalsIgnoreCase("NONE"))
-              {
-                gcol.setThreshType(AnnotationColourGradient.NO_THRESHOLD);
-              }
               if (ttyp.equalsIgnoreCase("ABOVE"))
               {
-                gcol.setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD);
+                gcol.setAboveThreshold(true);
               }
               if (ttyp.equalsIgnoreCase("BELOW"))
               {
-                gcol.setThreshType(AnnotationColourGradient.BELOW_THRESHOLD);
+                gcol.setBelowThreshold(true);
               }
             }
             fr.setColour(name = newcol.getName(), gcol);
           }
           else
           {
-            fr.setColour(name = jucs.getColour(i).getName(), new Color(
-                    Integer.parseInt(jucs.getColour(i).getRGB(), 16)));
+            Color color = new Color(
+                    Integer.parseInt(jucs.getColour(i).getRGB(), 16));
+            fr.setColour(name = jucs.getColour(i).getName(),
+                    new FeatureColour(color));
           }
           fr.setOrder(name, (i == 0) ? 0 : i / jucs.getColourCount());
         }
@@ -829,12 +813,9 @@ public class FeatureSettings extends JPanel implements
 
   void save()
   {
-    JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
-            new String[] { "fc" },
-            new String[] { "Sequence Feature Colours" },
+    JalviewFileChooser chooser = new JalviewFileChooser("fc",
             "Sequence Feature Colours");
-    chooser.setFileView(new jalview.io.JalviewFileView());
+    chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager
             .getString("label.save_feature_colours"));
     chooser.setToolTipText(MessageManager.getString("action.save"));
@@ -851,50 +832,40 @@ public class FeatureSettings extends JPanel implements
         PrintWriter out = new PrintWriter(new OutputStreamWriter(
                 new FileOutputStream(choice), "UTF-8"));
 
-        Set fr_colours = fr.getAllFeatureColours();
-        Iterator e = fr_colours.iterator();
+        Set<String> fr_colours = fr.getAllFeatureColours();
+        Iterator<String> e = fr_colours.iterator();
         float[] sortOrder = new float[fr_colours.size()];
         String[] sortTypes = new String[fr_colours.size()];
         int i = 0;
         while (e.hasNext())
         {
-          sortTypes[i] = e.next().toString();
+          sortTypes[i] = e.next();
           sortOrder[i] = fr.getOrder(sortTypes[i]);
           i++;
         }
-        jalview.util.QuickSort.sort(sortOrder, sortTypes);
+        QuickSort.sort(sortOrder, sortTypes);
         sortOrder = null;
-        Object fcol;
-        GraduatedColor gcol;
         for (i = 0; i < sortTypes.length; i++)
         {
           jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
           col.setName(sortTypes[i]);
-          col.setRGB(jalview.util.Format.getHexString(fr.getColour(col
-                  .getName())));
-          fcol = fr.getFeatureStyle(sortTypes[i]);
-          if (fcol instanceof GraduatedColor)
+          FeatureColourI fcol = fr.getFeatureStyle(sortTypes[i]);
+          if (fcol.isSimpleColour())
           {
-            gcol = (GraduatedColor) fcol;
-            col.setMin(gcol.getMin());
-            col.setMax(gcol.getMax());
-            col.setMinRGB(jalview.util.Format.getHexString(gcol
-                    .getMinColor()));
-            col.setAutoScale(gcol.isAutoScale());
-            col.setThreshold(gcol.getThresh());
-            col.setColourByLabel(gcol.isColourByLabel());
-            switch (gcol.getThreshType())
-            {
-            case AnnotationColourGradient.NO_THRESHOLD:
-              col.setThreshType("NONE");
-              break;
-            case AnnotationColourGradient.ABOVE_THRESHOLD:
-              col.setThreshType("ABOVE");
-              break;
-            case AnnotationColourGradient.BELOW_THRESHOLD:
-              col.setThreshType("BELOW");
-              break;
-            }
+            col.setRGB(Format.getHexString(fcol.getColour()));
+          }
+          else
+          {
+            col.setRGB(Format.getHexString(fcol.getMaxColour()));
+            col.setMin(fcol.getMin());
+            col.setMax(fcol.getMax());
+            col.setMinRGB(jalview.util.Format.getHexString(fcol
+                    .getMinColour()));
+            col.setAutoScale(fcol.isAutoScaled());
+            col.setThreshold(fcol.getThreshold());
+            col.setColourByLabel(fcol.isColourByLabel());
+            col.setThreshType(fcol.isAboveThreshold() ? "ABOVE" : (fcol
+                    .isBelowThreshold() ? "BELOW" : "NONE"));
           }
           ucs.addColour(col);
         }
@@ -930,7 +901,7 @@ public class FeatureSettings extends JPanel implements
     int num = 0;
     for (int i = 0; i < data.length; i++)
     {
-      awidth = (float[]) typeWidth.get(data[i][0]);
+      awidth = typeWidth.get(data[i][0]);
       if (awidth[0] > 0)
       {
         width[i] = awidth[1] / awidth[0];// *awidth[0]*awidth[2]; - better
@@ -1253,7 +1224,8 @@ public class FeatureSettings extends JPanel implements
     fetchDAS.setEnabled(false);
     cancelDAS.setEnabled(true);
     dassourceBrowser.setGuiEnabled(false);
-    Vector selectedSources = dassourceBrowser.getSelectedSources();
+    Vector<jalviewSourceI> selectedSources = dassourceBrowser
+            .getSelectedSources();
     doDasFeatureFetch(selectedSources, true, true);
   }
 
@@ -1312,7 +1284,7 @@ public class FeatureSettings extends JPanel implements
    *          Vector of Strings to resolve to DAS source nicknames.
    * @return sources that are present in source list.
    */
-  public List<jalviewSourceI> resolveSourceNicknames(Vector sources)
+  public List<jalviewSourceI> resolveSourceNicknames(Vector<String> sources)
   {
     return dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources);
   }
@@ -1323,7 +1295,7 @@ public class FeatureSettings extends JPanel implements
    * 
    * @return vector of selected das source nicknames
    */
-  public Vector getSelectedSources()
+  public Vector<jalviewSourceI> getSelectedSources()
   {
     return dassourceBrowser.getSelectedSources();
   }
@@ -1337,7 +1309,7 @@ public class FeatureSettings extends JPanel implements
    *          if true then runs in same thread, otherwise passes to the Swing
    *          executor
    */
-  public void fetchDasFeatures(Vector sources, boolean block)
+  public void fetchDasFeatures(Vector<String> sources, boolean block)
   {
     initDasSources();
     List<jalviewSourceI> resolved = dassourceBrowser.sourceRegistry
@@ -1398,15 +1370,15 @@ public class FeatureSettings extends JPanel implements
   public void noDasSourceActive()
   {
     complete();
-    JOptionPane
+    JvOptionPane
             .showInternalConfirmDialog(
                     Desktop.desktop,
                     MessageManager
                             .getString("label.no_das_sources_selected_warn"),
                     MessageManager
                             .getString("label.no_das_sources_selected_title"),
-                    JOptionPane.DEFAULT_OPTION,
-                    JOptionPane.INFORMATION_MESSAGE);
+                    JvOptionPane.DEFAULT_OPTION,
+                    JvOptionPane.INFORMATION_MESSAGE);
   }
 
   // ///////////////////////////////////////////////////////////////////////
@@ -1503,10 +1475,11 @@ public class FeatureSettings extends JPanel implements
     }
 
     @Override
-    public Component getTableCellRendererComponent(JTable table,
+    public Component getTableCellRendererComponent(JTable tbl,
             Object color, boolean isSelected, boolean hasFocus, int row,
             int column)
     {
+      FeatureColourI cellColour = (FeatureColourI) color;
       // JLabel comp = new JLabel();
       // comp.
       setOpaque(true);
@@ -1514,11 +1487,11 @@ public class FeatureSettings extends JPanel implements
       // setBounds(getBounds());
       Color newColor;
       setToolTipText(baseTT);
-      setBackground(table.getBackground());
-      if (color instanceof GraduatedColor)
+      setBackground(tbl.getBackground());
+      if (!cellColour.isSimpleColour())
       {
-        Rectangle cr = table.getCellRect(row, column, false);
-        FeatureSettings.renderGraduatedColor(this, (GraduatedColor) color,
+        Rectangle cr = tbl.getCellRect(row, column, false);
+        FeatureSettings.renderGraduatedColor(this, cellColour,
                 (int) cr.getWidth(), (int) cr.getHeight());
 
       }
@@ -1526,20 +1499,16 @@ public class FeatureSettings extends JPanel implements
       {
         this.setText("");
         this.setIcon(null);
-        newColor = (Color) color;
-        // comp.
+        newColor = cellColour.getColour();
         setBackground(newColor);
-        // comp.setToolTipText("RGB value: " + newColor.getRed() + ", "
-        // + newColor.getGreen() + ", " + newColor.getBlue());
       }
       if (isSelected)
       {
         if (selectedBorder == null)
         {
           selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
-                  table.getSelectionBackground());
+                  tbl.getSelectionBackground());
         }
-        // comp.
         setBorder(selectedBorder);
       }
       else
@@ -1547,9 +1516,8 @@ public class FeatureSettings extends JPanel implements
         if (unselectedBorder == null)
         {
           unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
-                  table.getBackground());
+                  tbl.getBackground());
         }
-        // comp.
         setBorder(unselectedBorder);
       }
 
@@ -1563,7 +1531,7 @@ public class FeatureSettings extends JPanel implements
    * @param comp
    * @param gcol
    */
-  public static void renderGraduatedColor(JLabel comp, GraduatedColor gcol)
+  public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol)
   {
     int w = comp.getWidth(), h = comp.getHeight();
     if (w < 20)
@@ -1579,23 +1547,23 @@ public class FeatureSettings extends JPanel implements
     renderGraduatedColor(comp, gcol, w, h);
   }
 
-  public static void renderGraduatedColor(JLabel comp, GraduatedColor gcol,
+  public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol,
           int w, int h)
   {
     boolean thr = false;
     String tt = "";
     String tx = "";
-    if (gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD)
+    if (gcol.isAboveThreshold())
     {
       thr = true;
       tx += ">";
-      tt += "Thresholded (Above " + gcol.getThresh() + ") ";
+      tt += "Thresholded (Above " + gcol.getThreshold() + ") ";
     }
-    if (gcol.getThreshType() == AnnotationColourGradient.BELOW_THRESHOLD)
+    if (gcol.isBelowThreshold())
     {
       thr = true;
       tx += "<";
-      tt += "Thresholded (Below " + gcol.getThresh() + ") ";
+      tt += "Thresholded (Below " + gcol.getThreshold() + ") ";
     }
     if (gcol.isColourByLabel())
     {
@@ -1609,7 +1577,7 @@ public class FeatureSettings extends JPanel implements
     }
     else
     {
-      Color newColor = gcol.getMaxColor();
+      Color newColor = gcol.getMaxColour();
       comp.setBackground(newColor);
       // System.err.println("Width is " + w / 2);
       Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr);
@@ -1637,7 +1605,7 @@ public class FeatureSettings extends JPanel implements
 
 class FeatureIcon implements Icon
 {
-  GraduatedColor gcol;
+  FeatureColourI gcol;
 
   Color backg;
 
@@ -1649,7 +1617,7 @@ class FeatureIcon implements Icon
 
   Color mpcolour = Color.white;
 
-  FeatureIcon(GraduatedColor gfc, Color bg, int w, int h, boolean mspace)
+  FeatureIcon(FeatureColourI gfc, Color bg, int w, int h, boolean mspace)
   {
     gcol = gfc;
     backg = bg;
@@ -1689,7 +1657,7 @@ class FeatureIcon implements Icon
       g.setColor(backg);
       g.fillRect(0, 0, width, height);
       // need an icon here.
-      g.setColor(gcol.getMaxColor());
+      g.setColor(gcol.getMaxColour());
 
       g.setFont(new Font("Verdana", Font.PLAIN, 9));
 
@@ -1703,7 +1671,7 @@ class FeatureIcon implements Icon
     }
     else
     {
-      Color minCol = gcol.getMinColor();
+      Color minCol = gcol.getMinColour();
       g.setColor(minCol);
       g.fillRect(0, 0, s1, height);
       if (midspace)
@@ -1711,7 +1679,7 @@ class FeatureIcon implements Icon
         g.setColor(Color.white);
         g.fillRect(s1, 0, e1 - s1, height);
       }
-      g.setColor(gcol.getMaxColor());
+      g.setColor(gcol.getMaxColour());
       g.fillRect(0, e1, width - e1, height);
     }
   }
@@ -1722,14 +1690,12 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor,
 {
   FeatureSettings me;
 
-  GraduatedColor currentGColor;
+  FeatureColourI currentColor;
 
   FeatureColourChooser chooser;
 
   String type;
 
-  Color currentColor;
-
   JButton button;
 
   JColorChooser colorChooser;
@@ -1769,11 +1735,11 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor,
     {
       // The user has clicked the cell, so
       // bring up the dialog.
-      if (currentColor != null)
+      if (currentColor.isSimpleColour())
       {
         // bring up simple color chooser
-        button.setBackground(currentColor);
-        colorChooser.setColor(currentColor);
+        button.setBackground(currentColor.getColour());
+        colorChooser.setColor(currentColor.getColour());
         dialog.setVisible(true);
       }
       else
@@ -1790,15 +1756,13 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor,
     }
     else
     { // User pressed dialog's "OK" button.
-      if (currentColor != null)
+      if (currentColor.isSimpleColour())
       {
-        currentColor = colorChooser.getColor();
+        currentColor = new FeatureColour(colorChooser.getColor());
       }
       else
       {
-        // class cast exceptions may be raised if the chooser created on a
-        // non-graduated color
-        currentGColor = (GraduatedColor) chooser.getLastColour();
+        currentColor = chooser.getLastColour();
       }
       me.table.setValueAt(getCellEditorValue(), selectedRow, 1);
       fireEditingStopped();
@@ -1810,10 +1774,6 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor,
   @Override
   public Object getCellEditorValue()
   {
-    if (currentColor == null)
-    {
-      return currentGColor;
-    }
     return currentColor;
   }
 
@@ -1822,18 +1782,16 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor,
   public Component getTableCellEditorComponent(JTable table, Object value,
           boolean isSelected, int row, int column)
   {
-    currentGColor = null;
-    currentColor = null;
+    currentColor = (FeatureColourI) value;
     this.selectedRow = row;
     type = me.table.getValueAt(row, 0).toString();
     button.setOpaque(true);
     button.setBackground(me.getBackground());
-    if (value instanceof GraduatedColor)
+    if (!currentColor.isSimpleColour())
     {
-      currentGColor = (GraduatedColor) value;
       JLabel btn = new JLabel();
       btn.setSize(button.getSize());
-      FeatureSettings.renderGraduatedColor(btn, currentGColor);
+      FeatureSettings.renderGraduatedColor(btn, currentColor);
       button.setBackground(btn.getBackground());
       button.setIcon(btn.getIcon());
       button.setText(btn.getText());
@@ -1842,8 +1800,7 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor,
     {
       button.setText("");
       button.setIcon(null);
-      currentColor = (Color) value;
-      button.setBackground(currentColor);
+      button.setBackground(currentColor.getColour());
     }
     return button;
   }