X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDasSourceBrowser.java;h=c6235301db319ec1ba8855a8be70073796b0f0c7;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=e23685cf1a005aef5c77deb5e882c291ff053d9c;hpb=cdefedf239cfb9d70f5e6a1ba6ff8993bbf9d1be;p=jalview.git

diff --git a/src/jalview/gui/DasSourceBrowser.java b/src/jalview/gui/DasSourceBrowser.java
index e23685c..c623530 100755
--- a/src/jalview/gui/DasSourceBrowser.java
+++ b/src/jalview/gui/DasSourceBrowser.java
@@ -1,38 +1,36 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.gui;
 
-import jalview.jbgui.*;
-import javax.swing.table.AbstractTableModel;
-import javax.swing.event.*;
-import jalview.util.TableSorter;
+import java.util.*;
+
+import java.awt.*;
 import java.awt.event.*;
 import javax.swing.*;
-import java.util.*;
-import java.net.*;
+import javax.swing.event.*;
+import javax.swing.table.*;
 
-import org.biojava.services.das.registry.DasCoordinateSystem;
-import org.biojava.services.das.registry.DasSource;
-import java.awt.BorderLayout;
+import org.biojava.dasobert.dasregistry.*;
+import jalview.jbgui.*;
+import jalview.util.*;
 
-public class DasSourceBrowser extends GDasSourceBrowser
-    implements Runnable, ListSelectionListener
+public class DasSourceBrowser extends GDasSourceBrowser implements
+        Runnable, ListSelectionListener
 {
   static DasSource[] dasSources = null;
 
@@ -40,30 +38,49 @@ public class DasSourceBrowser extends GDasSourceBrowser
 
   Vector selectedSources;
 
-  public DasSourceBrowser()
+  public static String DEFAULT_REGISTRY = "http://www.dasregistry.org/das1/sources/";
+
+  /**
+   * true if thread is running and we are talking to DAS registry service
+   */
+  public boolean loadingDasSources = false;
+
+  protected static String getDasRegistryURL()
+  {
+    String registry = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
+            DEFAULT_REGISTRY);
+
+    if (registry.indexOf("/registry/das1/sources/") > -1)
+    {
+      jalview.bin.Cache.setProperty(jalview.bin.Cache.DAS_REGISTRY_URL,
+              DEFAULT_REGISTRY);
+      registry = DEFAULT_REGISTRY;
+    }
+    return registry;
+  }
+
+  public DasSourceBrowser(FeatureSettings featureSettings)
   {
-    registryURL.setText(jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
-        "http://servlet.sanger.ac.uk/dasregistry/services/das_registry") );
+    fs = featureSettings;
+    String registry = getDasRegistryURL();
+
+    registryURL.setText(registry);
 
     setSelectedFromProperties();
 
     displayFullDetails(null);
     table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 
-    capabilities.addListSelectionListener(this);
-    coords1.addListSelectionListener(this);
-    coords2.addListSelectionListener(this);
+    filter1.addListSelectionListener(this);
+    filter2.addListSelectionListener(this);
+    filter3.addListSelectionListener(this);
 
-    //Ask to be notified of selection changes.
+    // Ask to be notified of selection changes.
     ListSelectionModel rowSM = table.getSelectionModel();
     rowSM.addListSelectionListener(new ListSelectionListener()
     {
       public void valueChanged(ListSelectionEvent e)
       {
-        //Ignore extra messages.
-        if (e.getValueIsAdjusting())
-          return;
-
         ListSelectionModel lsm = (ListSelectionModel) e.getSource();
         if (!lsm.isSelectionEmpty())
         {
@@ -74,24 +91,37 @@ public class DasSourceBrowser extends GDasSourceBrowser
     });
 
     table.addMouseListener(new MouseAdapter()
+    {
+      public void mouseClicked(MouseEvent evt)
+      {
+        if (evt.getClickCount() == 2
+                || SwingUtilities.isRightMouseButton(evt))
         {
-          public void mouseClicked(MouseEvent evt)
-          {
-            if(evt.getClickCount()==2
-               || SwingUtilities.isRightMouseButton(evt))
-              editRemoveLocalSource(evt);
-          }
-        });
+          editRemoveLocalSource(evt);
+        }
+      }
+    });
 
-    if(dasSources==null)
+    if (dasSources != null)
     {
-    Thread worker = new Thread(this);
-    worker.start();
+      init();
+    }
+  }
+
+  FeatureSettings fs = null;
+
+  public DasSourceBrowser()
+  {
+    this(null);
+  }
+
+  public void paintComponent(java.awt.Graphics g)
+  {
+    if (dasSources == null && !loadingDasSources)
+    {
+      Thread worker = new Thread(this);
+      worker.start();
     }
-    else
-     {
-       init();
-     }
   }
 
   void init()
@@ -101,22 +131,22 @@ public class DasSourceBrowser extends GDasSourceBrowser
     for (int i = 0; i < dSize; i++)
     {
       data[i][0] = dasSources[i].getNickname();
-      data[i][1] = new Boolean(selectedSources.contains(dasSources[i].
-          getNickname()));
+      data[i][1] = new Boolean(selectedSources.contains(dasSources[i]
+              .getNickname()));
     }
 
     refreshTableData(data);
     setCapabilities(dasSources);
 
     javax.swing.SwingUtilities.invokeLater(new Runnable()
-        {
-          public void run()
-          {
-            TableSorter sorter = (TableSorter)table.getModel();
-            sorter.setSortingStatus(1, TableSorter.DESCENDING);
-            sorter.setSortingStatus(1, TableSorter.NOT_SORTED);
-          }
-        });
+    {
+      public void run()
+      {
+        TableSorter sorter = (TableSorter) table.getModel();
+        sorter.setSortingStatus(1, TableSorter.DESCENDING);
+        sorter.setSortingStatus(1, TableSorter.NOT_SORTED);
+      }
+    });
 
     progressBar.setIndeterminate(false);
     progressBar.setVisible(false);
@@ -124,7 +154,6 @@ public class DasSourceBrowser extends GDasSourceBrowser
     refresh.setVisible(true);
   }
 
-
   public void refreshTableData(Object[][] data)
   {
     TableSorter sorter = new TableSorter(new DASTableModel(data));
@@ -136,13 +165,12 @@ public class DasSourceBrowser extends GDasSourceBrowser
   {
 
     StringBuffer text = new StringBuffer(
-        "<HTML><font size=\"2\" face=\"Verdana, Arial, Helvetica, sans-serif\">");
+            "<HTML><font size=\"2\" face=\"Verdana, Arial, Helvetica, sans-serif\">");
 
     if (nickName == null)
     {
-      fullDetails.setText(text +
-                          "Select a DAS service from the table"
-                          + " to read a full description here.</font></html>");
+      fullDetails.setText(text + "Select a DAS service from the table"
+              + " to read a full description here.</font></html>");
       return;
     }
 
@@ -150,48 +178,51 @@ public class DasSourceBrowser extends GDasSourceBrowser
     for (int i = 0; i < dSize; i++)
     {
       if (!dasSources[i].getNickname().equals(nickName))
+      {
         continue;
+      }
 
       DasSource ds = dasSources[i];
 
-      text.append("<font color=\"#0000FF\">Id:</font> " + dasSources[i].getId() +
-                  "<br>");
-      text.append("<font color=\"#0000FF\">Nickname:</font> " +
-                  dasSources[i].getNickname() + "<br>");
-      text.append("<font color=\"#0000FF\">URL:</font> " + dasSources[i].getUrl() +
-                  "<br>");
+      text.append("<font color=\"#0000FF\">Id:</font> "
+              + dasSources[i].getId() + "<br>");
+      text.append("<font color=\"#0000FF\">Nickname:</font> "
+              + dasSources[i].getNickname() + "<br>");
+      text.append("<font color=\"#0000FF\">URL:</font> "
+              + dasSources[i].getUrl() + "<br>");
 
       text.append("<font color=\"#0000FF\">Admin Email:</font> <a href=\"mailto:"
-                  +dasSources[i].getAdminemail()
-                  +"\">"+dasSources[i].getAdminemail()+"</a>" +
-                  "<br>");
-
+              + dasSources[i].getAdminemail()
+              + "\">"
+              + dasSources[i].getAdminemail() + "</a>" + "<br>");
 
-      text.append("<font color=\"#0000FF\">Registered at:</font> " + dasSources[i].getRegisterDate() +
-                        "<br>");
+      text.append("<font color=\"#0000FF\">Registered at:</font> "
+              + dasSources[i].getRegisterDate() + "<br>");
 
-      text.append("<font color=\"#0000FF\">Last successful test:</font> " + dasSources[i].getLeaseDate() +
-                        "<br>");
+      text.append("<font color=\"#0000FF\">Last successful test:</font> "
+              + dasSources[i].getLeaseDate() + "<br>");
 
       text.append("<font color=\"#0000FF\">Labels:</font> ");
-      for(int s=0; s<dasSources[i].getLabels().length; s++)
+      for (int s = 0; s < dasSources[i].getLabels().length; s++)
       {
-        text.append( dasSources[i].getLabels()[s]);
-        if(s<dasSources[i].getLabels().length-1)
+        text.append(dasSources[i].getLabels()[s]);
+        if (s < dasSources[i].getLabels().length - 1)
+        {
           text.append(",");
+        }
         text.append(" ");
       }
       text.append("<br>");
 
-
-
       text.append("<font color=\"#0000FF\">Capabilities:</font> ");
       String[] scap = dasSources[i].getCapabilities();
       for (int j = 0; j < scap.length; j++)
       {
         text.append(scap[j]);
         if (j < scap.length - 1)
+        {
           text.append(", ");
+        }
       }
       text.append("<br>");
 
@@ -200,23 +231,28 @@ public class DasSourceBrowser extends GDasSourceBrowser
       for (int j = 0; j < dcs.length; j++)
       {
         text.append("(" + dcs[j].getUniqueId() + ") "
-                    + dcs[j].getCategory() + ", " + dcs[j].getName());
+                + dcs[j].getCategory() + ", " + dcs[j].getName());
         if (dcs[j].getNCBITaxId() != 0)
+        {
           text.append(", " + dcs[j].getNCBITaxId());
+        }
         if (dcs[j].getOrganismName().length() > 0)
+        {
           text.append(", " + dcs[j].getOrganismName());
+        }
 
         text.append("<br>");
       }
 
-      text.append("<font color=\"#0000FF\">Description:</font> " +
-                  dasSources[i].getDescription() + "<br>");
+      text.append("<font color=\"#0000FF\">Description:</font> "
+              + dasSources[i].getDescription() + "<br>");
 
-      if (dasSources[i].getHelperurl().length() > 0)
+      if (dasSources[i].getHelperurl() != null
+              && dasSources[i].getHelperurl().length() > 0)
       {
-        text.append("<font color=\"#0000FF\"><a href=\"" +
-                    dasSources[i].getHelperurl()
-                    + "\">Go to site</a></font<br>");
+        text.append("<font color=\"#0000FF\"><a href=\""
+                + dasSources[i].getHelperurl()
+                + "\">Go to site</a></font<br>");
       }
 
       text.append("</font></html>");
@@ -234,27 +270,92 @@ public class DasSourceBrowser extends GDasSourceBrowser
     });
   }
 
-
   public void run()
   {
+    loadingDasSources = true;
+
     addLocal.setVisible(false);
     refresh.setVisible(false);
     progressBar.setVisible(true);
     progressBar.setIndeterminate(true);
+    setParentGuiEnabled(false);
+    // Refresh the source list.
+    dasSources = null;
+    getDASSource();
 
-    dasSources = jalview.io.DasSequenceFeatureFetcher.getDASSources();
+    init();
 
-    appendLocalSources();
+    setParentGuiEnabled(true);
+    loadingDasSources = false;
 
-    init();
   }
 
+  private void setParentGuiEnabled(boolean b)
+  {
+    if (fs != null)
+    {
+      fs.fetchDAS.setEnabled(b);
+      fs.saveDAS.setEnabled(b);
+    }
+  }
+
+  public Vector getSelectedSources()
+  {
+    // wait around if we're still loading.
+    while (dasSources == null)
+    {
+      if (!loadingDasSources)
+      {
+        new Thread(this).start();
+        try
+        {
+          Thread.sleep(5);
+        } catch (Exception e)
+        {
+        }
+        ;
+        while (loadingDasSources)
+        {
+          try
+          {
+            Thread.sleep(5);
+          } catch (Exception e)
+          {
+          }
+          ;
+        }
+        ;
+      }
+    }
+
+    Vector selected = new Vector();
+    for (int r = 0; r < selectedSources.size(); r++)
+    {
+      for (int i = 0; i < dasSources.length; i++)
+      {
+        if (dasSources[i].getNickname()
+                .equals(selectedSources.elementAt(r)))
+        {
+          selected.addElement(dasSources[i]);
+          break;
+        }
+      }
+    }
+
+    return selected;
+  }
+
+  /**
+   * retrieve das sources from registry and add local source list
+   * 
+   * @return
+   */
   public DasSource[] getDASSource()
   {
-    if(dasSources==null)
+    if (dasSources == null)
     {
-     dasSources = jalview.io.DasSequenceFeatureFetcher.getDASSources();
-     appendLocalSources();
+      dasSources = jalview.ws.DasSequenceFeatureFetcher.getDASSources();
+      appendLocalSources();
     }
 
     return dasSources;
@@ -270,49 +371,55 @@ public class DasSourceBrowser extends GDasSourceBrowser
 
   private void setCapabilities(DasSource[] sources)
   {
-    Vector vcapabilities = new Vector();
-    Vector vcoords = new Vector();
-    Vector vcoords2 = new Vector();
+    Vector authority = new Vector();
+    Vector type = new Vector();
+    Vector label = new Vector();
 
-    vcapabilities.addElement("All");
-    vcoords.addElement("All");
-    vcoords2.addElement("All");
+    authority.addElement("Any");
+    type.addElement("Any");
+    label.addElement("Any");
 
     for (int i = 0; i < sources.length; i++)
     {
       DasSource ds = sources[i];
-      String[] scap = ds.getCapabilities();
-      for (int s = 0; s < scap.length; s++)
-      {
-        if (!vcapabilities.contains(scap[s]))
-        {
-          vcapabilities.addElement(scap[s]);
-        }
-      }
 
       DasCoordinateSystem[] dcs = ds.getCoordinateSystem();
 
       for (int j = 0; j < dcs.length; j++)
       {
-        if (!vcoords.contains(dcs[j].getCategory()))
-          vcoords.addElement(dcs[j].getCategory());
+        if (!type.contains(dcs[j].getCategory()))
+        {
+          type.addElement(dcs[j].getCategory());
+        }
 
-        if (!vcoords2.contains(dcs[j].getName()))
-          vcoords2.addElement(dcs[j].getName());
+        if (!authority.contains(dcs[j].getName()))
+        {
+          authority.addElement(dcs[j].getName());
+        }
       }
+
+      String[] slabels = ds.getLabels();
+      for (int s = 0; s < slabels.length; s++)
+      {
+        if (!label.contains(slabels[s]))
+        {
+          label.addElement(slabels[s]);
+        }
+      }
+
     }
 
-    capabilities.setListData(vcapabilities);
-    coords1.setListData(vcoords);
-    coords2.setListData(vcoords2);
+    filter1.setListData(authority);
+    filter2.setListData(type);
+    filter3.setListData(label);
 
     javax.swing.SwingUtilities.invokeLater(new Runnable()
     {
       public void run()
       {
-        capabilities.setSelectedIndex(0);
-        coords1.setSelectedIndex(0);
-        coords2.setSelectedIndex(0);
+        filter1.setSelectedIndex(0);
+        filter2.setSelectedIndex(0);
+        filter3.setSelectedIndex(0);
       }
     });
   }
@@ -320,218 +427,234 @@ public class DasSourceBrowser extends GDasSourceBrowser
   public void amendLocal(boolean newSource)
   {
     String url = "http://localhost:8080/", nickname = "";
-
-    if(!newSource)
+    boolean seqsrc = false;
+    if (!newSource)
     {
       int selectedRow = table.getSelectionModel().getMinSelectionIndex();
       nickname = table.getValueAt(selectedRow, 0).toString();
-      url = ((DasSource)localSources.get(nickname)).getUrl();
+      url = ((DasSource) localSources.get(nickname)).getUrl();
+      seqsrc = ((DasSource) localSources.get(nickname))
+              .hasCapability("sequence");
     }
 
     JTextField nametf = new JTextField(nickname, 40);
     JTextField urltf = new JTextField(url, 40);
-
+    JCheckBox seqs = new JCheckBox("Sequence Source");
+    seqs.setSelected(seqsrc);
     JPanel panel = new JPanel(new BorderLayout());
     JPanel pane12 = new JPanel(new BorderLayout());
     pane12.add(new JLabel("Nickname: "), BorderLayout.CENTER);
     pane12.add(nametf, BorderLayout.EAST);
     panel.add(pane12, BorderLayout.NORTH);
     pane12 = new JPanel(new BorderLayout());
-    pane12.add(new JLabel("URL: "), BorderLayout.CENTER);
+    pane12.add(new JLabel("URL: "), BorderLayout.NORTH);
+    pane12.add(seqs, BorderLayout.SOUTH);
     pane12.add(urltf, BorderLayout.EAST);
     panel.add(pane12, BorderLayout.SOUTH);
 
-
     int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
-        panel, "Enter Nickname & URL of Local DAS Source",
-        JOptionPane.OK_CANCEL_OPTION);
+            panel, "Enter Nickname & URL of Local DAS Source",
+            JOptionPane.OK_CANCEL_OPTION);
 
-       if (reply != JOptionPane.OK_OPTION )
-       {
-           return;
-       }
+    if (reply != JOptionPane.OK_OPTION)
+    {
+      return;
+    }
 
-       if(!urltf.getText().endsWith("/"))
-         urltf.setText(urltf.getText()+"/");
+    if (!urltf.getText().endsWith("/"))
+    {
+      urltf.setText(urltf.getText() + "/");
+    }
 
-       DasSource local = new DasSource();
+    Das1Source local = new Das1Source();
 
-       local.setUrl(urltf.getText());
-       local.setNickname(nametf.getText());
+    local.setUrl(urltf.getText());
+    local.setNickname(nametf.getText());
+    if (seqs.isSelected())
+    {
+      local.setCapabilities(new String[]
+      { "features", "sequence" });
+    }
+    if (localSources == null)
+    {
+      localSources = new Hashtable();
+    }
 
+    localSources.put(local.getNickname(), local);
 
-       if(localSources==null)
-         localSources = new Hashtable();
+    if (!newSource && !nickname.equals(nametf.getText()))
+    {
+      localSources.remove(nickname);
+    }
 
-       localSources.put(local.getNickname(), local);
+    int size = dasSources.length;
+    int adjust = newSource ? 1 : 0;
 
-       if(!newSource && !nickname.equals(nametf.getText()))
-       {
-         localSources.remove(nickname);
-       }
+    Object[][] data = new Object[size + adjust][2];
+    for (int i = 0; i < size; i++)
+    {
+      if (!newSource && dasSources[i].getNickname().equals(nickname))
+      {
+        ((DasSource) dasSources[i]).setNickname(local.getNickname());
+        ((DasSource) dasSources[i]).setUrl(local.getUrl());
+        data[i][0] = local.getNickname();
+        data[i][1] = new Boolean(true);
+      }
+      else
+      {
+        data[i][0] = dasSources[i].getNickname();
+        data[i][1] = new Boolean(selectedSources.contains(dasSources[i]
+                .getNickname()));
+      }
+    }
 
-       int size = dasSources.length;
-       int adjust = newSource ? 1 : 0;
+    if (newSource)
+    {
+      data[size][0] = local.getNickname();
+      data[size][1] = new Boolean(true);
+      selectedSources.add(local.getNickname());
+    }
 
-       Object[][] data = new Object[size+adjust][2];
-       for (int i = 0; i < size; i++)
-       {
-         if(!newSource && dasSources[i].getNickname().equals(nickname))
-         {
-           ((DasSource)dasSources[i]).setNickname(local.getNickname());
-           ((DasSource)dasSources[i]).setUrl(local.getUrl());
-           data[i][0] = local.getNickname();
-           data[i][1] = new Boolean(true);
-         }
-         else
-         {
-           data[i][0] = dasSources[i].getNickname();
-           data[i][1] = new Boolean(selectedSources.contains(dasSources[i].
-               getNickname()));
-         }
-       }
+    DasSource[] tmp = new DasSource[size + adjust];
 
-       if(newSource)
-       {
-         data[size][0] = local.getNickname();
-         data[size][1] = new Boolean(true);
-         selectedSources.add(local.getNickname());
-       }
+    System.arraycopy(dasSources, 0, tmp, 0, size);
 
-       DasSource [] tmp = new DasSource[size+adjust];
+    if (newSource)
+    {
+      tmp[size] = local;
+    }
 
-       System.arraycopy(dasSources, 0, tmp, 0, size);
+    dasSources = tmp;
 
-       if(newSource)
-         tmp[size] = local;
+    refreshTableData(data);
 
-       dasSources = tmp;
+    SwingUtilities.invokeLater(new Runnable()
+    {
+      public void run()
+      {
+        scrollPane.getVerticalScrollBar().setValue(
+                scrollPane.getVerticalScrollBar().getMaximum());
+      }
+    });
 
-       refreshTableData(data);
+    displayFullDetails(local.getNickname());
+  }
 
-       SwingUtilities.invokeLater(new Runnable()
-       {
-         public void run()
-         {
-           scrollPane.getVerticalScrollBar().setValue(
-               scrollPane.getVerticalScrollBar().getMaximum()
-               );
-         }
-       });
+  public void editRemoveLocalSource(MouseEvent evt)
+  {
+    int selectedRow = table.getSelectionModel().getMinSelectionIndex();
+    if (selectedRow == -1)
+    {
+      return;
+    }
 
-       displayFullDetails(local.getNickname());
-     }
+    String nickname = table.getValueAt(selectedRow, 0).toString();
 
-    public void editRemoveLocalSource(MouseEvent evt)
+    if (!localSources.containsKey(nickname))
     {
-      int selectedRow = table.getSelectionModel().getMinSelectionIndex();
-      if(selectedRow==-1)
-        return;
+      JOptionPane.showInternalMessageDialog(Desktop.desktop,
+              "You can only edit or remove local DAS Sources!",
+              "Public DAS source - not editable",
+              JOptionPane.WARNING_MESSAGE);
+      return;
+    }
 
-      String nickname = table.getValueAt(selectedRow, 0).toString();
+    Object[] options =
+    { "Edit", "Remove", "Cancel" };
+    int choice = JOptionPane.showInternalOptionDialog(Desktop.desktop,
+            "Do you want to edit or remove " + nickname + "?",
+            "Edit / Remove Local DAS Source",
+            JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE,
+            null, options, options[2]);
 
-      if (!localSources.containsKey(nickname))
+    switch (choice)
+    {
+    case 0:
+      amendLocal(false);
+      break;
+    case 1:
+      localSources.remove(nickname);
+      selectedSources.remove(nickname);
+      Object[][] data = new Object[dasSources.length - 1][2];
+      DasSource[] tmp = new DasSource[dasSources.length - 1];
+      int index = 0;
+      for (int i = 0; i < dasSources.length; i++)
       {
-        JOptionPane.showInternalMessageDialog(Desktop.desktop,
-        "You can only edit or remove local DAS Sources!",
-         "Public DAS source - not editable",
-         JOptionPane.WARNING_MESSAGE);
-        return;
+        if (dasSources[i].getNickname().equals(nickname))
+        {
+          continue;
+        }
+        else
+        {
+          tmp[index] = dasSources[i];
+          data[index][0] = dasSources[i].getNickname();
+          data[index][1] = new Boolean(
+                  selectedSources.contains(dasSources[i].getNickname()));
+          index++;
+        }
       }
-
-
-      Object[] options = {"Edit", "Remove", "Cancel"};
-      int choice = JOptionPane.showInternalOptionDialog(Desktop.desktop,
-    "Do you want to edit or remove "+nickname+"?",
-    "Edit / Remove Local DAS Source",
-    JOptionPane.YES_NO_CANCEL_OPTION,
-    JOptionPane.QUESTION_MESSAGE,
-    null,
-    options,
-    options[2]);
-
-      switch(choice)
+      dasSources = tmp;
+      refreshTableData(data);
+      SwingUtilities.invokeLater(new Runnable()
       {
-        case 0: amendLocal(false);   break;
-        case 1:
-          localSources.remove(nickname);
-          selectedSources.remove(nickname);
-          Object[][] data = new Object[dasSources.length-1][2];
-          DasSource [] tmp = new DasSource[dasSources.length-1];
-          int index = 0;
-          for (int i = 0; i < dasSources.length; i++)
-          {
-            if (dasSources[i].getNickname().equals(nickname))
-            {
-              continue;
-            }
-            else
-            {
-              tmp[index] = dasSources[i];
-              data[index][0] = dasSources[i].getNickname();
-              data[index][1] = new Boolean(selectedSources.contains(dasSources[i].
-                  getNickname()));
-              index++;
-            }
-          }
-           dasSources = tmp;
-           refreshTableData(data);
-           SwingUtilities.invokeLater(new Runnable()
-           {
-             public void run()
-             {
-               scrollPane.getVerticalScrollBar().setValue(
-                   scrollPane.getVerticalScrollBar().getMaximum()
-                   );
-             }
-           });
+        public void run()
+        {
+          scrollPane.getVerticalScrollBar().setValue(
+                  scrollPane.getVerticalScrollBar().getMaximum());
+        }
+      });
 
-          break;
-      }
+      break;
     }
+  }
 
-    void appendLocalSources()
+  void appendLocalSources()
+  {
+    if (localSources == null)
     {
-      if(localSources==null)
-        return;
-
-      int size = dasSources!=null ? dasSources.length : 0;
-      int lsize = localSources.size();
-
-      Object[][] data = new Object[size+lsize][2];
-      for (int i = 0; i < size; i++)
-      {
-        data[i][0] = dasSources[i].getNickname();
-        data[i][1] = new Boolean(selectedSources.contains(dasSources[i].
-            getNickname()));
-      }
+      return;
+    }
+    // note - we add all das sources to list so they can be filtered for the
+    // standard fetchDbRefs function
+    int size = dasSources != null ? dasSources.length : 0;
+    int lsize = localSources.size();
 
-      DasSource [] tmp = new DasSource[size+lsize];
-      if(dasSources!=null)
-        System.arraycopy(dasSources, 0, tmp, 0, size);
+    Object[][] data = new Object[size + lsize][2];
+    for (int i = 0; i < size; i++)
+    {
+      data[i][0] = dasSources[i].getNickname();
+      data[i][1] = new Boolean(selectedSources.contains(dasSources[i]
+              .getNickname()));
+    }
 
-      Enumeration en = localSources.keys();
-      int index = size;
-      while(en.hasMoreElements())
-      {
-        String key = en.nextElement().toString();
-        data[index][0] = key;
-        data[index][1] = new Boolean(false);
-        tmp[index] = new DasSource();
-        tmp[index].setNickname(key);
-        tmp[index].setUrl( ((DasSource)localSources.get(key)).getUrl() );
+    DasSource[] tmp = new DasSource[size + lsize];
+    if (dasSources != null)
+    {
+      System.arraycopy(dasSources, 0, tmp, 0, size);
+    }
 
-        index++;
-      }
+    Enumeration en = localSources.keys();
+    int index = size;
+    while (en.hasMoreElements())
+    {
+      String key = en.nextElement().toString();
+      data[index][0] = key;
+      data[index][1] = new Boolean(false);
+      tmp[index] = new Das1Source();
+      tmp[index].setNickname(key);
+      tmp[index].setUrl(((DasSource) localSources.get(key)).getUrl());
+
+      index++;
+    }
 
-         dasSources = tmp;
+    dasSources = tmp;
 
-         refreshTableData(data);
+    refreshTableData(data);
   }
 
   public void valueChanged(ListSelectionEvent evt)
   {
-    //Called when the MainTable selection changes
+    // Called when the MainTable selection changes
     if (evt.getValueIsAdjusting())
     {
       return;
@@ -541,31 +664,52 @@ public class DasSourceBrowser extends GDasSourceBrowser
 
     // Filter the displayed data sources
     int dSize = dasSources.length;
+
     ArrayList names = new ArrayList();
     ArrayList selected = new ArrayList();
     DasSource ds;
 
-    // capabilities.get
+    // The features filter is not visible, but we must still
+    // filter the das source list here.
+    // July 2006 - only 6 sources fo not serve features
+    Object[] dummyFeatureList = new Object[]
+    { "features" };
+
     for (int i = 0; i < dSize; i++)
     {
       ds = dasSources[i];
+      DasCoordinateSystem[] dcs = ds.getCoordinateSystem();
 
-      if (!selectedInList(capabilities, ds.getCapabilities()))
+      if (dcs.length == 0 && ds.getCapabilities().length == 0
+              && filter1.getSelectedIndex() == 0
+              && filter2.getSelectedIndex() == 0
+              && filter3.getSelectedIndex() == 0)
+      {
+        // THIS IS A FIX FOR LOCAL SOURCES WHICH DO NOT
+        // HAVE COORDINATE SYSTEMS, INFO WHICH AT PRESENT
+        // IS ADDED FROM THE REGISTRY
+        names.add(ds.getNickname());
+        selected.add(new Boolean(selectedSources.contains(ds.getNickname())));
+        continue;
+      }
+
+      if (!selectedInList(dummyFeatureList, ds.getCapabilities())
+              || !selectedInList(filter3.getSelectedValues(),
+                      ds.getLabels()))
       {
         continue;
       }
 
-      DasCoordinateSystem[] dcs = ds.getCoordinateSystem();
       for (int j = 0; j < dcs.length; j++)
       {
-        if (selectedInList(coords1, new String[]
-                           {dcs[j].getCategory()})
-            && selectedInList(coords2, new String[]
-                              {dcs[j].getName()}))
+        if (selectedInList(filter1.getSelectedValues(), new String[]
+        { dcs[j].getName() })
+                && selectedInList(filter2.getSelectedValues(), new String[]
+                { dcs[j].getCategory() }))
         {
           names.add(ds.getNickname());
-          selected.add(new Boolean(
-              selectedSources.contains(ds.getNickname())));
+          selected.add(new Boolean(selectedSources.contains(ds
+                  .getNickname())));
           break;
         }
       }
@@ -582,18 +726,21 @@ public class DasSourceBrowser extends GDasSourceBrowser
     refreshTableData(data);
   }
 
-  boolean selectedInList(JList list, String[] items)
+  boolean selectedInList(Object[] selection, String[] items)
   {
-    Object[] selection = list.getSelectedValues();
     for (int i = 0; i < selection.length; i++)
     {
-      if (selection[i].equals("All"))
+      if (selection[i].equals("Any"))
+      {
         return true;
+      }
 
       for (int j = 0; j < items.length; j++)
       {
         if (selection[i].equals(items[j]))
+        {
           return true;
+        }
       }
     }
 
@@ -602,69 +749,86 @@ public class DasSourceBrowser extends GDasSourceBrowser
 
   void setSelectedFromProperties()
   {
-     String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");
-     StringTokenizer st = new StringTokenizer(active, "\t");
-     selectedSources = new Vector();
-     while(st.hasMoreTokens())
-     {
-       selectedSources.addElement(st.nextToken());
-     }
-
-     String local = jalview.bin.Cache.getProperty("DAS_LOCAL_SOURCE");
-     if(local!=null)
-     {
-       if(localSources == null)
-         localSources = new Hashtable();
-
-       st = new StringTokenizer(local, "\t");
-       while(st.hasMoreTokens())
-       {
-         String token = st.nextToken();
-         int bar = token.indexOf("|");
-         DasSource source = new DasSource();
-
-         source.setUrl(token.substring(bar + 1));
-         source.setNickname(token.substring(0, bar));
-
-         localSources.put(source.getNickname(), source);
-       }
-     }
+    String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE",
+            "uniprot");
+    StringTokenizer st = new StringTokenizer(active, "\t");
+    selectedSources = new Vector();
+    while (st.hasMoreTokens())
+    {
+      selectedSources.addElement(st.nextToken());
+    }
+
+    Vector _localSources = jalview.bin.Cache.getLocalDasSources();
+    if (_localSources != null)
+    {
+      if (localSources == null)
+      {
+        localSources = new Hashtable();
+      }
+      Enumeration sources = _localSources.elements();
+      while (sources.hasMoreElements())
+      {
+        Das1Source source = (Das1Source) sources.nextElement();
+        localSources.put(source.getNickname(), source);
+      }
+    }
   }
 
-  void saveProperties(Properties properties)
+  public void reset_actionPerformed(ActionEvent e)
   {
-    properties.setProperty("DAS_REGISTRY_URL", registryURL.getText());
+    registryURL.setText(DEFAULT_REGISTRY);
+  }
+
+  /**
+   * set the DAS source settings in the given jalview properties.
+   * 
+   * @param properties
+   */
+  public void saveProperties(Properties properties)
+  {
+    if (registryURL.getText() == null || registryURL.getText().length() < 1)
+    {
+      properties.remove(jalview.bin.Cache.DAS_REGISTRY_URL);
+    }
+    else
+    {
+      properties.setProperty(jalview.bin.Cache.DAS_REGISTRY_URL,
+              registryURL.getText());
+    }
 
     StringBuffer sb = new StringBuffer();
-    for(int r=0; r<table.getModel().getRowCount(); r++)
+    for (int r = 0; r < table.getModel().getRowCount(); r++)
     {
-      if( ((Boolean)table.getValueAt(r,1)).booleanValue())
+      if (((Boolean) table.getValueAt(r, 1)).booleanValue())
       {
-        sb.append(table.getValueAt(r,0)+"\t");
+        sb.append(table.getValueAt(r, 0) + "\t");
       }
     }
 
-    properties.setProperty("DAS_ACTIVE_SOURCE", sb.toString() );
+    properties.setProperty(jalview.bin.Cache.DAS_ACTIVE_SOURCE,
+            sb.toString());
 
-    if(localSources!=null)
+    if (localSources != null)
     {
       sb = new StringBuffer();
       Enumeration en = localSources.keys();
-      while(en.hasMoreElements())
+      while (en.hasMoreElements())
       {
         String token = en.nextElement().toString();
-        sb.append(token+"|"
-                  + ((DasSource)localSources.get(token)).getUrl()
-                  +"\t");
+        sb.append(token
+                + "|"
+                + (((DasSource) localSources.get(token))
+                        .hasCapability("sequence") ? "sequence:" : "")
+                + ((DasSource) localSources.get(token)).getUrl() + "\t");
       }
 
-      properties.setProperty("DAS_LOCAL_SOURCE", sb.toString());
+      properties.setProperty(jalview.bin.Cache.DAS_LOCAL_SOURCE,
+              sb.toString());
     }
 
   }
 
-  class DASTableModel
-      extends AbstractTableModel
+  class DASTableModel extends AbstractTableModel
   {
 
     public DASTableModel(Object[][] data)
@@ -672,7 +836,8 @@ public class DasSourceBrowser extends GDasSourceBrowser
       this.data = data;
     }
 
-    private String[] columnNames = new String[]  {"Nickname", "Use Source"};
+    private String[] columnNames = new String[]
+    { "Nickname", "Use Source" };
 
     private Object[][] data;
 
@@ -697,10 +862,9 @@ public class DasSourceBrowser extends GDasSourceBrowser
     }
 
     /*
-     * JTable uses this method to determine the default renderer/
-     * editor for each cell.  If we didn't implement this method,
-     * then the last column would contain text ("true"/"false"),
-     * rather than a check box.
+     * JTable uses this method to determine the default renderer/ editor for
+     * each cell. If we didn't implement this method, then the last column would
+     * contain text ("true"/"false"), rather than a check box.
      */
     public Class getColumnClass(int c)
     {
@@ -708,36 +872,91 @@ public class DasSourceBrowser extends GDasSourceBrowser
     }
 
     /*
-     * Don't need to implement this method unless your table's
-     * editable.
+     * Don't need to implement this method unless your table's editable.
      */
     public boolean isCellEditable(int row, int col)
     {
-      //Note that the data/cell address is constant,
-      //no matter where the cell appears onscreen.
+      // Note that the data/cell address is constant,
+      // no matter where the cell appears onscreen.
       return col == 1;
 
     }
 
     /*
-     * Don't need to implement this method unless your table's
-     * data can change.
+     * Don't need to implement this method unless your table's data can change.
      */
     public void setValueAt(Object value, int row, int col)
     {
       data[row][col] = value;
       fireTableCellUpdated(row, col);
 
-      String name = getValueAt(row,0).toString();
-      boolean selected = ((Boolean)value).booleanValue();
+      String name = getValueAt(row, 0).toString();
+      boolean selected = ((Boolean) value).booleanValue();
 
-      if(selectedSources.contains(name) && !selected)
+      if (selectedSources.contains(name) && !selected)
+      {
         selectedSources.remove(name);
+      }
 
-      if(!selectedSources.contains(name) && selected)
+      if (!selectedSources.contains(name) && selected)
+      {
         selectedSources.add(name);
+      }
+    }
+  }
+
+  public void initDasSources()
+  {
+
+    Thread thr = new Thread(new Runnable()
+    {
+      public void run()
+      {
+        // this actually initialises the das source list
+        paintComponent(null); // yuk
+      }
+    });
+    thr.start();
+    while (loadingDasSources || dasSources == null)
+    {
+      try
+      {
+        Thread.sleep(10);
+      } catch (Exception e)
+      {
+      }
+      ;
     }
   }
-}
 
+  public Vector resolveSourceNicknames(Vector sources)
+  {
 
+    Vector resolved = new Vector();
+    if (sources != null)
+    {
+      for (int i = 0; i < dasSources.length; i++)
+      {
+        if (sources.contains(dasSources[i].getNickname()))
+        {
+          if (!resolved.contains(dasSources[i]))
+          {
+            resolved.addElement(dasSources[i]);
+          }
+        }
+      }
+    }
+    return resolved;
+  }
+
+  /**
+   * disable or enable the buttons on the source browser
+   * 
+   * @param b
+   */
+  public void setGuiEnabled(boolean b)
+  {
+    refresh.setEnabled(b);
+    addLocal.setEnabled(b);
+  }
+}