From: kiramt <k.mourao@dundee.ac.uk>
Date: Wed, 7 Dec 2016 11:43:28 +0000 (+0000)
Subject: JAL-2316 Restructure identifiers.org download
X-Git-Tag: Release_2_10_3b1~346^2~25
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=e63a4d52c27252dfb83efeeee1bda6c89b6dddec

JAL-2316 Restructure identifiers.org download
---

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index a52e6a4..1f5bdeb 100644
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -1277,6 +1277,7 @@ exception.url_cannot_have_miriam_id = {0} is a MIRIAM id and cannot be used as a
 exception.url_cannot_have_duplicate_id = {0} cannot be used as a label for more than one line
 label.filter = Filter text:
 action.customfilter = Custom only
+action.showall = Show All
 label.insert = Insert:
 action.seq_id = $SEQUENCE_ID$
 action.db_acc = $DB_ACCESSION$
diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties
index f1339f8..b0194b9 100644
--- a/resources/lang/Messages_es.properties
+++ b/resources/lang/Messages_es.properties
@@ -1278,6 +1278,7 @@ exception.url_cannot_have_miriam_id = {0} is a MIRIAM id and cannot be used as a
 exception.url_cannot_have_duplicate_id = {0} cannot be used as a label for more than one link
 label.filter = Filter text:
 action.customfilter = Custom only
+action.showall = Show All
 label.insert = Insert:
 action.seq_id = $SEQUENCE_ID$
 action.db_acc = $DB_ACCESSION$
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 8412dab..fe21406 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -22,6 +22,7 @@ package jalview.bin;
 
 import jalview.datamodel.PDBEntry;
 import jalview.structure.StructureImportSettings;
+import jalview.urls.IdOrgSettings;
 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
 import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
 import jalview.ws.sifts.SiftsSettings;
@@ -220,6 +221,9 @@ public class Cache
 
   public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
 
+  /**
+   * Sifts settings
+   */
   public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
           .getProperty("user.home")
           + File.separatorChar
@@ -230,6 +234,14 @@ public class Cache
   private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
 
   /**
+   * Identifiers.org download settings
+   */
+  private static final String ID_ORG_FILE = System.getProperty("user.home")
+          + File.separatorChar + ".jalview_identifiers";
+
+  private static final String ID_ORG_URL = "http://identifiers.org/rest/collections/";
+
+  /**
    * Allowed values are PDB or mmCIF
    */
   private final static String PDB_DOWNLOAD_FORMAT = PDBEntry.Type.MMCIF
@@ -440,6 +452,9 @@ public class Cache
             "sifts_cache_threshold_in_days",
             DEFAULT_CACHE_THRESHOLD_IN_DAYS));
 
+    IdOrgSettings.setUrl(ID_ORG_URL);
+    IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
+
     System.out
             .println("Jalview Version: " + codeVersion + codeInstallation);
 
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index e0abe93..41ce9a7 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -34,11 +34,13 @@ import jalview.io.JalviewFileView;
 import jalview.jbgui.GSplitFrame;
 import jalview.jbgui.GStructureViewer;
 import jalview.structure.StructureSelectionManager;
+import jalview.urls.IdOrgSettings;
 import jalview.util.ImageMaker;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.util.UrlConstants;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.ws.UrlDownloadClient;
 import jalview.ws.params.ParamManager;
 
 import java.awt.BorderLayout;
@@ -74,6 +76,7 @@ import java.beans.PropertyChangeListener;
 import java.io.BufferedInputStream;
 import java.io.File;
 import java.io.FileOutputStream;
+import java.io.IOException;
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.Hashtable;
@@ -389,6 +392,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
     showNews.setVisible(false);
 
+    getIdentifiersOrgData();
+
     checkURLLinks();
 
     this.addWindowListener(new WindowAdapter()
@@ -525,6 +530,29 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     });
   }
 
+  public void getIdentifiersOrgData()
+  {
+    // Thread off the identifiers fetcher
+    addDialogThread(new Runnable()
+    {
+      @Override
+      public void run()
+      {
+        Cache.log.debug("Downloading data from identifiers.org");
+        UrlDownloadClient client = new UrlDownloadClient();
+        try
+        {
+          client.download(IdOrgSettings.getUrl(),
+                  IdOrgSettings.getDownloadLocation());
+        } catch (IOException e)
+        {
+          Cache.log.debug("Exception downloading identifiers.org data"
+                  + e.getMessage());
+        }
+      }
+    });
+  }
+
   @Override
   protected void showNews_actionPerformed(ActionEvent e)
   {
diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 550f324..efe1ed6 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -128,10 +128,13 @@ public class Preferences extends GPreferences
   public static List<String> groupURLLinks;
   static
   {
-    String string = Cache.getDefault("SEQUENCE_LINKS",
+    String inMenuString = Cache.getDefault("SEQUENCE_LINKS",
             UrlConstants.DEFAULT_STRING);
-    UrlProviderFactoryI factory = new DesktopUrlProviderFactory(
-            UrlConstants.DEFAULT_LABEL, string);
+    String notInMenuString = Cache.getDefault("STORED_LINKS", "");
+    String defaultUrl = Cache.getDefault("DEFAULT_URL",
+            UrlConstants.DEFAULT_LABEL);
+    UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
+            inMenuString, notInMenuString);
     sequenceUrlLinks = factory.createUrlProvider();
     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 
@@ -414,7 +417,7 @@ public class Preferences extends GPreferences
 
     // set up radio buttons
     linkUrlTable.getColumn("Default").setCellRenderer(
-            new RadioButtonRenderer());
+               new RadioButtonRenderer());
     linkUrlTable.getColumn("Default")
             .setCellEditor(new RadioButtonEditor());
 
@@ -635,17 +638,31 @@ public class Preferences extends GPreferences
     jalview.util.BrowserLauncher.resetBrowser();
 
     // save user-defined and selected links
-    String links = linkUrlTable.getModel().toString();
-    if (links.isEmpty())
+    String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
+    if (menuLinks.isEmpty())
     {
       Cache.applicationProperties.remove("SEQUENCE_LINKS");
     }
     else
     {
       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
-              links.toString());
+              menuLinks.toString());
     }
 
+    String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
+    if (nonMenuLinks.isEmpty())
+    {
+      Cache.applicationProperties.remove("STORED_LINKS");
+    }
+    else
+    {
+      Cache.applicationProperties.setProperty("STORED_LINKS",
+              nonMenuLinks.toString());
+    }
+
+    Cache.applicationProperties.setProperty("DEFAULT_URL",
+            sequenceUrlLinks.getDefaultUrlId());
+
     Cache.applicationProperties.setProperty("USE_PROXY",
             Boolean.toString(useProxy.isSelected()));
 
diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index 3fe1939..6fe6be2 100755
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -654,6 +654,12 @@ public class GPreferences extends JPanel
     linkUrlTable.setAutoCreateRowSorter(true);
     linkUrlTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 
+    // adjust row height so radio buttons actually fit
+    // don't do this in the renderer, it causes the awt thread to activate
+    // constantly
+    JRadioButton temp = new JRadioButton();
+    linkUrlTable.setRowHeight(temp.getMinimumSize().height);
+
     // Table in scrollpane so that the table is given a scrollbar
     JScrollPane linkScrollPane = new JScrollPane(linkUrlTable);
     linkScrollPane.setBorder(null);
@@ -706,7 +712,7 @@ public class GPreferences extends JPanel
     filterTB.setFont(LABEL_FONT);
     filterTB.setText("");
 
-    doReset.setText(MessageManager.getString("action.reset"));
+    doReset.setText(MessageManager.getString("action.showall"));
     userOnly.setText(MessageManager.getString("action.customfilter"));
 
     // Panel for filter functionality
@@ -1515,54 +1521,51 @@ public class GPreferences extends JPanel
 
       // set colours to match rest of table
       if (isSelected)
-      {
-        setBackground(table.getSelectionBackground());
-        setForeground(table.getSelectionForeground());
-      }
-      else
-      {
-        setBackground(table.getBackground());
-        setForeground(table.getForeground());
+       {
+         setBackground(table.getSelectionBackground());
+         setForeground(table.getSelectionForeground());
+       }
+       else
+       {
+         setBackground(table.getBackground());
+         setForeground(table.getForeground());
       }
 
-      // adjust row height so radio buttons actually fit
-      table.setRowHeight(row, getMinimumSize().height);
-
       return this;
     }
   }
 
   public class RadioButtonEditor extends AbstractCellEditor implements
-          TableCellEditor
-  {
-    private JRadioButton button = new JRadioButton();
-
-    public RadioButtonEditor()
+            TableCellEditor
     {
-      this.button.setHorizontalAlignment(SwingConstants.CENTER);
-      this.button.addActionListener(new ActionListener()
+      private JRadioButton button = new JRadioButton();
+
+      public RadioButtonEditor()
       {
-        @Override
-        public void actionPerformed(ActionEvent e)
+        // this.button.setHorizontalAlignment(SwingConstants.CENTER);
+      this.button.addActionListener(new ActionListener()
         {
-          fireEditingStopped();
-        }
-      });
-    }
+          @Override
+          public void actionPerformed(ActionEvent e)
+          {
+            fireEditingStopped();
+          }
+        });
+      }
 
-    @Override
-    public Component getTableCellEditorComponent(JTable table,
-            Object value, boolean isSelected, int row, int column)
-    {
+      @Override
+      public Component getTableCellEditorComponent(JTable table,
+              Object value, boolean isSelected, int row, int column)
+      {
       button.setSelected((boolean) value);
-      return button;
-    }
+        return button;
+      }
 
-    @Override
-    public Object getCellEditorValue()
-    {
+      @Override
+      public Object getCellEditorValue()
+      {
       return button.isSelected();
-    }
+      }
 
   }
 }
diff --git a/src/jalview/urls/AppletUrlProviderFactory.java b/src/jalview/urls/AppletUrlProviderFactory.java
index 6faf9c0..db1206c 100644
--- a/src/jalview/urls/AppletUrlProviderFactory.java
+++ b/src/jalview/urls/AppletUrlProviderFactory.java
@@ -49,11 +49,11 @@ public class AppletUrlProviderFactory implements UrlProviderFactoryI
   {
     // create all the UrlProviders we need
     List<UrlProviderI> providers = new ArrayList<UrlProviderI>();
-    UrlProviderI customProvider = new CustomUrlProvider(provUrlList);
+    UrlProviderI customProvider = new CustomUrlProvider(provUrlList, null);
     providers.add(customProvider);
 
     UrlProviderI prov = new UrlProvider(provDefaultUrl, providers);
-    return null;
+    return prov;
   }
 
 }
diff --git a/src/jalview/urls/CustomUrlProvider.java b/src/jalview/urls/CustomUrlProvider.java
index ec594b6..ab84be2 100644
--- a/src/jalview/urls/CustomUrlProvider.java
+++ b/src/jalview/urls/CustomUrlProvider.java
@@ -52,84 +52,107 @@ public class CustomUrlProvider extends UrlProviderImpl
   // Default sequence URL link label for SRS
   private static final String SRS_LABEL = "SRS";
 
-  // map of string ids to urlLinks
-  private HashMap<String, UrlLink> urls;
+  // map of string ids to urlLinks (selected)
+  private HashMap<String, UrlLink> selectedUrls;
+
+  // map of string ids to urlLinks (not selected)
+  private HashMap<String, UrlLink> nonselectedUrls;
 
   /**
    * Construct UrlProvider for custom (user-entered) URLs
    * 
-   * @param cachedUrlList
-   *          list of URLs in form stored in Cache. i.e. SEP delimited string
+   * @param inMenuUrlList
+   *          list of URLs set to be displayed in menu, in form stored in Cache.
+   *          i.e. SEP delimited string
+   * @param storedUrlList
+   *          list of custom URLs entered by user but not currently displayed in
+   *          menu, in form stored in Cache
    */
-  public CustomUrlProvider(String cachedUrlList)
+  public CustomUrlProvider(String inMenuUrlList, String storedUrlList)
   {
     try
     {
-      urls = new HashMap<String, UrlLink>();
-
-      // cachedUrlList is in form <label>|<url>|<label>|<url>...
-      // parse cachedUrlList into labels (used as id) and url links
-      StringTokenizer st = new StringTokenizer(cachedUrlList, SEP);
-      while (st.hasMoreElements())
-      {
-        String name = st.nextToken();
-
-        if (!isMiriamId(name))
-        {
-          // this one of our custom urls
-          String url = st.nextToken();
-          // check for '|' within a regex
-          int rxstart = url.indexOf(DELIM + DB_ACCESSION + DELIM);
-          if (rxstart == -1)
-          {
-            rxstart = url.indexOf(DELIM + SEQUENCE_ID + DELIM);
-          }
-          while (rxstart == -1 && url.indexOf("/=" + DELIM) == -1
-                  && st.hasMoreTokens())
-          {
-            url = url + SEP + st.nextToken();
-          }
-          urls.put(name, new UrlLink(name + SEP + url));
-        }
-      }
+      selectedUrls = parseUrlStrings(inMenuUrlList);
+      nonselectedUrls = parseUrlStrings(storedUrlList);
     } catch (Exception ex)
     {
       System.out.println(ex + "\nError parsing sequence links");
     }
-    upgradeOldLinks();
-
   }
 
   /**
    * Construct UrlProvider for custom (user-entered) URLs
    * 
    * @param urlList
-   *          list of URLs as (label,url) pairs
+   *          list of URLs to be displayed in menu, as (label,url) pairs
+   * @param storedUrlList
+   *          list of custom URLs entered by user but not currently displayed in
+   *          menu, as (label,url) pairs
    */
-  public CustomUrlProvider(Map<String, String> urlList)
+  public CustomUrlProvider(Map<String, String> inMenuUrlList,
+          Map<String, String> storedUrlList)
   {
     try
     {
-      urls = new HashMap<String, UrlLink>();
-      Iterator<Map.Entry<String, String>> it = urlList.entrySet()
-              .iterator();
-      while (it.hasNext())
-      {
-        Map.Entry<String, String> pair = it.next();
-        urls.put(pair.getKey(),
-                new UrlLink(pair.getKey() + SEP + pair.getValue()));
-      }
+      selectedUrls = parseUrlList(inMenuUrlList);
+      nonselectedUrls = parseUrlList(storedUrlList);
     } catch (Exception ex)
     {
       System.out.println(ex + "\nError parsing sequence links");
     }
-    upgradeOldLinks();
+  }
+
+  private HashMap<String, UrlLink> parseUrlStrings(String urlStrings)
+  {
+    // cachedUrlList is in form <label>|<url>|<label>|<url>...
+    // parse cachedUrlList into labels (used as id) and url links
+    HashMap<String, UrlLink> urls = new HashMap<String, UrlLink>();
+
+    StringTokenizer st = new StringTokenizer(urlStrings, SEP);
+    while (st.hasMoreElements())
+    {
+      String name = st.nextToken();
+
+      if (!isMiriamId(name))
+      {
+        // this one of our custom urls
+        String url = st.nextToken();
+        // check for '|' within a regex
+        int rxstart = url.indexOf(DELIM + DB_ACCESSION + DELIM);
+        if (rxstart == -1)
+        {
+          rxstart = url.indexOf(DELIM + SEQUENCE_ID + DELIM);
+        }
+        while (rxstart == -1 && url.indexOf("/=" + DELIM) == -1
+                && st.hasMoreTokens())
+        {
+          url = url + SEP + st.nextToken();
+        }
+        urls.put(name, new UrlLink(name + SEP + url));
+      }
+    }
+    upgradeOldLinks(urls);
+    return urls;
+  }
+
+  private HashMap<String, UrlLink> parseUrlList(Map<String, String> urlList)
+  {
+    HashMap<String, UrlLink> urls = new HashMap<String, UrlLink>();
+    Iterator<Map.Entry<String, String>> it = urlList.entrySet().iterator();
+    while (it.hasNext())
+    {
+      Map.Entry<String, String> pair = it.next();
+      urls.put(pair.getKey(),
+              new UrlLink(pair.getKey() + SEP + pair.getValue()));
+    }
+    upgradeOldLinks(urls);
+    return urls;
   }
 
   /*
    * Upgrade any legacy links which may have been left lying around
    */
-  private void upgradeOldLinks()
+  private void upgradeOldLinks(HashMap<String, UrlLink> urls)
   {
     // upgrade old SRS link
     if (urls.containsKey(SRS_LABEL))
@@ -143,7 +166,8 @@ public class CustomUrlProvider extends UrlProviderImpl
   public Vector<String> getLinksForMenu()
   {
     Vector<String> links = new Vector<String>();
-    Iterator<Map.Entry<String, UrlLink>> it = urls.entrySet().iterator();
+    Iterator<Map.Entry<String, UrlLink>> it = selectedUrls.entrySet()
+            .iterator();
     while (it.hasNext())
     {
       Map.Entry<String, UrlLink> pair = it.next();
@@ -156,45 +180,55 @@ public class CustomUrlProvider extends UrlProviderImpl
   public List<UrlLinkDisplay> getLinksForTable()
   {
     ArrayList<UrlLinkDisplay> displayLinks = new ArrayList<UrlLinkDisplay>();
-    for (Entry<String, UrlLink> entry : urls.entrySet())
-    {
-      String key = entry.getKey();
-      boolean isDefault = (key.equals(defaultUrl));
-      boolean isSelected = true; // custom urls always selected
-      String displayLink = entry.getValue().toString().split("\\|")[1]; // TODO
-                                                                        // sort
-                                                                        // this
-                                                                        // out
-                                                                        // properly!
-      displayLinks.add(new UrlLinkDisplay(key, key, displayLink,
-              isSelected, isDefault));
-    }
+    displayLinks = getLinksForTable(selectedUrls, true);
+    displayLinks.addAll(getLinksForTable(nonselectedUrls, false));
     return displayLinks;
   }
 
+  private ArrayList<UrlLinkDisplay> getLinksForTable(
+          HashMap<String, UrlLink> urlList, boolean selected)
+  {
+    return super.getLinksForTable(urlList, null, selected);
+  }
+
   @Override
   public boolean setDefaultUrl(String id)
   {
-    if (urls.containsKey(id))
+    if (selectedUrls.containsKey(id))
+    {
+      defaultUrl = id;
+    }
+    else if (nonselectedUrls.containsKey(id))
     {
+      selectedUrls.put(id, nonselectedUrls.get(id));
+      nonselectedUrls.remove(id);
       defaultUrl = id;
     }
     else
     {
       defaultUrl = null;
     }
-    return urls.containsKey(id);
+    return (defaultUrl != null);
   }
 
   @Override
-  public String writeUrlsAsString()
+  public String writeUrlsAsString(boolean selected)
   {
     StringBuffer links = new StringBuffer();
+    HashMap<String, UrlLink> urls;
+    if (selected)
+    {
+      urls = selectedUrls;
+    }
+    else
+    {
+      urls = nonselectedUrls;
+    }
     if (urls.size() > 0)
     {
-      for (UrlLink link : urls.values())
+      for (Entry<String, UrlLink> entry : urls.entrySet())
       {
-        links.append(link.toString());
+        links.append(entry.getValue().toString());
         links.append(SEP);
       }
 
@@ -211,37 +245,26 @@ public class CustomUrlProvider extends UrlProviderImpl
   @Override
   public String getDefaultUrl(String seqid)
   {
-    if (defaultUrl == null)
-    {
-      return null;
-    }
+    return super.getDefaultUrl(seqid, selectedUrls);
+  }
 
-    String url = null;
-    UrlLink urlLink = urls.get(defaultUrl);
-    String[] defaultUrls = urlLink.makeUrls(seqid, true);
-    if (defaultUrls == null || defaultUrls[0] == null
-            || defaultUrls[0].length() < MIN_SUBST_LENGTH)
-    {
-      url = null;
-    }
-    else
-    {
-      // just take first URL made from regex
-      url = defaultUrls[1];
-    }
-    return url;
+  @Override
+  public String getDefaultUrlId()
+  {
+    return defaultUrl;
   }
 
   @Override
   public String getDefaultTarget(String seqid)
   {
-    return urls.get(defaultUrl).getTarget();
+    return selectedUrls.get(defaultUrl).getTarget();
   }
 
   @Override
   public void setUrlData(List<UrlLinkDisplay> links)
   {
-    HashMap<String, UrlLink> newurls = new HashMap<String, UrlLink>();
+    HashMap<String, UrlLink> unselurls = new HashMap<String, UrlLink>();
+    HashMap<String, UrlLink> selurls = new HashMap<String, UrlLink>();
 
     Iterator<UrlLinkDisplay> it = links.iterator();
     while (it.hasNext())
@@ -251,16 +274,16 @@ public class CustomUrlProvider extends UrlProviderImpl
       // MIRIAM ids will be handled by a different UrlProvider class
       if (!isMiriamId(link.getId()))
       {
-
         // don't allow duplicate key names as entries will be overwritten
-        if (newurls.containsKey(link.getId()))
+        if (unselurls.containsKey(link.getId())
+                || selurls.containsKey(link.getId()))
         {
           throw new IllegalArgumentException(MessageManager.formatMessage(
                   "exception.url_cannot_have_duplicate_id", link.getId()));
         }
         if (link.getIsSelected())
         {
-          newurls.put(link.getId(),
+          selurls.put(link.getId(),
                   new UrlLink(link.getId() + SEP + link.getUrl()));
 
           // sort out default and selected ids
@@ -269,12 +292,16 @@ public class CustomUrlProvider extends UrlProviderImpl
             setDefaultUrl(link.getId());
           }
         }
-          // TODO KM make it possible to set and save selected custom urls
-
+        else
+        {
+          unselurls.put(link.getId(),
+                new UrlLink(link.getId() + SEP + link.getUrl()));
+        }
       }
 
     }
-    urls = newurls;
+    nonselectedUrls = unselurls;
+    selectedUrls = selurls;
   }
 
   @Override
@@ -282,9 +309,16 @@ public class CustomUrlProvider extends UrlProviderImpl
   {
     // unilaterally set the default id to the EMBL_EBI link
     
-    if (!urls.containsKey(UrlConstants.DEFAULT_LABEL))
+    if (nonselectedUrls.containsKey(UrlConstants.DEFAULT_LABEL))
     {
-      urls.put(UrlConstants.DEFAULT_LABEL, new UrlLink(UrlConstants.DEFAULT_STRING));
+      // default key must be selected so remove from nonselected list
+      nonselectedUrls.remove(UrlConstants.DEFAULT_LABEL);
+    }
+
+    if (!selectedUrls.containsKey(UrlConstants.DEFAULT_LABEL))
+    {
+      selectedUrls.put(UrlConstants.DEFAULT_LABEL, new UrlLink(
+              UrlConstants.DEFAULT_STRING));
     }
     defaultUrl = UrlConstants.DEFAULT_LABEL;
     return UrlConstants.DEFAULT_LABEL;
diff --git a/src/jalview/urls/DesktopUrlProviderFactory.java b/src/jalview/urls/DesktopUrlProviderFactory.java
index ee05376..0c5cefc 100644
--- a/src/jalview/urls/DesktopUrlProviderFactory.java
+++ b/src/jalview/urls/DesktopUrlProviderFactory.java
@@ -35,13 +35,16 @@ public class DesktopUrlProviderFactory implements UrlProviderFactoryI
 
   private String provDefaultUrl;
 
-  private String provUrlList;
+  private String menuUrlList;
+
+  private String nonMenuUrlList;
 
   public DesktopUrlProviderFactory(String defaultUrlString,
-          String cachedUrlList)
+          String cachedUrlList, String userUrlList)
   {
     provDefaultUrl = defaultUrlString;
-    provUrlList = cachedUrlList;
+    menuUrlList = cachedUrlList;
+    nonMenuUrlList = userUrlList;
   }
 
   @Override
@@ -50,9 +53,9 @@ public class DesktopUrlProviderFactory implements UrlProviderFactoryI
     // create all the UrlProviders we need
     List<UrlProviderI> providers = new ArrayList<UrlProviderI>();
 
-    UrlProviderI idProvider = new IdentifiersUrlProvider(provUrlList,
-            IdentifiersUrlProvider.ID_ORG_FILE);
-    UrlProviderI customProvider = new CustomUrlProvider(provUrlList);
+    UrlProviderI idProvider = new IdentifiersUrlProvider(menuUrlList);
+    UrlProviderI customProvider = new CustomUrlProvider(menuUrlList,
+            nonMenuUrlList);
     providers.add(idProvider);
     providers.add(customProvider);
 
diff --git a/src/jalview/urls/IdOrgSettings.java b/src/jalview/urls/IdOrgSettings.java
new file mode 100644
index 0000000..7dd1a19
--- /dev/null
+++ b/src/jalview/urls/IdOrgSettings.java
@@ -0,0 +1,55 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
+package jalview.urls;
+
+/**
+ * Holds settings for identifiers.org e.g. url, download location
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class IdOrgSettings
+{
+  private static String url;
+
+  private static String location;
+
+  public static void setUrl(String seturl)
+  {
+    url = seturl;
+  }
+
+  public static void setDownloadLocation(String setloc)
+  {
+    location = setloc;
+  }
+
+  public static String getUrl()
+  {
+    return url;
+  }
+
+  public static String getDownloadLocation()
+  {
+    return location;
+  }
+}
diff --git a/src/jalview/urls/IdentifiersUrlProvider.java b/src/jalview/urls/IdentifiersUrlProvider.java
index 3501169..45d3863 100644
--- a/src/jalview/urls/IdentifiersUrlProvider.java
+++ b/src/jalview/urls/IdentifiersUrlProvider.java
@@ -25,19 +25,16 @@ import static jalview.util.UrlConstants.DB_ACCESSION;
 import static jalview.util.UrlConstants.DELIM;
 import static jalview.util.UrlConstants.SEP;
 
-import java.io.BufferedInputStream;
-import java.io.File;
+import jalview.util.UrlLink;
+
 import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
 import java.io.FileReader;
 import java.io.IOException;
-import java.io.InputStream;
-import java.net.URL;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.Iterator;
 import java.util.List;
-import java.util.Map.Entry;
+import java.util.StringTokenizer;
 import java.util.Vector;
 
 import org.json.simple.JSONArray;
@@ -57,62 +54,37 @@ public class IdentifiersUrlProvider extends UrlProviderImpl
 {
 
   // map of string ids to urls
-  private HashMap<String, HashMap<String, String>> urls;
+  private HashMap<String, UrlLink> urls;
 
   // list of selected urls
   private ArrayList<String> selectedUrls;
 
-  /*
-   * Location of file for identifiers.org download
-   */
-  public static final String ID_ORG_FILE = System.getProperty("user.home")
-          + File.separatorChar + ".jalview_identifiers";
-
-  public IdentifiersUrlProvider(String cachedUrlList, String idFileName)
-  {
-    try
-    {
-      // File idFile = getIdentifiers();
-      urls = readIdentifiers(new FileReader(idFileName));
-      selectedUrls = new ArrayList<String>();
-      checkSelectionMatchesUrls(cachedUrlList);
-
-    } catch (IOException e)
-    {
-      System.out.println("Exception reading URLs from identifiers.org");
-      System.out.println(e.getMessage());
-    }
-  }
-
-  private File getIdentifiers() throws IOException
+  public IdentifiersUrlProvider(String cachedUrlList)
   {
-    String identifiersorgUrl = "http://identifiers.org/rest/collections/";
-    String outfile = "identifiers.json";
-    int BUFFER_SIZE = 4096;
-    
-    URL url = new URL(identifiersorgUrl);
-    InputStream is = new BufferedInputStream(url.openStream());
-    FileOutputStream os = new FileOutputStream(outfile);
-    byte[] buffer = new byte[BUFFER_SIZE];
-    int bytesRead = -1;
-    while ((bytesRead = is.read(buffer)) != -1)
-    {
-      os.write(buffer, 0, bytesRead);
-    }
-    os.close();
-    is.close();
-    
-    return new File(outfile);
+    urls = readIdentifiers(IdOrgSettings.getDownloadLocation());
+    selectedUrls = new ArrayList<String>();
+    checkSelectionMatchesUrls(cachedUrlList);
   }
 
-  private HashMap<String, HashMap<String, String>> readIdentifiers(
-          FileReader reader)
+  /**
+   * Read data from an identifiers.org download file
+   * 
+   * @param idFileName
+   *          name of identifiers.org download file
+   * @return hashmap of identifiers.org data, keyed by MIRIAM id
+   */
+  private HashMap<String, UrlLink> readIdentifiers(
+          String idFileName)
   {
     JSONParser parser = new JSONParser();
-    HashMap<String, HashMap<String, String>> idData = new HashMap<String, HashMap<String, String>>();
+
+    // identifiers.org data
+    HashMap<String, UrlLink> idData = new HashMap<String, UrlLink>();
 
     try
     {
+      FileReader reader = new FileReader(idFileName);
+
       JSONArray jsonarray = (JSONArray) parser.parse(reader);
 
       // loop over each entry in JSON array and build HashMap entry
@@ -120,10 +92,10 @@ public class IdentifiersUrlProvider extends UrlProviderImpl
       {
         JSONObject item = (JSONObject) jsonarray.get(i);
 
-        HashMap<String, String> idEntry = new HashMap<String, String>();
-        idEntry.put("name", (String) item.get("name"));
-        idEntry.put("url", (String) item.get("url"));
-        idData.put((String) item.get("id"), idEntry);
+        String url = (String) item.get("url") + "/" + DELIM + DB_ACCESSION
+                + DELIM;
+        UrlLink link = new UrlLink((String) item.get("name") + SEP + url);
+        idData.put((String) item.get("id"), link);
       }
     } catch (FileNotFoundException e)
     {
@@ -140,29 +112,18 @@ public class IdentifiersUrlProvider extends UrlProviderImpl
 
   private void checkSelectionMatchesUrls(String cachedUrlList)
   {
-
-    String[] prevSelected = cachedUrlList.split("\\" + SEP);
-    for (String id : prevSelected)
+    StringTokenizer st = new StringTokenizer(cachedUrlList, SEP);
+    while (st.hasMoreElements())
     {
-      if (urls.containsKey(id))
-      {
-        selectedUrls.add(id);
-      }
-    }
-
-    // reset defaultUrl in case it is no longer selected
-    setDefaultUrl(defaultUrl);
-  }
+      String id = st.nextToken();
 
-  private void checkSelectionMatchesUrls(Vector<String> idList)
-  {
-    String[] prevSelected = new String[idList.size()];
-    idList.toArray(prevSelected);
-    for (String id : prevSelected)
-    {
-      if (urls.containsKey(id))
+      if (isMiriamId(id))
       {
-        selectedUrls.add(id);
+        // this is an identifiers.org MIRIAM id
+        if (urls.containsKey(id))
+        {
+          selectedUrls.add(id);
+        }
       }
     }
 
@@ -185,11 +146,16 @@ public class IdentifiersUrlProvider extends UrlProviderImpl
   }
 
   @Override
-  public String writeUrlsAsString()
+  public String writeUrlsAsString(boolean selected)
   {
+    if (!selected)
+    {
+      return ""; // we don't cache unselected identifiers.org urls
+    }
+
+    StringBuffer links = new StringBuffer();
     if (!selectedUrls.isEmpty())
     {
-      StringBuffer links = new StringBuffer();
       for (String k : selectedUrls)
       {
         links.append(k);
@@ -197,9 +163,8 @@ public class IdentifiersUrlProvider extends UrlProviderImpl
       }
       // remove last SEP
       links.setLength(links.length() - 1);
-      return links.toString();
     }
-    return "";
+    return links.toString();
   }
 
   @Override
@@ -208,9 +173,7 @@ public class IdentifiersUrlProvider extends UrlProviderImpl
     Vector<String> links = new Vector<String>();
     for (String key : selectedUrls)
     {
-      links.add(urls.get(key).get("name") + SEP + urls.get(key).get("url")
-              + "/" + DELIM
-              + DB_ACCESSION + DELIM);
+      links.add(urls.get(key).toString());
     }
     return links;
   }
@@ -218,18 +181,7 @@ public class IdentifiersUrlProvider extends UrlProviderImpl
   @Override
   public List<UrlLinkDisplay> getLinksForTable()
   {
-    ArrayList<UrlLinkDisplay> displayLinks = new ArrayList<UrlLinkDisplay>();
-    for (Entry<String, HashMap<String, String>> entry : urls.entrySet())
-    {
-      String key = entry.getKey();
-      boolean isDefault = (key == defaultUrl);
-      boolean isSelected = (selectedUrls.contains(key));
-      displayLinks.add(new UrlLinkDisplay(key,
-              entry.getValue().get("name"),
-              entry.getValue().get("url")
-              + "/" + DELIM + DB_ACCESSION + DELIM, isSelected, isDefault));
-    }
-    return displayLinks;
+    return super.getLinksForTable(urls, selectedUrls, false);
   }
 
   @Override
@@ -243,7 +195,7 @@ public class IdentifiersUrlProvider extends UrlProviderImpl
       UrlLinkDisplay link = it.next();
 
       // Handle links with MIRIAM ids only
-      if (isMiriamId(link.getId())) // TODO separate use of name and id
+      if (isMiriamId(link.getId()))
       {
         // select/deselect links accordingly and set default url
 
@@ -267,18 +219,13 @@ public class IdentifiersUrlProvider extends UrlProviderImpl
   @Override
   public String getDefaultUrl(String seqid)
   {
-    if (seqid.length() < MIN_SUBST_LENGTH)
-    {
-      return null;
-    }
-    else if (defaultUrl == null)
-    {
-      return null;
-    }
-    else
-    {
-      return urls.get(defaultUrl).get("url") + "/" + seqid;
-    }
+    return super.getDefaultUrl(seqid, urls);
+  }
+
+  @Override
+  public String getDefaultUrlId()
+  {
+    return defaultUrl;
   }
 
   @Override
diff --git a/src/jalview/urls/UrlLinkTableModel.java b/src/jalview/urls/UrlLinkTableModel.java
index edf2561..0605f02 100644
--- a/src/jalview/urls/UrlLinkTableModel.java
+++ b/src/jalview/urls/UrlLinkTableModel.java
@@ -24,6 +24,8 @@ package jalview.urls;
 import java.util.Iterator;
 import java.util.List;
 
+import javax.swing.event.TableModelEvent;
+import javax.swing.event.TableModelListener;
 import javax.swing.table.AbstractTableModel;
 
 /**
@@ -80,6 +82,17 @@ public class UrlLinkTableModel extends AbstractTableModel
         defaultRow++;
       }
     }
+
+    this.addTableModelListener(new TableModelListener()
+    {
+      @Override
+      public void tableChanged(TableModelEvent e)
+      {
+        // update the UrlProvider from data list
+        dataProvider.setUrlData(data);
+      }
+    });
+
   }
 
   @Override
@@ -164,15 +177,6 @@ public class UrlLinkTableModel extends AbstractTableModel
     return displayColumns.get(columnIndex);
   }
 
-  @Override
-  public String toString()
-  {
-    // update the UrlProvider from data list
-    dataProvider.setUrlData(data);
-
-    return dataProvider.writeUrlsAsString();
-  }
-
   public void removeRow(int rowIndex)
   {
     // remove the row from data
@@ -196,4 +200,5 @@ public class UrlLinkTableModel extends AbstractTableModel
     fireTableRowsInserted(index, index);
     return index;
   }
+
 }
diff --git a/src/jalview/urls/UrlProvider.java b/src/jalview/urls/UrlProvider.java
index f93656f..fcda198 100644
--- a/src/jalview/urls/UrlProvider.java
+++ b/src/jalview/urls/UrlProvider.java
@@ -84,27 +84,35 @@ public class UrlProvider implements UrlProviderI
   @Override
   public boolean setDefaultUrl(String id)
   {
+    boolean outcome = false;
     for (UrlProviderI p : providers)
     {
       if (p.setDefaultUrl(id))
       {
-        return true;
+        outcome = true;
       }
     }
-    return false;
+    return outcome;
   }
   
   @Override
-  public String writeUrlsAsString()
+  public String writeUrlsAsString(boolean selected)
   {
     String result = "";
     for (UrlProviderI p : providers)
     {
-      result += p.writeUrlsAsString();
-      result += SEP;
+      String next = p.writeUrlsAsString(selected);
+      if (!next.isEmpty())
+      {
+        result += next;
+        result += SEP;
+      }
     }
     // remove last sep
-    result = result.substring(0, result.length() - 1);
+    if (!result.isEmpty())
+    {
+      result = result.substring(0, result.length() - 1);
+    }
     return result;
   }
 
@@ -141,6 +149,7 @@ public class UrlProvider implements UrlProviderI
   {
     for (UrlProviderI p : providers)
     {
+      p.setDefaultUrl(null);
       p.setUrlData(links);
     }
   }
@@ -165,6 +174,25 @@ public class UrlProvider implements UrlProviderI
   }
 
   @Override
+  public String getDefaultUrlId()
+  {
+    String id = null;
+    for (UrlProviderI p : providers)
+    {
+      if (p.getDefaultUrlId() == null)
+      {
+        continue;
+      }
+      else
+      {
+        id = p.getDefaultUrlId();
+        break;
+      }
+    }
+    return id;
+  }
+
+  @Override
   public String getDefaultTarget(String seqid)
   {
     String target = null;
diff --git a/src/jalview/urls/UrlProviderI.java b/src/jalview/urls/UrlProviderI.java
index 25303a6..595f98d 100644
--- a/src/jalview/urls/UrlProviderI.java
+++ b/src/jalview/urls/UrlProviderI.java
@@ -58,6 +58,13 @@ public interface UrlProviderI
   String getDefaultUrl(String seqid);
 
   /**
+   * Get the default URL id
+   * 
+   * @return id for default URL
+   */
+  String getDefaultUrlId();
+
+  /**
    * Get the target of thelink for the default URL
    * 
    * @seqid sequence id for which to build link
@@ -79,7 +86,7 @@ public interface UrlProviderI
    * 
    * @return string representation of available URLs
    */
-  String writeUrlsAsString();
+  String writeUrlsAsString(boolean selected);
 
   /**
    * Choose the default URL in the event of the selected default being
diff --git a/src/jalview/urls/UrlProviderImpl.java b/src/jalview/urls/UrlProviderImpl.java
index 82eeee9..b846976 100644
--- a/src/jalview/urls/UrlProviderImpl.java
+++ b/src/jalview/urls/UrlProviderImpl.java
@@ -20,7 +20,12 @@
  */
 package jalview.urls;
 
+import jalview.util.UrlLink;
+
+import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map.Entry;
 import java.util.Vector;
 import java.util.regex.Pattern;
 
@@ -62,6 +67,35 @@ public class UrlProviderImpl implements UrlProviderI
     return null;
   }
 
+  protected String getDefaultUrl(String seqid, HashMap<String, UrlLink> urls)
+  {
+    if (seqid.length() < MIN_SUBST_LENGTH)
+    {
+      return null;
+    }
+    else if (defaultUrl == null)
+    {
+      return null;
+    }
+    else
+    {
+      String url = null;
+      UrlLink urlLink = urls.get(defaultUrl);
+      String[] defaultUrls = urlLink.makeUrls(seqid, true);
+      if (defaultUrls == null || defaultUrls[0] == null
+              || defaultUrls[0].length() < MIN_SUBST_LENGTH)
+      {
+        url = null;
+      }
+      else
+      {
+        // just take first URL made from regex
+        url = defaultUrls[1];
+      }
+      return url;
+    }
+  }
+
   @Override
   public boolean setDefaultUrl(String id)
   {
@@ -70,7 +104,7 @@ public class UrlProviderImpl implements UrlProviderI
   }
 
   @Override
-  public String writeUrlsAsString()
+  public String writeUrlsAsString(boolean selected)
   {
     // TODO Auto-generated method stub
     return null;
@@ -89,6 +123,31 @@ public class UrlProviderImpl implements UrlProviderI
     return null;
   }
 
+  protected ArrayList<UrlLinkDisplay> getLinksForTable(
+          HashMap<String, UrlLink> urls, ArrayList<String> selectedUrls,
+          boolean selected)
+  {
+    ArrayList<UrlLinkDisplay> displayLinks = new ArrayList<UrlLinkDisplay>();
+    for (Entry<String, UrlLink> entry : urls.entrySet())
+    {
+      String key = entry.getKey();
+      boolean isDefault = (key.equals(defaultUrl));
+      boolean isSelected;
+      if (selectedUrls != null)
+      {
+        isSelected = selectedUrls.contains(key);
+      }
+      else
+      {
+        isSelected = selected;
+      }
+      String displayLink = entry.getValue().getUrlWithToken();
+      displayLinks.add(new UrlLinkDisplay(key, entry.getValue().getLabel(),
+              displayLink, isSelected, isDefault));
+    }
+    return displayLinks;
+  }
+
   @Override
   public void setUrlData(List<UrlLinkDisplay> links)
   {
@@ -106,4 +165,11 @@ public class UrlProviderImpl implements UrlProviderI
     return !isMiriamId(id);
   }
 
+  @Override
+  public String getDefaultUrlId()
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
 }
diff --git a/src/jalview/util/UrlLink.java b/src/jalview/util/UrlLink.java
index c889287..34070dd 100644
--- a/src/jalview/util/UrlLink.java
+++ b/src/jalview/util/UrlLink.java
@@ -135,6 +135,16 @@ public class UrlLink
     return label;
   }
 
+  public String getUrlWithToken()
+  {
+    String var = (usesDBaccession ? DB_ACCESSION : SEQUENCE_ID);
+
+    return urlPrefix
+            + (dynamic ? (DELIM + var + ((regexReplace != null) ? "="
+                    + regexReplace + "=" + DELIM : DELIM)) : "")
+            + ((urlSuffix == null) ? "" : urlSuffix);
+  }
+
   /**
    * @return the regexReplace
    */
@@ -304,14 +314,7 @@ public class UrlLink
   @Override
   public String toString()
   {
-    String var = (usesDBaccession ? DB_ACCESSION : SEQUENCE_ID);
-
-    return label
-            + SEP
-            + urlPrefix
-            + (dynamic ? (DELIM + var + ((regexReplace != null) ? "="
-                    + regexReplace + "=" + DELIM : DELIM)) : "")
-            + ((urlSuffix == null) ? "" : urlSuffix);
+    return label + SEP + getUrlWithToken();
   }
 
   /**
diff --git a/src/jalview/ws/UrlDownloadClient.java b/src/jalview/ws/UrlDownloadClient.java
new file mode 100644
index 0000000..4787c26
--- /dev/null
+++ b/src/jalview/ws/UrlDownloadClient.java
@@ -0,0 +1,109 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
+package jalview.ws;
+
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.net.URL;
+import java.nio.channels.Channels;
+import java.nio.channels.ReadableByteChannel;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.nio.file.StandardCopyOption;
+
+public class UrlDownloadClient
+{
+  public UrlDownloadClient()
+  {
+
+  }
+
+  /**
+   * Download persistent database URLs from identifiers.org
+   * 
+   * @param urlstring
+   *          url to download from, as string
+   * @param outfile
+   *          the name of file to save the URLs to
+   * @throws IOException
+   */
+  public void download(String urlstring, String outfile) throws IOException
+  {
+    FileOutputStream fos = null;
+    ReadableByteChannel rbc = null;
+    Path temp = null;
+    try
+    {
+      temp = Files.createTempFile(".jalview_", ".tmp");
+
+      URL url = new URL(urlstring);
+      rbc = Channels.newChannel(url.openStream());
+      fos = new FileOutputStream(temp.toString());
+      fos.getChannel().transferFrom(rbc, 0, Long.MAX_VALUE);
+
+      // copy tempfile to outfile once our download completes
+      // incase something goes wrong
+      Files.copy(temp, Paths.get(outfile),
+              StandardCopyOption.REPLACE_EXISTING);
+    } catch (IOException e)
+    {
+      throw e;
+    } finally
+    {
+      try
+      {
+        if (fos != null)
+        {
+          fos.close();
+        }
+      } catch (IOException e)
+      {
+        System.out
+                .println("Exception while closing download file output stream: "
+                        + e.getMessage());
+      }
+      try
+      {
+        if (rbc != null)
+        {
+          rbc.close();
+        }
+      } catch (IOException e)
+      {
+        System.out.println("Exception while closing download channel: "
+                        + e.getMessage());
+      }
+      try
+      {
+        if (temp != null)
+        {
+          Files.deleteIfExists(temp);
+        }
+      } catch (IOException e)
+      {
+        System.out.println("Exception while deleting download temp file: "
+                        + e.getMessage());
+      }
+    }
+  }
+}
diff --git a/test/jalview/urls/CustomUrlProviderTest.java b/test/jalview/urls/CustomUrlProviderTest.java
index 35ec5ff..52b3fcd 100644
--- a/test/jalview/urls/CustomUrlProviderTest.java
+++ b/test/jalview/urls/CustomUrlProviderTest.java
@@ -40,6 +40,9 @@ public class CustomUrlProviderTest
           + "TEST2|http://address/$SEQUENCE_ID$|SRS|"
           + "http://theSRSlink/$SEQUENCE_ID$";
 
+  private static final String unselectedList = "NON1|http://x/y/$DB_ACCESSION$|"
+          + "NON2|http://a/b/c/$DB_ACCESSION";
+
   private static final HashMap<String, String> urlMap = new HashMap<String, String>()
   {
     {
@@ -50,15 +53,29 @@ public class CustomUrlProviderTest
     }
   };
   
+  private static final HashMap<String, String> unselUrlMap = new HashMap<String, String>()
+  {
+    {
+      put("NON1", "http://x/y/$DB_ACCESSION$");
+      put("NON2", "http://a/b/c/$DB_ACCESSION");
+    }
+  };
+
   private static final String[] dlinks = {
       "TEST|http://someurl.blah/$DB_ACCESSION$",
       "ANOTHER|http://test/t$SEQUENCE_ID$",
       "TEST2|http://address/$SEQUENCE_ID$",
  UrlConstants.DEFAULT_STRING };
 
+  private static final String[] unselDlinks = {
+      "NON1|http://x/y/$DB_ACCESSION$", "NON2|http://a/b/c/$DB_ACCESSION" };
+
   private static final Vector<String> displayLinks = new Vector<String>(
           Arrays.asList(dlinks));
 
+  private static final Vector<String> unselDisplayLinks = new Vector<String>(
+          Arrays.asList(unselDlinks));
+
   private static final String[] dlinks2 = { "a|http://x.y.z/$SEQUENCE_ID$" };
 
   private static final Vector<String> displayLinks2 = new Vector<String>(
@@ -80,7 +97,8 @@ public class CustomUrlProviderTest
   @Test(groups = { "Functional" })
   public void testDefaultUrl()
   {
-    UrlProviderI customProv = new CustomUrlProvider(cachedList);
+    UrlProviderI customProv = new CustomUrlProvider(cachedList,
+            unselectedList);
     
     // default url can be set
     assertTrue(customProv.setDefaultUrl("ANOTHER"));
@@ -114,22 +132,31 @@ public class CustomUrlProviderTest
   public void testUrlLinks()
   {
     // creation from cached url list works + old links upgraded
-    UrlProviderI customProv = new CustomUrlProvider(cachedList);
+    UrlProviderI customProv = new CustomUrlProvider(cachedList,
+            unselectedList);
     assertTrue(displayLinks.containsAll(customProv.getLinksForMenu()));
 
     // creation from map works + old links upgraded
-    UrlProviderI customProv2 = new CustomUrlProvider(urlMap);
+    UrlProviderI customProv2 = new CustomUrlProvider(urlMap, unselUrlMap);
     assertTrue(displayLinks.containsAll(customProv2.getLinksForMenu()));
 
     // writing url links as a string works
     // because UrlProvider does not guarantee order of links, we can't just
     // compare the output of writeUrlsAsString to a string, hence the hoops here
-    String result = customProv.writeUrlsAsString();
-    UrlProviderI up = new CustomUrlProvider(result);
+    String result = customProv.writeUrlsAsString(true);
+    UrlProviderI up = new CustomUrlProvider(result, "");
     assertTrue(displayLinks.containsAll(up.getLinksForMenu()));
 
-    result = customProv2.writeUrlsAsString();
-    UrlProviderI up2 = new CustomUrlProvider(result);
+    result = customProv.writeUrlsAsString(false);
+    up = new CustomUrlProvider("", result);
+    assertTrue(unselDisplayLinks.containsAll(up.getLinksForMenu()));
+
+    result = customProv2.writeUrlsAsString(true);
+    UrlProviderI up2 = new CustomUrlProvider(result, "");
+    assertTrue(displayLinks.containsAll(up2.getLinksForMenu()));
+
+    result = customProv2.writeUrlsAsString(false);
+    up2 = new CustomUrlProvider("", result);
     assertTrue(displayLinks.containsAll(up2.getLinksForMenu()));
   }
 }
diff --git a/test/jalview/urls/IdentifiersUrlProviderTest.java b/test/jalview/urls/IdentifiersUrlProviderTest.java
index 8ea47c9..2e1387c 100644
--- a/test/jalview/urls/IdentifiersUrlProviderTest.java
+++ b/test/jalview/urls/IdentifiersUrlProviderTest.java
@@ -64,9 +64,14 @@ public class IdentifiersUrlProviderTest
           + "MIR:00000011|http://identifiers.org/interpro/$DB_ACCESSION$"
           + "MIR:00000372|http://identifiers.org/ena.embl/$DB_ACCESSION$";
 
+  private static final String[] unselDlinks = { "ChEBI|http://identifiers.org/chebi/$DB_ACCESSION$" };
+
   private static final Vector<String> displayLinks = new Vector<String>(
         Arrays.asList(dlinks));
   
+  private static final Vector<String> unselDisplayLinks = new Vector<String>(
+          Arrays.asList(unselDlinks));
+
   private static final Vector<String> displayLinks1 = new Vector<String>(
           Arrays.asList(dlinks1));
 
@@ -105,6 +110,8 @@ public class IdentifiersUrlProviderTest
     {
       System.err.println(ex);
     }
+
+    IdOrgSettings.setDownloadLocation(testfile);
   }
 
   /*
@@ -115,16 +122,20 @@ public class IdentifiersUrlProviderTest
   {
     // creation from cached id list
     String idList = "MIR:00000005|MIR:00000011|MIR:00000372";
-    UrlProviderI idProv = new IdentifiersUrlProvider(idList, testfile);
+    UrlProviderI idProv = new IdentifiersUrlProvider(idList);
     
     assertTrue(displayLinks.containsAll(idProv.getLinksForMenu()));
 
     // because UrlProvider does not guarantee order of links, we can't just
     // compare the output of writeUrlsAsString to a string, hence the hoops here
-    String result = idProv.writeUrlsAsString();
-    UrlProviderI up = new IdentifiersUrlProvider(result, testfile);
+    String result = idProv.writeUrlsAsString(true);
+    UrlProviderI up = new IdentifiersUrlProvider(result);
     assertTrue(displayLinks.containsAll(up.getLinksForMenu()));
 
+    result = idProv.writeUrlsAsString(false);
+    up = new IdentifiersUrlProvider(result);
+    assertTrue(unselDisplayLinks.containsAll(up.getLinksForMenu()));
+
   }
 
   /*
@@ -135,7 +146,7 @@ public class IdentifiersUrlProviderTest
   {
     // creation from cached id list
     String idList = "MIR:00000005|MIR:00000011|MIR:00000372";
-    UrlProviderI idProv = new IdentifiersUrlProvider(idList, testfile);
+    UrlProviderI idProv = new IdentifiersUrlProvider(idList);
     
     // initially no default
     assertEquals(null, idProv.getDefaultUrl("seqid"));