X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDasSourceBrowser.java;h=7f41d3cba535e49c22115dd2d28e447b5e68d564;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=58580eb03dc89b79461e25a9f87f22e1b9543686;hpb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;p=jalview.git

diff --git a/src/jalview/gui/DasSourceBrowser.java b/src/jalview/gui/DasSourceBrowser.java
index 58580eb..7f41d3c 100755
--- a/src/jalview/gui/DasSourceBrowser.java
+++ b/src/jalview/gui/DasSourceBrowser.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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
@@ -18,22 +18,20 @@
  */
 package jalview.gui;
 
-import jalview.jbgui.*;
-import javax.swing.table.AbstractTableModel;
-import javax.swing.event.*;
-import jalview.util.TableSorter;
-import java.awt.event.*;
-import javax.swing.*;
 import java.util.*;
 
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+import javax.swing.event.*;
+import javax.swing.table.*;
 
-import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
-import org.biojava.dasobert.dasregistry.DasSource;
-import org.biojava.dasobert.dasregistry.Das1Source;
-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;
 
@@ -41,23 +39,23 @@ public class DasSourceBrowser extends GDasSourceBrowser
 
   Vector selectedSources;
 
-  public static String DEFAULT_REGISTRY = "http://www.dasregistry.org/das1/sources/";
+  public static String DEFAULT_REGISTRY =
+      "http://www.dasregistry.org/das1/sources/";
 
   boolean loadingDasSources = false;
 
-
   public DasSourceBrowser()
   {
     String registry = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
         DEFAULT_REGISTRY);
 
-    if(registry.indexOf("/registry/das1/sources/")>-1)
+    if (registry.indexOf("/registry/das1/sources/") > -1)
     {
       jalview.bin.Cache.setProperty("DAS_REGISTRY_URL", DEFAULT_REGISTRY);
       registry = DEFAULT_REGISTRY;
     }
 
-    registryURL.setText( registry );
+    registryURL.setText(registry);
 
     setSelectedFromProperties();
 
@@ -84,18 +82,20 @@ 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)
     {
-       init();
+      init();
     }
   }
 
@@ -123,14 +123,14 @@ public class DasSourceBrowser extends GDasSourceBrowser
     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);
@@ -138,7 +138,6 @@ public class DasSourceBrowser extends GDasSourceBrowser
     refresh.setVisible(true);
   }
 
-
   public void refreshTableData(Object[][] data)
   {
     TableSorter sorter = new TableSorter(new DASTableModel(data));
@@ -164,7 +163,9 @@ public class DasSourceBrowser extends GDasSourceBrowser
     for (int i = 0; i < dSize; i++)
     {
       if (!dasSources[i].getNickname().equals(nickName))
+      {
         continue;
+      }
 
       DasSource ds = dasSources[i];
 
@@ -175,37 +176,41 @@ public class DasSourceBrowser extends GDasSourceBrowser
       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>");
-
+      text.append(
+          "<font color=\"#0000FF\">Admin Email:</font> <a href=\"mailto:"
+          + 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>");
 
@@ -216,9 +221,13 @@ public class DasSourceBrowser extends GDasSourceBrowser
         text.append("(" + dcs[j].getUniqueId() + ") "
                     + 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>");
       }
@@ -226,8 +235,7 @@ public class DasSourceBrowser extends GDasSourceBrowser
       text.append("<font color=\"#0000FF\">Description:</font> " +
                   dasSources[i].getDescription() + "<br>");
 
-
-      if (dasSources[i].getHelperurl()!=null
+      if (dasSources[i].getHelperurl() != null
           && dasSources[i].getHelperurl().length() > 0)
       {
         text.append("<font color=\"#0000FF\"><a href=\"" +
@@ -250,7 +258,6 @@ public class DasSourceBrowser extends GDasSourceBrowser
     });
   }
 
-
   public void run()
   {
     loadingDasSources = true;
@@ -275,15 +282,15 @@ public class DasSourceBrowser extends GDasSourceBrowser
     Vector selected = new Vector();
     for (int r = 0; r < selectedSources.size(); r++)
     {
-        for (int i = 0; i < dasSources.length; i++)
+      for (int i = 0; i < dasSources.length; i++)
+      {
+        if (dasSources[i].getNickname().equals(
+            selectedSources.elementAt(r)))
         {
-          if (dasSources[i].getNickname().equals(
-              selectedSources.elementAt(r)))
-          {
-            selected.addElement(dasSources[i]);
-            break;
-          }
+          selected.addElement(dasSources[i]);
+          break;
         }
+      }
     }
 
     return selected;
@@ -291,10 +298,10 @@ public class DasSourceBrowser extends GDasSourceBrowser
 
   public DasSource[] getDASSource()
   {
-    if(dasSources==null)
+    if (dasSources == null)
     {
-     dasSources = jalview.io.DasSequenceFeatureFetcher.getDASSources();
-     appendLocalSources();
+      dasSources = jalview.io.DasSequenceFeatureFetcher.getDASSources();
+      appendLocalSources();
     }
 
     return dasSources;
@@ -327,10 +334,14 @@ public class DasSourceBrowser extends GDasSourceBrowser
       for (int j = 0; j < dcs.length; j++)
       {
         if (!type.contains(dcs[j].getCategory()))
+        {
           type.addElement(dcs[j].getCategory());
+        }
 
         if (!authority.contains(dcs[j].getName()))
+        {
           authority.addElement(dcs[j].getName());
+        }
       }
 
       String[] slabels = ds.getLabels();
@@ -363,11 +374,11 @@ public class DasSourceBrowser extends GDasSourceBrowser
   {
     String url = "http://localhost:8080/", nickname = "";
 
-    if(!newSource)
+    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();
     }
 
     JTextField nametf = new JTextField(nickname, 40);
@@ -383,209 +394,220 @@ public class DasSourceBrowser extends GDasSourceBrowser
     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);
 
-       if (reply != JOptionPane.OK_OPTION )
-       {
-           return;
-       }
-
-       if(!urltf.getText().endsWith("/"))
-         urltf.setText(urltf.getText()+"/");
-
-       Das1Source local = new Das1Source();
-
-       local.setUrl(urltf.getText());
-       local.setNickname(nametf.getText());
+    if (reply != JOptionPane.OK_OPTION)
+    {
+      return;
+    }
 
+    if (!urltf.getText().endsWith("/"))
+    {
+      urltf.setText(urltf.getText() + "/");
+    }
 
-       if(localSources==null)
-         localSources = new Hashtable();
+    Das1Source local = new Das1Source();
 
-       localSources.put(local.getNickname(), local);
+    local.setUrl(urltf.getText());
+    local.setNickname(nametf.getText());
 
-       if(!newSource && !nickname.equals(nametf.getText()))
-       {
-         localSources.remove(nickname);
-       }
+    if (localSources == null)
+    {
+      localSources = new Hashtable();
+    }
 
-       int size = dasSources.length;
-       int adjust = newSource ? 1 : 0;
+    localSources.put(local.getNickname(), local);
 
-       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()));
-         }
-       }
+    if (!newSource && !nickname.equals(nametf.getText()))
+    {
+      localSources.remove(nickname);
+    }
 
-       if(newSource)
-       {
-         data[size][0] = local.getNickname();
-         data[size][1] = new Boolean(true);
-         selectedSources.add(local.getNickname());
-       }
+    int size = dasSources.length;
+    int adjust = newSource ? 1 : 0;
 
-       DasSource [] tmp = new DasSource[size+adjust];
+    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()));
+      }
+    }
 
-       System.arraycopy(dasSources, 0, tmp, 0, size);
+    if (newSource)
+    {
+      data[size][0] = local.getNickname();
+      data[size][1] = new Boolean(true);
+      selectedSources.add(local.getNickname());
+    }
 
-       if(newSource)
-         tmp[size] = local;
+    DasSource[] tmp = new DasSource[size + adjust];
 
-       dasSources = tmp;
+    System.arraycopy(dasSources, 0, tmp, 0, size);
 
-       refreshTableData(data);
+    if (newSource)
+    {
+      tmp[size] = local;
+    }
 
-       SwingUtilities.invokeLater(new Runnable()
-       {
-         public void run()
-         {
-           scrollPane.getVerticalScrollBar().setValue(
-               scrollPane.getVerticalScrollBar().getMaximum()
-               );
-         }
-       });
+    dasSources = tmp;
 
-       displayFullDetails(local.getNickname());
-     }
+    refreshTableData(data);
 
-    public void editRemoveLocalSource(MouseEvent evt)
+    SwingUtilities.invokeLater(new Runnable()
     {
-      int selectedRow = table.getSelectionModel().getMinSelectionIndex();
-      if(selectedRow==-1)
-        return;
-
-      String nickname = table.getValueAt(selectedRow, 0).toString();
-
-      if (!localSources.containsKey(nickname))
+      public void run()
       {
-        JOptionPane.showInternalMessageDialog(Desktop.desktop,
-        "You can only edit or remove local DAS Sources!",
-         "Public DAS source - not editable",
-         JOptionPane.WARNING_MESSAGE);
-        return;
+        scrollPane.getVerticalScrollBar().setValue(
+            scrollPane.getVerticalScrollBar().getMaximum()
+            );
       }
+    });
 
+    displayFullDetails(local.getNickname());
+  }
 
-      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]);
+  public void editRemoveLocalSource(MouseEvent evt)
+  {
+    int selectedRow = table.getSelectionModel().getMinSelectionIndex();
+    if (selectedRow == -1)
+    {
+      return;
+    }
 
-      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++)
+    String nickname = table.getValueAt(selectedRow, 0).toString();
+
+    if (!localSources.containsKey(nickname))
+    {
+      JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                            "You can only edit or remove local DAS Sources!",
+                                            "Public DAS source - not editable",
+                                            JOptionPane.WARNING_MESSAGE);
+      return;
+    }
+
+    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)
+    {
+      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
           {
-            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++;
-            }
+            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()
-                   );
-             }
-           });
+        }
+        dasSources = tmp;
+        refreshTableData(data);
+        SwingUtilities.invokeLater(new Runnable()
+        {
+          public void run()
+          {
+            scrollPane.getVerticalScrollBar().setValue(
+                scrollPane.getVerticalScrollBar().getMaximum()
+                );
+          }
+        });
 
-          break;
-      }
+        break;
     }
+  }
 
-    void appendLocalSources()
+  void appendLocalSources()
+  {
+    if (localSources == null)
     {
-      if(localSources==null)
-        return;
+      return;
+    }
 
-      int size = dasSources!=null ? dasSources.length : 0;
-      int lsize = localSources.size();
+    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()));
-      }
+    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()));
+    }
 
-      DasSource [] tmp = new DasSource[size+lsize];
-      if(dasSources!=null)
-        System.arraycopy(dasSources, 0, tmp, 0, size);
+    DasSource[] tmp = new DasSource[size + lsize];
+    if (dasSources != null)
+    {
+      System.arraycopy(dasSources, 0, tmp, 0, size);
+    }
 
-      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++;
-      }
+    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
-    if (evt.getValueIsAdjusting() )
+    if (evt.getValueIsAdjusting())
     {
       return;
     }
 
-
     displayFullDetails(null);
 
     // Filter the displayed data sources
     int dSize = dasSources.length;
 
-
     ArrayList names = new ArrayList();
     ArrayList selected = new ArrayList();
     DasSource ds;
@@ -593,7 +615,9 @@ public class DasSourceBrowser extends GDasSourceBrowser
     //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"};
+    Object[] dummyFeatureList = new Object[]
+        {
+        "features"};
 
     for (int i = 0; i < dSize; i++)
     {
@@ -610,21 +634,20 @@ public class DasSourceBrowser extends GDasSourceBrowser
         //IS ADDED FROM THE REGISTRY
         names.add(ds.getNickname());
         selected.add(new Boolean(
-              selectedSources.contains(ds.getNickname())));
+            selectedSources.contains(ds.getNickname())));
         continue;
       }
 
-
       if (!selectedInList(dummyFeatureList, ds.getCapabilities())
-      ||  !selectedInList(filter3.getSelectedValues(),
-                          ds.getLabels()))
+          || !selectedInList(filter3.getSelectedValues(),
+                             ds.getLabels()))
       {
         continue;
       }
 
       for (int j = 0; j < dcs.length; j++)
       {
-        if (   selectedInList(filter1.getSelectedValues(),
+        if (selectedInList(filter1.getSelectedValues(),
                            new String[]
                            {dcs[j].getName()})
             && selectedInList(filter2.getSelectedValues(),
@@ -650,17 +673,21 @@ public class DasSourceBrowser extends GDasSourceBrowser
     refreshTableData(data);
   }
 
-  boolean selectedInList(Object [] selection, String[] items)
+  boolean selectedInList(Object[] selection, String[] items)
   {
     for (int i = 0; i < selection.length; i++)
     {
-      if (selection[i].equals("Any") )
+      if (selection[i].equals("Any"))
+      {
         return true;
+      }
 
       for (int j = 0; j < items.length; j++)
       {
         if (selection[i].equals(items[j]))
+        {
           return true;
+        }
       }
     }
 
@@ -669,33 +696,35 @@ 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("|");
-         Das1Source source = new Das1Source();
-
-         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());
+    }
+
+    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("|");
+        Das1Source source = new Das1Source();
+
+        source.setUrl(token.substring(bar + 1));
+        source.setNickname(token.substring(0, bar));
+
+        localSources.put(source.getNickname(), source);
+      }
+    }
   }
 
   public void reset_actionPerformed(ActionEvent e)
@@ -706,31 +735,35 @@ public class DasSourceBrowser extends GDasSourceBrowser
   public void saveProperties(Properties properties)
   {
     if (registryURL.getText() == null || registryURL.getText().length() < 1)
+    {
       properties.remove("DAS_REGISTRY_URL");
+    }
     else
+    {
       properties.setProperty("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("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)).getUrl()
+                  + "\t");
       }
 
       properties.setProperty("DAS_LOCAL_SOURCE", sb.toString());
@@ -747,7 +780,9 @@ 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;
 
@@ -803,16 +838,18 @@ public class DasSourceBrowser extends GDasSourceBrowser
       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);
+      }
     }
   }
 }
-
-