X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=6c5990a80aff82a1adec14bc38264c7c8fbfd115;hb=2bc54fc3fc79e09819a6e650ecd38446322a5f3c;hp=bbaaa5a2ff1e606c99dc8da97c8d54470c4d6c49;hpb=d03971168d7f0192862cf5b57602ecf3e341b457;p=jalview.git

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index bbaaa5a..6c5990a 100755
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -1,500 +1,982 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.gui;
-
-import jalview.datamodel.*;
-import javax.swing.*;
-import javax.swing.event.*;
-import java.awt.*;
-import java.util.*;
-import javax.swing.BorderFactory;
-import java.awt.event.*;
-import javax.swing.table.*;
-import java.io.*;
-import jalview.io.JalviewFileChooser;
-
-public class FeatureSettings extends JPanel
-{
-
-  final FeatureRenderer fr;
-  final AlignmentPanel ap;
-  final AlignViewport av;
-  Object [][] originalData;
-  final JInternalFrame frame;
-  JScrollPane scrollPane = new JScrollPane();
-  JTable table;
-
-  public FeatureSettings(AlignViewport av, final AlignmentPanel ap)
-  {
-    this.ap = ap;
-    this.av = av;
-    fr = ap.seqPanel.seqCanvas.getFeatureRenderer();
-    av.alignment.getSequences();
-    frame = new JInternalFrame();
-    frame.setContentPane(this);
-    Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 300);
-
-    setTableData();
-
-    final JSlider transparency = new JSlider(0, 70, 0);
-    transparency.addChangeListener(new ChangeListener()
-    {
-      public void stateChanged(ChangeEvent evt)
-      {
-        fr.setTransparency( (float) (100 - transparency.getValue()) / 100f);
-        ap.repaint();
-      }
-    });
-
-    JPanel transPanel = new JPanel(new FlowLayout());
-    transPanel.add(new JLabel("Transparency"));
-    transPanel.add(transparency);
-
-    //////////////////////////////////////////////
-    //We're going to need those OK cancel buttons
-    JPanel buttonPanel = new JPanel(new FlowLayout());
-    JButton button = new JButton("OK");
-    button.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent evt)
-      {
-        try
-        {
-          frame.setClosed(true);
-        }
-        catch (Exception exe)
-        {}
-      }
-    });
-    buttonPanel.add(button);
-    button = new JButton("Cancel");
-    button.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent evt)
-      {
-        try
-        {
-          updateFeatureRenderer(originalData);
-          frame.setClosed(true);
-        }
-        catch (Exception exe)
-        {}
-      }
-    });
-    buttonPanel.add(button);
-
-    button = new JButton("Load Colours");
-    button.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent evt)
-      {
-        load();
-      }
-    });
-    buttonPanel.add(button);
-    button = new JButton("Save Colours");
-    button.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent evt)
-      {
-        save();
-      }
-    });
-    buttonPanel.add(button);
-
-    this.setLayout(new BorderLayout());
-    JPanel bigPanel = new JPanel(new BorderLayout());
-    bigPanel.add(transPanel, BorderLayout.SOUTH);
-    bigPanel.add(scrollPane, BorderLayout.CENTER);
-
-    add(bigPanel, BorderLayout.CENTER);
-    add(buttonPanel, BorderLayout.SOUTH);
-
-
-  }
-
-  void setTableData()
-  {
-    Vector allFeatures = new Vector();
-    Vector features;
-    Enumeration e;
-    SequenceFeature sf;
-
-  for (int i = 0; i < av.alignment.getHeight(); i++)
-  {
-    features = av.alignment.getSequenceAt(i).getDatasetSequence().
-        getSequenceFeatures();
-    if (features == null)
-      continue;
-
-    e = features.elements();
-    while (e.hasMoreElements())
-    {
-      sf = (SequenceFeature) e.nextElement();
-      if (!allFeatures.contains(sf.getType()))
-      {
-        allFeatures.addElement(sf.getType());
-      }
-    }
-
-    if(allFeatures.size()<1)
-     {
-       try{
-         frame.setClosed(true);
-       }catch(Exception ex){}
-       return;
-     }
-
-    int fSize = allFeatures.size();
-
-    String type;
-    boolean originalExists = false;
-    if(originalData!=null)
-      originalExists = true;
-    else
-      originalData = new Object[fSize][3];
-
-    Object [][] data = new Object[fSize][3];
-    for(int i=0; i<fSize; i++)
-    {
-      type = allFeatures.elementAt(i).toString();
-      Color col = fr.getColour(type);
-      data[i][0]=type;
-      data[i][1]=col;
-      if(fr.featuresDisplayed!=null)
-         data[i][2] = new Boolean(fr.featuresDisplayed.contains(type));
-      else
-        data[i][2] = new Boolean(true);
-
-      if(!originalExists)
-      {
-        originalData[i][0] = type;
-        originalData[i][1] = col;
-        if (fr.featuresDisplayed != null)
-          originalData[i][2] = new Boolean(fr.featuresDisplayed.contains(type));
-        else
-          originalData[i][2] = new Boolean(true);
-      }
-    }
-    ////////////////////////////////////
-        //Now build the table
-        table = new JTable(new FeatureTableModel(data));
-        scrollPane.setViewportView(table);
-        table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));
-        table.setFont(new Font("Verdana", Font.PLAIN, 12));
-        table.setDefaultRenderer(Color.class,
-                             new ColorRenderer());
-
-        table.setDefaultEditor(Color.class,
-                          new ColorEditor());
-
-        table.getColumnModel().getColumn(0).setPreferredWidth(200);
-
-        table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
-
-        table.addMouseListener(new MouseAdapter()
-            {
-              public void mousePressed(MouseEvent evt)
-              {
-                selectedRow = table.rowAtPoint(evt.getPoint());
-              }
-            });
-
-        table.addMouseMotionListener(new MouseMotionAdapter()
-            {
-              public void mouseDragged(MouseEvent evt)
-              {
-                int newRow = table.rowAtPoint(evt.getPoint());
-                if(newRow!=selectedRow
-                   && selectedRow!=-1
-                   && newRow!=-1)
-                {
-                  Object[] temp = new Object[3];
-                  temp[0] = table.getValueAt(selectedRow, 0);
-                  temp[1] = table.getValueAt(selectedRow, 1);
-                  temp[2] = table.getValueAt(selectedRow, 2);
-
-                  table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0);
-                  table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1);
-                  table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2);
-
-                  table.setValueAt(temp[0], newRow, 0);
-                  table.setValueAt(temp[1], newRow, 1);
-                  table.setValueAt(temp[2], newRow, 2);
-
-                  selectedRow = newRow;
-                }
-              }
-        });
-
-  }
-
-  void load()
-  {
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
-                 "LAST_DIRECTORY"), new String[] { "fc" },
-             new String[] { "Sequence Feature Colours" }, "Sequence Feature Colours");
-     chooser.setFileView(new jalview.io.JalviewFileView());
-     chooser.setDialogTitle("Load Feature Colours");
-     chooser.setToolTipText("Load");
-
-     int value = chooser.showOpenDialog(this);
-
-     if (value == JalviewFileChooser.APPROVE_OPTION)
-     {
-       File file = chooser.getSelectedFile();
-
-       try
-       {
-         InputStreamReader in = new InputStreamReader(new FileInputStream(
-             file), "UTF-8");
-
-         jalview.binding.JalviewUserColours jucs = new jalview.binding.
-             JalviewUserColours();
-         jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
-
-
-         for (int i = 0; i < jucs.getColourCount(); i++)
-         {
-           fr.setColour( jucs.getColour(i).getName(),
-                          new Color(Integer.parseInt( jucs.getColour(i).getRGB(), 16)));
-         }
-
-         setTableData();
-         ap.repaint();
-       }
-       catch (Exception ex)
-       {
-         System.out.println("Error loading User ColourFile\n" + ex);
-       }
-     }
-  }
-
-  void save()
-  {
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
-                "LAST_DIRECTORY"), new String[] { "fc" },
-            new String[] { "Sequence Feature Colours" }, "Sequence Feature Colours");
-    chooser.setFileView(new jalview.io.JalviewFileView());
-    chooser.setDialogTitle("Save Feature Colour Scheme");
-    chooser.setToolTipText("Save");
-
-    int value = chooser.showSaveDialog(this);
-
-    if (value == JalviewFileChooser.APPROVE_OPTION)
-    {
-        String choice = chooser.getSelectedFile().getPath();
-        jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours();
-        ucs.setSchemeName("Sequence Features");
-        try
-        {
-            PrintWriter out = new PrintWriter(new OutputStreamWriter(
-                        new FileOutputStream(choice), "UTF-8"));
-
-            Enumeration e = fr.featureColours.keys();
-           while(e.hasMoreElements())
-           {
-
-
-                jalview.binding.Colour col = new jalview.binding.Colour();
-                col.setName(e.nextElement().toString());
-                col.setRGB(jalview.util.Format.getHexString(
-                        fr.getColour(col.getName())));
-                ucs.addColour(col);
-            }
-
-            ucs.marshal(out);
-            out.close();
-        }
-        catch (Exception ex)
-        {
-            ex.printStackTrace();
-        }
-    }
-
-  }
-
-  public void updateFeatureRenderer(Object [][] data)
-  {
-    fr.setFeaturePriority( data );
-    ap.repaint();
-
-    if(ap.overviewPanel!=null)
-      ap.overviewPanel.updateOverviewImage();
-  }
-
-  int selectedRow =-1;
-
-
-  /////////////////////////////////////////////////////////////////////////
-  // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html
-  /////////////////////////////////////////////////////////////////////////
-  class FeatureTableModel
-      extends AbstractTableModel
-  {
-    FeatureTableModel(Object[][] data)
-    {
-      this.data = data;
-    }
-
-    private String[] columnNames = {"Feature Type", "Colour","Display"};
-          private Object[][] data;
-
-          public Object[][] getData()
-          {
-            return data;
-          }
-
-          public int getColumnCount() {
-              return columnNames.length;
-          }
-
-          public Object[] getRow(int row)
-          {
-            return data[row];
-          }
-
-          public int getRowCount() {
-              return data.length;
-          }
-
-          public String getColumnName(int col) {
-              return columnNames[col];
-          }
-
-          public Object getValueAt(int row, int col) {
-              return data[row][col];
-          }
-
-          public Class getColumnClass(int c) {
-              return getValueAt(0, c).getClass();
-          }
-
-          public boolean isCellEditable(int row, int col) {
-              return col==0 ? false:true;
-          }
-
-          public void setValueAt(Object value, int row, int col) {
-              data[row][col] = value;
-              fireTableCellUpdated(row, col);
-              updateFeatureRenderer(data);
-          }
-
-    }
-    class ColorRenderer extends JLabel
-                              implements TableCellRenderer {
-       javax.swing.border.Border unselectedBorder = null;
-       javax.swing.border.Border selectedBorder = null;
-
-       public ColorRenderer() {
-           setOpaque(true); //MUST do this for background to show up.
-       }
-
-       public Component getTableCellRendererComponent(
-                               JTable table, Object color,
-                               boolean isSelected, boolean hasFocus,
-                               int row, int column) {
-           Color newColor = (Color)color;
-           setBackground(newColor);
-               if (isSelected) {
-                   if (selectedBorder == null) {
-                       selectedBorder = BorderFactory.createMatteBorder(2,5,2,5,
-                                                 table.getSelectionBackground());
-                   }
-                   setBorder(selectedBorder);
-               } else {
-                   if (unselectedBorder == null) {
-                       unselectedBorder = BorderFactory.createMatteBorder(2,5,2,5,
-                                                 table.getBackground());
-                   }
-                   setBorder(unselectedBorder);
-               }
-
-           setToolTipText("RGB value: " + newColor.getRed() + ", "
-                                        + newColor.getGreen() + ", "
-                                        + newColor.getBlue());
-           return this;
-       }
-   }
-}
-
- class ColorEditor extends AbstractCellEditor
-                          implements TableCellEditor,
-                                     ActionListener {
-     Color currentColor;
-     JButton button;
-     JColorChooser colorChooser;
-     JDialog dialog;
-     protected static final String EDIT = "edit";
-
-     public ColorEditor() {
-         //Set up the editor (from the table's point of view),
-         //which is a button.
-         //This button brings up the color chooser dialog,
-         //which is the editor from the user's point of view.
-         button = new JButton();
-         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,
-                                         "Select new 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.
-      */
-     public void actionPerformed(ActionEvent e) {
-
-          if (EDIT.equals(e.getActionCommand())) {
-             //The user has clicked the cell, so
-             //bring up the dialog.
-             button.setBackground(currentColor);
-             colorChooser.setColor(currentColor);
-             dialog.setVisible(true);
-
-             //Make the renderer reappear.
-             fireEditingStopped();
-
-         } else { //User pressed dialog's "OK" button.
-             currentColor = colorChooser.getColor();
-         }
-     }
-
-     //Implement the one CellEditor method that AbstractCellEditor doesn't.
-     public Object getCellEditorValue() {
-         return currentColor;
-     }
-
-     //Implement the one method defined by TableCellEditor.
-     public Component getTableCellEditorComponent(JTable table,
-                                                  Object value,
-                                                  boolean isSelected,
-                                                  int row,
-                                                  int column) {
-         currentColor = (Color)value;
-         return button;
-     }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.gui;
+
+import java.io.*;
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+
+import javax.swing.*;
+import javax.swing.event.*;
+import javax.swing.table.*;
+
+import jalview.datamodel.*;
+import jalview.io.*;
+
+public class FeatureSettings
+    extends JPanel
+{
+  DasSourceBrowser dassourceBrowser;
+  jalview.io.DasSequenceFeatureFetcher dasFeatureFetcher;
+  JPanel settingsPane = new JPanel();
+  JPanel dasSettingsPane = new JPanel();
+
+  final FeatureRenderer fr;
+  public final AlignFrame af;
+  Object[][] originalData;
+  final JInternalFrame frame;
+  JScrollPane scrollPane = new JScrollPane();
+  JTable table;
+  JPanel groupPanel;
+  JSlider transparency = new JSlider();
+
+  JPanel transPanel = new JPanel(new FlowLayout());
+
+  public FeatureSettings(AlignFrame af)
+  {
+    this.af = af;
+    fr = af.getFeatureRenderer();
+
+    transparency.setMaximum(100 - (int) (fr.transparency * 100));
+
+    try
+    {
+      jbInit();
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+
+    table = new JTable();
+    table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));
+    table.setFont(new Font("Verdana", Font.PLAIN, 12));
+    table.setDefaultRenderer(Color.class,
+                             new ColorRenderer());
+
+    table.setDefaultEditor(Color.class,
+                           new ColorEditor());
+
+    table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+
+    table.addMouseListener(new MouseAdapter()
+    {
+      public void mousePressed(MouseEvent evt)
+      {
+        selectedRow = table.rowAtPoint(evt.getPoint());
+      }
+    });
+
+    table.addMouseMotionListener(new MouseMotionAdapter()
+    {
+      public void mouseDragged(MouseEvent evt)
+      {
+        int newRow = table.rowAtPoint(evt.getPoint());
+        if (newRow != selectedRow
+            && selectedRow != -1
+            && newRow != -1)
+        {
+          Object[] temp = new Object[3];
+          temp[0] = table.getValueAt(selectedRow, 0);
+          temp[1] = table.getValueAt(selectedRow, 1);
+          temp[2] = table.getValueAt(selectedRow, 2);
+
+          table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0);
+          table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1);
+          table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2);
+
+          table.setValueAt(temp[0], newRow, 0);
+          table.setValueAt(temp[1], newRow, 1);
+          table.setValueAt(temp[2], newRow, 2);
+
+          selectedRow = newRow;
+        }
+      }
+    });
+
+    scrollPane.setViewportView(table);
+
+    dassourceBrowser = new DasSourceBrowser();
+    dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER);
+
+    if (af.getViewport().featuresDisplayed == null || fr.renderOrder == null)
+    {
+      fr.findAllFeatures(true); // display everything!
+    }
+
+    setTableData();
+    final PropertyChangeListener change;
+    final FeatureSettings fs=this;
+    fr.addPropertyChangeListener(change=new PropertyChangeListener() {
+      public void propertyChange(PropertyChangeEvent evt)
+      {
+        if (!fs.resettingTable && !fs.handlingUpdate) {
+          fs.handlingUpdate=true;
+          fs.resetTable(new String[] {}); // groups may be added
+          fs.handlingUpdate=false;
+        }
+      }
+      
+    });
+    
+    frame = new JInternalFrame();
+    frame.setContentPane(this);
+    Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 450);
+    frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+    {
+      public void internalFrameClosed(
+          javax.swing.event.InternalFrameEvent evt)
+      {
+        fr.removePropertyChangeListener(change);
+      }
+      ;
+    });
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);
+  }
+  /**
+   * true when Feature Settings are updating from feature renderer
+   */
+  private boolean handlingUpdate=false;
+  
+  /**
+   * contains a float[3] for each feature type string. created by setTableData
+   */
+  Hashtable typeWidth=null;
+  synchronized public void setTableData()
+  {
+    if (fr.featureGroups == null)
+    {
+      fr.featureGroups = new Hashtable();
+    }
+    Vector allFeatures = new Vector();
+    Vector allGroups = new Vector();
+    SequenceFeature[] tmpfeatures;
+    String group;
+    for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
+    {
+      if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence().
+          getSequenceFeatures() == null)
+      {
+        continue;
+      }
+
+      tmpfeatures = af.getViewport().alignment.getSequenceAt(i).
+          getDatasetSequence().getSequenceFeatures();
+
+      int index = 0;
+      while (index < tmpfeatures.length)
+      {
+        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);
+
+            boolean visible;
+            if (fr.featureGroups.containsKey(group))
+            {
+              visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();
+            } else {
+              visible=true; //initGroups || fr.av.featuresDisplayed.containsKey(tmpfeatures[index].getType());
+            }
+
+            if (groupPanel == null)
+            {
+              groupPanel = new JPanel();
+            }
+
+            boolean alreadyAdded = false;
+            for (int g = 0; g < groupPanel.getComponentCount(); g++)
+            {
+              if ( ( (JCheckBox) groupPanel.getComponent(g))
+                  .getText().equals(group))
+              {
+                alreadyAdded = true;
+                break;
+              }
+            }
+
+            if (alreadyAdded)
+            {
+              
+              continue;
+            }
+
+            fr.featureGroups.put(group, new Boolean(visible));
+            final String grp = group;
+            final JCheckBox check = new JCheckBox(group, visible);
+            check.setFont(new Font("Serif", Font.BOLD, 12));
+            check.addItemListener(new ItemListener()
+            {
+              public void itemStateChanged(ItemEvent evt)
+              {
+                fr.featureGroups.put(check.getText(),
+                                     new Boolean(check.isSelected()));
+                af.alignPanel.seqPanel.seqCanvas.repaint();
+                if (af.alignPanel.overviewPanel != null)
+                {
+                  af.alignPanel.overviewPanel.updateOverviewImage();
+                }
+
+                resetTable(new String[] { grp } );
+              }
+            });
+            groupPanel.add(check);
+          }
+        }
+
+        if (!allFeatures.contains(tmpfeatures[index].getType()))
+        {
+          allFeatures.addElement(tmpfeatures[index].getType());
+        }
+        index++;
+      }
+    }
+    
+    resetTable(null);
+
+    validate();
+  }
+  boolean resettingTable=false;
+  void resetTable(String[] groupChanged)
+  {
+    resettingTable=true;
+    typeWidth=new Hashtable();
+    Vector groupchanged = new Vector();
+    // 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
+    for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
+    {
+
+      tmpfeatures = af.getViewport().alignment.getSequenceAt(i).
+          getDatasetSequence().getSequenceFeatures();
+      if (tmpfeatures == null)
+      {
+        continue;
+      }
+
+      int index = 0;
+      while (index < tmpfeatures.length)
+      {
+        group = tmpfeatures[index].featureGroup;
+
+        if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0)
+        {
+          index++;
+          continue;
+        }
+
+        if (group == null || fr.featureGroups.get(group) == null ||
+            ( (Boolean) fr.featureGroups.get(group)).booleanValue())
+        {
+          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());
+        }
+        avWidth[0]++;
+        if (tmpfeatures[index].getBegin()>tmpfeatures[index].getEnd())
+        {
+          avWidth[1]+=1+tmpfeatures[index].getBegin()-tmpfeatures[index].getEnd();
+        } else {
+          avWidth[1]+=1+tmpfeatures[index].getEnd()-tmpfeatures[index].getBegin();
+        }
+        index++;
+      }
+    }
+
+    int fSize = visibleChecks.size();
+    Object[][] data = new Object[fSize][3];
+    int dataIndex = 0;
+
+    if (fr.renderOrder != null)
+    {
+      if (!handlingUpdate)
+        fr.findAllFeatures(groupChanged!=null); // prod to update colourschemes. but don't affect display
+      //First add the checks in the previous render order,
+      //in case the window has been closed and reopened
+      for (int ro = fr.renderOrder.length - 1; ro > -1; ro--)
+      {
+        type = fr.renderOrder[ro];
+
+        if (!visibleChecks.contains(type))
+        {
+          continue;
+        }
+
+        data[dataIndex][0] = type;
+        data[dataIndex][1] = fr.getColour(type);
+        data[dataIndex][2] = new Boolean(af.getViewport().featuresDisplayed.containsKey(type));
+        dataIndex++;
+        visibleChecks.removeElement(type);
+      }
+    }
+
+    fSize = visibleChecks.size();
+    for (int i = 0; i < fSize; i++)
+    {
+      //These must be extra features belonging to the group
+      //which was just selected
+      type = visibleChecks.elementAt(i).toString();
+      data[dataIndex][0] = type;
+
+      data[dataIndex][1] = fr.getColour(type);
+      if (data[dataIndex][1] == null)
+      {
+        //"Colour has been updated in another view!!"
+        fr.renderOrder = null;
+        return;
+      }
+
+      data[dataIndex][2] = new Boolean(true);
+      dataIndex++;
+    }
+
+    if (originalData == null)
+    {
+      originalData = new Object[data.length][3];
+      System.arraycopy(data, 0, originalData, 0, data.length);
+    }
+
+    table.setModel(new FeatureTableModel(data));
+    table.getColumnModel().getColumn(0).setPreferredWidth(200);
+
+    if (groupPanel != null)
+    {
+      groupPanel.setLayout(
+          new GridLayout(fr.featureGroups.size() / 4 + 1, 4));
+
+      groupPanel.validate();
+      bigPanel.add(groupPanel, BorderLayout.NORTH);
+    }
+
+    updateFeatureRenderer(data, groupChanged!=null);
+    resettingTable=false;
+  }
+  /**
+   * reorder data based on the featureRenderers global priority list.
+   * @param data
+   */
+  private void ensureOrder(Object[][] data)
+  {
+    boolean sort=false;
+    float[] order = new float[data.length];
+    for (int i=0;i<order.length; i++)
+    {
+      order[i] = fr.getOrder(data[i][0].toString());
+      if (order[i]<0)
+        order[i] = fr.setOrder(data[i][0].toString(), i/order.length);
+      if (i>1)
+        sort = sort || order[i-1]>order[i];
+    }
+    if (sort)
+      jalview.util.QuickSort.sort(order, data);
+  }
+
+  void load()
+  {
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+        getProperty(
+            "LAST_DIRECTORY"), new String[]
+        {"fc"},
+        new String[]
+        {"Sequence Feature Colours"}, "Sequence Feature Colours");
+    chooser.setFileView(new jalview.io.JalviewFileView());
+    chooser.setDialogTitle("Load Feature Colours");
+    chooser.setToolTipText("Load");
+
+    int value = chooser.showOpenDialog(this);
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      File file = chooser.getSelectedFile();
+
+      try
+      {
+        InputStreamReader in = new InputStreamReader(new FileInputStream(
+            file), "UTF-8");
+
+        jalview.binding.JalviewUserColours jucs = new jalview.binding.
+            JalviewUserColours();
+        jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
+
+        for (int i = jucs.getColourCount()-1; i >=0; i--)
+        {
+          String name;
+          fr.setColour(name=jucs.getColour(i).getName(),
+                       new Color(Integer.parseInt(jucs.getColour(i).getRGB(),
+                                                  16)));
+          fr.setOrder(name,(i==0) ? 0 : i/jucs.getColourCount());
+        }
+        if (table!=null) {
+          resetTable(null);
+          Object[][] data=((FeatureTableModel) table.getModel()).getData();
+          ensureOrder(data);
+          updateFeatureRenderer(data,false);
+          table.repaint();
+        }
+      }
+      catch (Exception ex)
+      {
+        System.out.println("Error loading User Colour File\n" + ex);
+      }
+    }
+  }
+
+  void save()
+  {
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+        getProperty(
+            "LAST_DIRECTORY"), new String[]
+        {"fc"},
+        new String[]
+        {"Sequence Feature Colours"}, "Sequence Feature Colours");
+    chooser.setFileView(new jalview.io.JalviewFileView());
+    chooser.setDialogTitle("Save Feature Colour Scheme");
+    chooser.setToolTipText("Save");
+
+    int value = chooser.showSaveDialog(this);
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      String choice = chooser.getSelectedFile().getPath();
+      jalview.binding.JalviewUserColours ucs = new jalview.binding.
+          JalviewUserColours();
+      ucs.setSchemeName("Sequence Features");
+      try
+      {
+        PrintWriter out = new PrintWriter(new OutputStreamWriter(
+            new FileOutputStream(choice), "UTF-8"));
+
+        Enumeration e = fr.featureColours.keys();
+        float[] sortOrder = new float[fr.featureColours.size()];
+        String[] sortTypes = new String[fr.featureColours.size()];
+        int i=0;
+        while (e.hasMoreElements())
+        {
+          sortTypes[i] = e.nextElement().toString();
+          sortOrder[i]  = fr.getOrder(sortTypes[i]);
+          i++;
+        }
+        jalview.util.QuickSort.sort(sortOrder, sortTypes);
+        sortOrder=null;
+        for (i=0; i<sortTypes.length; i++) {
+          jalview.binding.Colour col = new jalview.binding.Colour();
+          col.setName(sortTypes[i]);
+          col.setRGB(jalview.util.Format.getHexString(
+              fr.getColour(col.getName())));
+          ucs.addColour(col);
+        }
+        ucs.marshal(out);
+        out.close();
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+    }
+  }
+
+  public void invertSelection()
+  {
+    for (int i = 0; i < table.getRowCount(); i++)
+    {
+      Boolean value = (Boolean) table.getValueAt(i, 2);
+
+      table.setValueAt(
+          new Boolean(!value.booleanValue()),
+          i, 2);
+    }
+  }
+  public void orderByAvWidth() {
+    if (table==null || table.getModel()==null)
+      return;
+    Object[][] data = ((FeatureTableModel) table.getModel()).getData();
+    float[] width = new float[data.length];
+    float[] awidth;
+    float max=0;
+    int num=0;
+    for (int i=0;i<data.length;i++) {
+       awidth = (float[]) typeWidth.get(data[i][0]);
+       if (awidth[0]>0) {
+         width[i] = awidth[1]/awidth[0];// *awidth[0]*awidth[2]; - better weight - but have to make per sequence, too (awidth[2])
+         //if (width[i]==1) // hack to distinguish single width sequences.
+         num++;
+       } else {
+         width[i]=0;
+       }
+       if (max<width[i])
+         max=width[i];
+    }
+    boolean sort=false;
+    for (int i=0;i<width.length; i++) {
+      //awidth = (float[]) typeWidth.get(data[i][0]);
+      if (width[i]==0) 
+      {
+        width[i] = fr.getOrder(data[i][0].toString());
+        if (width[i]<0)
+        {
+          width[i] = fr.setOrder(data[i][0].toString(), i/data.length);
+        }
+      } else { 
+        width[i] /=max; // normalize
+        fr.setOrder(data[i][0].toString(), width[i]); // store for later 
+      }
+      if (i>0)
+        sort = sort || width[i-1]>width[i];
+    }
+    if (sort)
+      jalview.util.QuickSort.sort(width, data);
+    // update global priority order
+    
+    updateFeatureRenderer(data,false);
+    table.repaint();
+  }
+  public void close()
+  {
+    try
+    {
+      frame.setClosed(true);
+    }
+    catch (Exception exe)
+    {}
+
+  }
+
+  public void updateFeatureRenderer(Object[][] data)
+  {
+    updateFeatureRenderer(data, true);
+  }
+  private void updateFeatureRenderer(Object[][] data, boolean visibleNew)
+  {
+    fr.setFeaturePriority(data, visibleNew);
+    af.alignPanel.paintAlignment(true);
+
+    if (af.alignPanel.overviewPanel != null)
+    {
+      af.alignPanel.overviewPanel.updateOverviewImage();
+    }
+  }
+
+  int selectedRow = -1;
+  JTabbedPane tabbedPane = new JTabbedPane();
+  BorderLayout borderLayout1 = new BorderLayout();
+  BorderLayout borderLayout2 = new BorderLayout();
+  BorderLayout borderLayout3 = new BorderLayout();
+  JPanel bigPanel = new JPanel();
+  BorderLayout borderLayout4 = new BorderLayout();
+  JButton invert = new JButton();
+  JPanel buttonPanel = new JPanel();
+  JButton cancel = new JButton();
+  JButton ok = new JButton();
+  JButton loadColours = new JButton();
+  JButton saveColours = new JButton();
+  JPanel dasButtonPanel = new JPanel();
+  JButton fetchDAS = new JButton();
+  JButton saveDAS = new JButton();
+  JButton cancelDAS = new JButton();
+  JButton optimizeOrder = new JButton();
+  JPanel transbuttons = new JPanel(new BorderLayout());
+  private void jbInit()
+      throws Exception
+  {
+    this.setLayout(borderLayout1);
+    settingsPane.setLayout(borderLayout2);
+    dasSettingsPane.setLayout(borderLayout3);
+    bigPanel.setLayout(borderLayout4);
+    invert.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    invert.setText("Invert Selection");
+    invert.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        invertSelection();
+      }
+    });
+    optimizeOrder.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    optimizeOrder.setText("Optimise Order");
+    optimizeOrder.addActionListener(new ActionListener() {
+      public void actionPerformed(ActionEvent e) {
+        orderByAvWidth();
+      }
+    });
+    cancel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    cancel.setText("Cancel");
+    cancel.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        updateFeatureRenderer(originalData);
+        close();
+      }
+    });
+    ok.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    ok.setText("OK");
+    ok.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        close();
+      }
+    });
+    loadColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    loadColours.setText("Load Colours");
+    loadColours.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        load();
+      }
+    });
+    saveColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    saveColours.setText("Save Colours");
+    saveColours.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        save();
+      }
+    });
+    transparency.addChangeListener(new ChangeListener()
+    {
+      public void stateChanged(ChangeEvent evt)
+      {
+        fr.setTransparency( (float) (100 - transparency.getValue()) / 100f);
+        af.alignPanel.paintAlignment(true);
+      }
+    });
+
+    transparency.setMaximum(70);
+    fetchDAS.setText("Fetch DAS Features");
+    fetchDAS.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        fetchDAS_actionPerformed(e);
+      }
+    });
+    saveDAS.setText("Save as default");
+    saveDAS.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        saveDAS_actionPerformed(e);
+      }
+    });
+    dasButtonPanel.setBorder(BorderFactory.createEtchedBorder());
+    dasSettingsPane.setBorder(null);
+    cancelDAS.setEnabled(false);
+    cancelDAS.setText("Cancel Fetch");
+    cancelDAS.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        cancelDAS_actionPerformed(e);
+      }
+    });
+    this.add(tabbedPane, java.awt.BorderLayout.CENTER);
+    tabbedPane.addTab("Feature Settings", settingsPane);
+    tabbedPane.addTab("DAS Settings", dasSettingsPane);
+    bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH);
+    transPanel.add(transparency);
+    transbuttons.add(invert, java.awt.BorderLayout.NORTH);
+    transbuttons.add(optimizeOrder,java.awt.BorderLayout.SOUTH);
+    transPanel.add(transbuttons);
+    buttonPanel.add(ok);
+    buttonPanel.add(cancel);
+    buttonPanel.add(loadColours);
+    buttonPanel.add(saveColours);
+    bigPanel.add(scrollPane, java.awt.BorderLayout.CENTER);
+    dasSettingsPane.add(dasButtonPanel, java.awt.BorderLayout.SOUTH);
+    dasButtonPanel.add(fetchDAS);
+    dasButtonPanel.add(cancelDAS);
+    dasButtonPanel.add(saveDAS);
+    settingsPane.add(bigPanel, java.awt.BorderLayout.CENTER);
+    settingsPane.add(buttonPanel, java.awt.BorderLayout.SOUTH);
+  }
+
+  public void fetchDAS_actionPerformed(ActionEvent e)
+  {
+    fetchDAS.setEnabled(false);
+    cancelDAS.setEnabled(true);
+    Vector selectedSources = dassourceBrowser.getSelectedSources();
+
+    SequenceI[] dataset, seqs;
+    int iSize;
+
+    if (af.getViewport().getSelectionGroup() != null
+        && af.getViewport().getSelectionGroup().getSize() > 0)
+    {
+      iSize = af.getViewport().getSelectionGroup().getSize();
+      dataset = new SequenceI[iSize];
+      seqs = af.getViewport().getSelectionGroup().
+          getSequencesInOrder(
+              af.getViewport().getAlignment());
+    }
+    else
+    {
+      iSize = af.getViewport().getAlignment().getHeight();
+      seqs = af.getViewport().getAlignment().getSequencesArray();
+    }
+
+    dataset = new SequenceI[iSize];
+    for (int i = 0; i < iSize; i++)
+    {
+      dataset[i] = seqs[i].getDatasetSequence();
+    }
+
+    dasFeatureFetcher =
+        new jalview.io.DasSequenceFeatureFetcher(
+            dataset,
+            this,
+            selectedSources);
+    cancelDAS.setEnabled(true);
+    af.getViewport().setShowSequenceFeatures(true);
+    af.showSeqFeatures.setSelected(true);
+  }
+
+  public void saveDAS_actionPerformed(ActionEvent e)
+  {
+    dassourceBrowser.saveProperties(jalview.bin.Cache.applicationProperties);
+  }
+
+  public void complete()
+  {
+    fetchDAS.setEnabled(true);
+    cancelDAS.setEnabled(false);
+  }
+
+  public void cancelDAS_actionPerformed(ActionEvent e)
+  {
+    dasFeatureFetcher.cancel();
+    fetchDAS.setEnabled(true);
+    cancelDAS.setEnabled(false);
+  }
+
+  /////////////////////////////////////////////////////////////////////////
+  // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html
+  /////////////////////////////////////////////////////////////////////////
+  class FeatureTableModel
+      extends AbstractTableModel
+  {
+    FeatureTableModel(Object[][] data)
+    {
+      this.data = data;
+    }
+
+    private String[] columnNames =
+        {
+        "Feature Type", "Colour", "Display"};
+    private Object[][] data;
+
+    public Object[][] getData()
+    {
+      return data;
+    }
+
+    public void setData(Object[][] data)
+    {
+      this.data = data;
+    }
+
+    public int getColumnCount()
+    {
+      return columnNames.length;
+    }
+
+    public Object[] getRow(int row)
+    {
+      return data[row];
+    }
+
+    public int getRowCount()
+    {
+      return data.length;
+    }
+
+    public String getColumnName(int col)
+    {
+      return columnNames[col];
+    }
+
+    public Object getValueAt(int row, int col)
+    {
+      return data[row][col];
+    }
+
+    public Class getColumnClass(int c)
+    {
+      return getValueAt(0, c).getClass();
+    }
+
+    public boolean isCellEditable(int row, int col)
+    {
+      return col == 0 ? false : true;
+    }
+
+    public void setValueAt(Object value, int row, int col)
+    {
+      data[row][col] = value;
+      fireTableCellUpdated(row, col);
+      updateFeatureRenderer(data);
+    }
+
+  }
+
+  class ColorRenderer
+      extends JLabel implements TableCellRenderer
+  {
+    javax.swing.border.Border unselectedBorder = null;
+    javax.swing.border.Border selectedBorder = null;
+
+    public ColorRenderer()
+    {
+      setOpaque(true); //MUST do this for background to show up.
+    }
+
+    public Component getTableCellRendererComponent(
+        JTable table, Object color,
+        boolean isSelected, boolean hasFocus,
+        int row, int column)
+    {
+      Color newColor = (Color) color;
+      setBackground(newColor);
+      if (isSelected)
+      {
+        if (selectedBorder == null)
+        {
+          selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
+              table.getSelectionBackground());
+        }
+        setBorder(selectedBorder);
+      }
+      else
+      {
+        if (unselectedBorder == null)
+        {
+          unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
+              table.getBackground());
+        }
+        setBorder(unselectedBorder);
+      }
+
+      setToolTipText("RGB value: " + newColor.getRed() + ", "
+                     + newColor.getGreen() + ", "
+                     + newColor.getBlue());
+      return this;
+    }
+  }
+}
+
+class ColorEditor
+    extends AbstractCellEditor implements TableCellEditor,
+    ActionListener
+{
+  Color currentColor;
+  JButton button;
+  JColorChooser colorChooser;
+  JDialog dialog;
+  protected static final String EDIT = "edit";
+
+  public ColorEditor()
+  {
+    //Set up the editor (from the table's point of view),
+    //which is a button.
+    //This button brings up the color chooser dialog,
+    //which is the editor from the user's point of view.
+    button = new JButton();
+    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,
+                                        "Select new 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.
+   */
+  public void actionPerformed(ActionEvent e)
+  {
+
+    if (EDIT.equals(e.getActionCommand()))
+    {
+      //The user has clicked the cell, so
+      //bring up the dialog.
+      button.setBackground(currentColor);
+      colorChooser.setColor(currentColor);
+      dialog.setVisible(true);
+
+      //Make the renderer reappear.
+      fireEditingStopped();
+
+    }
+    else
+    { //User pressed dialog's "OK" button.
+      currentColor = colorChooser.getColor();
+    }
+  }
+
+  //Implement the one CellEditor method that AbstractCellEditor doesn't.
+  public Object getCellEditorValue()
+  {
+    return currentColor;
+  }
+
+  //Implement the one method defined by TableCellEditor.
+  public Component getTableCellEditorComponent(JTable table,
+                                               Object value,
+                                               boolean isSelected,
+                                               int row,
+                                               int column)
+  {
+    currentColor = (Color) value;
+    return button;
+  }
+}