X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=955684c7cd175bfe919052d3e63ea2a8f7f4e8fc;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=556529206921c08b183314207a618d3a46155dc3;hpb=cd1face8eb59fa71e3c639237f4b7afbc80d3312;p=jalview.git

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 5565292..955684c 100755
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,398 +18,381 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.*;
-import javax.swing.*;
-import javax.swing.event.*;
-import java.awt.*;
+import java.io.*;
 import java.util.*;
-import javax.swing.BorderFactory;
+
+import java.awt.*;
 import java.awt.event.*;
+import javax.swing.*;
+import javax.swing.event.*;
 import javax.swing.table.*;
-import java.io.*;
-import jalview.io.JalviewFileChooser;
 
-public class FeatureSettings extends JPanel
+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;
-  final AlignmentPanel ap;
-  final AlignViewport av;
-  Object [][] originalData;
+  public final AlignFrame af;
+  Object[][] originalData;
   final JInternalFrame frame;
   JScrollPane scrollPane = new JScrollPane();
   JTable table;
   JPanel groupPanel;
+  JSlider transparency = new JSlider();
 
-  boolean alignmentHasFeatures = false;
+  JPanel transPanel = new JPanel(new FlowLayout());
 
-  public FeatureSettings(AlignViewport av, final AlignmentPanel ap)
+  public FeatureSettings(AlignFrame af)
   {
-    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);
-    frame.setLayer(JLayeredPane.PALETTE_LAYER);
+    this.af = af;
+    fr = af.getFeatureRenderer();
 
-    setTableData();
+    transparency.setMaximum(100 - (int) (fr.transparency * 100));
 
-    final JSlider transparency = new JSlider(0, 70, 100 - (int)(fr.transparency*100)   );
-    transparency.addChangeListener(new ChangeListener()
+    try
     {
-      public void stateChanged(ChangeEvent evt)
-      {
-        fr.setTransparency( (float) (100 - transparency.getValue()) / 100f);
-        ap.repaint();
-      }
-    });
+      jbInit();
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
 
-    JPanel transPanel = new JPanel(new FlowLayout());
-    transPanel.add(new JLabel("Transparency"));
-    transPanel.add(transparency);
-    JButton button = new JButton("Invert Selection");
-    transPanel.add(button);
-    button.addActionListener(new ActionListener()
-        {
-          public void actionPerformed(ActionEvent evt)
-          {
-            invertSelection();
-          }
-        });
+    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);
 
-    //////////////////////////////////////////////
-    //We're going to need those OK cancel buttons
-    JPanel buttonPanel = new JPanel(new FlowLayout());
-    button = new JButton("OK");
-    button.addActionListener(new ActionListener()
+    table.addMouseListener(new MouseAdapter()
     {
-      public void actionPerformed(ActionEvent evt)
+      public void mousePressed(MouseEvent evt)
       {
-        try
-        {
-          frame.setClosed(true);
-        }
-        catch (Exception exe)
-        {}
+        selectedRow = table.rowAtPoint(evt.getPoint());
       }
     });
-    buttonPanel.add(button);
-    button = new JButton("Cancel");
-    button.addActionListener(new ActionListener()
+
+    table.addMouseMotionListener(new MouseMotionAdapter()
     {
-      public void actionPerformed(ActionEvent evt)
+      public void mouseDragged(MouseEvent evt)
       {
-        try
+        int newRow = table.rowAtPoint(evt.getPoint());
+        if (newRow != selectedRow
+            && selectedRow != -1
+            && newRow != -1)
         {
-          updateFeatureRenderer(originalData);
-          frame.setClosed(true);
+          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;
         }
-        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);
+    scrollPane.setViewportView(table);
 
-    this.setLayout(new BorderLayout());
-    JPanel bigPanel = new JPanel(new BorderLayout());
-    bigPanel.add(transPanel, BorderLayout.SOUTH);
-    bigPanel.add(scrollPane, BorderLayout.CENTER);
-    if(groupPanel!=null)
-    {
-      groupPanel.setLayout(
-          new GridLayout(fr.featureGroups.size() / 4 + 1, 4));
+    dassourceBrowser = new DasSourceBrowser();
+    dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER);
 
-      groupPanel.validate();
-      bigPanel.add(groupPanel, BorderLayout.NORTH);
+    if (af.getViewport().featuresDisplayed == null || fr.renderOrder == null)
+    {
+      fr.findAllFeatures();
     }
-    add(bigPanel, BorderLayout.CENTER);
-    add(buttonPanel, BorderLayout.SOUTH);
 
+    setTableData();
 
+    frame = new JInternalFrame();
+    frame.setContentPane(this);
+    Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 450);
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);
   }
 
-  void setTableData()
+  synchronized public void setTableData()
   {
-    alignmentHasFeatures = false;
-
     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 < av.alignment.getHeight(); i++)
+    for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
     {
-      if (av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures() == null)
+      if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence().
+          getSequenceFeatures() == null)
+      {
         continue;
+      }
 
-      alignmentHasFeatures = true;
+      tmpfeatures = af.getViewport().alignment.getSequenceAt(i).
+          getDatasetSequence().getSequenceFeatures();
 
-      tmpfeatures = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
       int index = 0;
       while (index < tmpfeatures.length)
       {
-        if(tmpfeatures[index].getFeatureGroup()!=null)
+        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 = true;
-             if (fr.featureGroups.containsKey(group))
-             {
-               visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();
-             }
-
-             fr.featureGroups.put(group, new Boolean(visible));
-
-             if (groupPanel == null)
-             {
-               groupPanel = new JPanel();
-             }
-
-             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()));
-                 ap.seqPanel.seqCanvas.repaint();
-                 if (ap.overviewPanel != null)
-                   ap.overviewPanel.updateOverviewImage();
-
-                 resetTable(true);
-               }
-             });
-             groupPanel.add(check);
-
-           }
-
-       }
-
-       if (!allFeatures.contains(tmpfeatures[index].getType()))
-       {
-           allFeatures.addElement(tmpfeatures[index].getType());
-       }
-       index ++;
-    }
-  }
+          if (!allGroups.contains(group))
+          {
+            allGroups.addElement(group);
+
+            boolean visible = true;
+            if (fr.featureGroups.containsKey(group))
+            {
+              visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();
+            }
 
+            if (groupPanel == null)
+            {
+              groupPanel = new JPanel();
+            }
 
-    if(!alignmentHasFeatures)
-     {
-       try
-       { frame.setClosed(true);  }
-       catch (Exception ex){}
+            boolean alreadyAdded = false;
+            for (int g = 0; g < groupPanel.getComponentCount(); g++)
+            {
+              if ( ( (JCheckBox) groupPanel.getComponent(g))
+                  .getText().equals(group))
+              {
+                alreadyAdded = true;
+                break;
+              }
+            }
 
-       JOptionPane.showInternalMessageDialog(
-           Desktop.desktop, "No features have been added to this alignment!",
-           "No Sequence Features", JOptionPane.WARNING_MESSAGE);
+            if (alreadyAdded)
+            {
+              continue;
+            }
 
-       return;
-     }
+            fr.featureGroups.put(group, new Boolean(visible));
 
-     resetTable(false);
+            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(true);
+              }
+            });
+            groupPanel.add(check);
+          }
+        }
+
+        if (!allFeatures.contains(tmpfeatures[index].getType()))
+        {
+          allFeatures.addElement(tmpfeatures[index].getType());
+        }
+        index++;
+      }
+    }
+
+    resetTable(false);
+
+    validate();
   }
 
   void resetTable(boolean groupsChanged)
   {
-   SequenceFeature [] tmpfeatures;
-   String group=null, type;
-   Vector visibleChecks = new Vector();
+    SequenceFeature[] tmpfeatures;
+    String group = null, type;
+    Vector visibleChecks = new Vector();
 
-   //Find out which features should be visible depending on which groups
-   //are selected / deselected
-    for (int i = 0; i < av.alignment.getHeight(); i++)
+    //Find out which features should be visible depending on which groups
+    //are selected / deselected
+    for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
     {
-        if (av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures() == null)
-          continue;
 
-        tmpfeatures = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
-        int index = 0;
-        while (index < tmpfeatures.length)
+      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)
         {
-          group = tmpfeatures[index].featureGroup;
+          index++;
+          continue;
+        }
 
-          if (group==null || fr.featureGroups.get(group)==null ||
-              ((Boolean) fr.featureGroups.get(group)).booleanValue())
+        if (group == null || fr.featureGroups.get(group) == null ||
+            ( (Boolean) fr.featureGroups.get(group)).booleanValue())
+        {
+          type = tmpfeatures[index].getType();
+          if (!visibleChecks.contains(type))
           {
-            type = tmpfeatures[index].getType();
-            if(!visibleChecks.contains(type) )
-            {
-              visibleChecks.addElement(type);
-            }
+            visibleChecks.addElement(type);
           }
-          index++;
         }
+        index++;
+      }
     }
 
     int fSize = visibleChecks.size();
-    Object [][] data = new Object[fSize][3];
+    Object[][] data = new Object[fSize][3];
     int dataIndex = 0;
 
-    if(fr.renderOrder!=null)
+    if (fr.renderOrder != null)
     {
       //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--)
+      for (int ro = fr.renderOrder.length - 1; ro > -1; ro--)
       {
-           type = fr.renderOrder[ro];
+        type = fr.renderOrder[ro];
 
-           if(!visibleChecks.contains(type))
-             continue;
+        if (!visibleChecks.contains(type))
+        {
+          continue;
+        }
 
-           data[dataIndex][0] = type;
-           data[dataIndex][1] = fr.getColour(type);
-           data[dataIndex][2] = new Boolean(av.featuresDisplayed.containsKey(type));
-           dataIndex++;
-           visibleChecks.removeElement(type);
+        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++)
+    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)
+    if (originalData == null)
     {
       originalData = new Object[data.length][3];
-      System.arraycopy(data,0,originalData,0,data.length);
+      System.arraycopy(data, 0, originalData, 0, data.length);
     }
 
-    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.setModel(new FeatureTableModel(data));
+    table.getColumnModel().getColumn(0).setPreferredWidth(200);
 
-    table.setDefaultEditor(Color.class,
-                      new ColorEditor());
+    if (groupPanel != null)
+    {
+      groupPanel.setLayout(
+          new GridLayout(fr.featureGroups.size() / 4 + 1, 4));
 
-    table.getColumnModel().getColumn(0).setPreferredWidth(200);
+      groupPanel.validate();
+      bigPanel.add(groupPanel, BorderLayout.NORTH);
+    }
 
-    table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+    updateFeatureRenderer(data);
 
-    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);
+  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");
 
-              table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0);
-              table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1);
-              table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2);
+    int value = chooser.showOpenDialog(this);
 
-              table.setValueAt(temp[0], newRow, 0);
-              table.setValueAt(temp[1], newRow, 1);
-              table.setValueAt(temp[2], newRow, 2);
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      File file = chooser.getSelectedFile();
 
-              selectedRow = newRow;
-            }
-          }
-    });
+      try
+      {
+        InputStreamReader in = new InputStreamReader(new FileInputStream(
+            file), "UTF-8");
 
-    updateFeatureRenderer(data);
+        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)));
+        }
 
-  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);
-       }
-     }
+        setTableData();
+        af.alignPanel.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");
+    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");
@@ -418,60 +401,252 @@ public class FeatureSettings extends JPanel
 
     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);
-            }
+      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"));
 
-            ucs.marshal(out);
-            out.close();
-        }
-        catch (Exception ex)
+        Enumeration e = fr.featureColours.keys();
+        while (e.hasMoreElements())
         {
-            ex.printStackTrace();
+          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 invertSelection()
   {
-    for(int i=0; i<table.getRowCount(); i++)
+    for (int i = 0; i < table.getRowCount(); i++)
     {
-      Boolean value = (Boolean)table.getValueAt(i,2);
+      Boolean value = (Boolean) table.getValueAt(i, 2);
 
       table.setValueAt(
           new Boolean(!value.booleanValue()),
-                       i,2);
+          i, 2);
+    }
+  }
+
+  public void close()
+  {
+    try
+    {
+      frame.setClosed(true);
     }
+    catch (Exception exe)
+    {}
 
   }
 
-  public void updateFeatureRenderer(Object [][] data)
+  public void updateFeatureRenderer(Object[][] data)
   {
-    fr.setFeaturePriority( data );
-    ap.repaint();
+    fr.setFeaturePriority(data);
+    af.alignPanel.repaint();
 
-    if(ap.overviewPanel!=null)
-      ap.overviewPanel.updateOverviewImage();
+    if (af.alignPanel.overviewPanel != null)
+    {
+      af.alignPanel.overviewPanel.updateOverviewImage();
+    }
   }
 
-  int selectedRow =-1;
+  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();
+  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();
+      }
+    });
+    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.repaint();
+      }
+    });
+
+    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);
+    transPanel.add(invert);
+    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);
+
+    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
@@ -484,153 +659,179 @@ public class FeatureSettings extends JPanel
       this.data = data;
     }
 
-    private String[] columnNames = {"Feature Type", "Colour","Display"};
-          private Object[][] data;
+    private String[] columnNames =
+        {
+        "Feature Type", "Colour", "Display"};
+    private Object[][] data;
 
-          public Object[][] getData()
-          {
-            return data;
-          }
+    public Object[][] getData()
+    {
+      return data;
+    }
 
-          public void setData(Object[][] data)
-          {
-            this.data = data;
-          }
+    public void setData(Object[][] data)
+    {
+      this.data = data;
+    }
 
-          public int getColumnCount() {
-              return columnNames.length;
-          }
+    public int getColumnCount()
+    {
+      return columnNames.length;
+    }
 
-          public Object[] getRow(int row)
-          {
-            return data[row];
-          }
+    public Object[] getRow(int row)
+    {
+      return data[row];
+    }
 
-          public int getRowCount() {
-              return data.length;
-          }
+    public int getRowCount()
+    {
+      return data.length;
+    }
 
-          public String getColumnName(int col) {
-              return columnNames[col];
-          }
+    public String getColumnName(int col)
+    {
+      return columnNames[col];
+    }
 
-          public Object getValueAt(int row, int col) {
-              return data[row][col];
-          }
+    public Object getValueAt(int row, int col)
+    {
+      return data[row][col];
+    }
 
-          public Class getColumnClass(int c) {
-              return getValueAt(0, c).getClass();
-          }
+    public Class getColumnClass(int c)
+    {
+      return getValueAt(0, c).getClass();
+    }
 
-          public boolean isCellEditable(int row, int col) {
-              return col==0 ? false:true;
-          }
+    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);
-          }
+    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 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;
-     }
+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;
+  }
 }