X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=21d5205ebb719d98172708389d0958b278984f59;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=bae40cac24fc154a50a3fc7c952a69eb326902a0;hpb=cf2d81d34ca92dc583974065b88b23cf8fe6b237;p=jalview.git

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index bae40ca..21d5205 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -1,28 +1,47 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
- * 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 file is part of Jalview.
  * 
- * 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.bin;
 
-import java.io.*;
-import java.util.*;
-
-import org.apache.log4j.*;
-import org.biojava.dasobert.dasregistry.Das1Source;
+import jalview.ws.dbsources.das.api.DasSourceRegistryI;
+import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
+
+import java.awt.Color;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.text.DateFormat;
+import java.text.SimpleDateFormat;
+import java.util.Collections;
+import java.util.Date;
+import java.util.Enumeration;
+import java.util.Properties;
+import java.util.TreeSet;
+
+import org.apache.log4j.ConsoleAppender;
+import org.apache.log4j.Level;
+import org.apache.log4j.Logger;
+import org.apache.log4j.SimpleLayout;
 
 /**
  * Stores and retrieves Jalview Application Properties Lists and fields within
@@ -40,75 +59,136 @@ import org.biojava.dasobert.dasregistry.Das1Source;
  * </li>
  * <li>logs.Jalview.Level - Cache.log stringified level. <br>
  * </li>
- * <li>DISCOVERY_START - Boolean - controls if discovery services are queried
- * on startup </li>
- * <li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
- * </li>
- * <li>SCREEN_WIDTH </li>
- * <li>SCREEN_HEIGHT </li>
- * <li>SCREEN_Y=285 </li>
- * <li>SCREEN_X=371 </li>
- * <li>SHOW_FULLSCREEN boolean </li>
- * <li>FONT_NAME java font name for alignment text display </li>
- * <li>FONT_SIZE size of displayed alignment text </li>
- * <li>FONT_STYLE style of font displayed (sequence labels are always italic)
- * </li>
- * <li>GAP_SYMBOL character to treat as gap symbol (usually -,.,' ') </li>
- * <li>LAST_DIRECTORY last directory for browsing alignment </li>
- * <li>USER_DEFINED_COLOURS list of user defined colour scheme files </li>
- * <li>SHOW_FULL_ID show id with '/start-end' numbers appended </li>
- * <li>SHOW_IDENTITY show percentage identity annotation </li>
- * <li>SHOW_QUALITY show alignment quality annotation </li>
- * <li>SHOW_ANNOTATIONS show alignment annotation rows </li>
- * <li>SHOW_CONSERVATION show alignment conservation annotation </li>
+ * <li>SCREEN_WIDTH</li>
+ * <li>SCREEN_HEIGHT</li>
+ * <li>SCREEN_Y=285</li>
+ * <li>SCREEN_X=371</li>
+ * <li>SHOW_FULLSCREEN boolean</li>
+ * <li>FONT_NAME java font name for alignment text display</li>
+ * <li>FONT_SIZE size of displayed alignment text</li>
+ * <li>FONT_STYLE style of font displayed (sequence labels are always italic)</li>
+ * <li>GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')</li>
+ * <li>LAST_DIRECTORY last directory for browsing alignment</li>
+ * <li>USER_DEFINED_COLOURS list of user defined colour scheme files</li>
+ * <li>SHOW_FULL_ID show id with '/start-end' numbers appended</li>
+ * <li>SHOW_IDENTITY show percentage identity annotation</li>
+ * <li>SHOW_QUALITY show alignment quality annotation</li>
+ * <li>SHOW_ANNOTATIONS show alignment annotation rows</li>
+ * <li>SHOW_CONSERVATION show alignment conservation annotation</li>
+ * <li>SORT_ANNOTATIONS currently either SEQUENCE_AND_LABEL or
+ * LABEL_AND_SEQUENCE</li>
+ * <li>SHOW_AUTOCALC_ABOVE true to show autocalculated annotations above
+ * sequence annotations</li>
  * <li>CENTRE_COLUMN_LABELS centre the labels at each column in a displayed
- * annotation row </li>
- * <li>DEFAULT_COLOUR default colour scheme to apply for a new alignment </li>
- * <li>DEFAULT_FILE_FORMAT file format used to save </li>
- * <li>STARTUP_FILE file loaded on startup (may be a fully qualified url) </li>
- * <li>SHOW_STARTUP_FILE flag to control loading of startup file </li>
- * <li>VERSION the version of the jalview build </li>
- * <li>BUILD_DATE date of this build </li>
+ * annotation row</li>
+ * <li>DEFAULT_COLOUR default colour scheme to apply for a new alignment</li>
+ * <li>DEFAULT_FILE_FORMAT file format used to save</li>
+ * <li>STARTUP_FILE file loaded on startup (may be a fully qualified url)</li>
+ * <li>SHOW_STARTUP_FILE flag to control loading of startup file</li>
+ * <li>VERSION the version of the jalview build</li>
+ * <li>BUILD_DATE date of this build</li>
  * <li>LATEST_VERSION the latest jalview version advertised on the
- * www.jalview.org </li>
+ * www.jalview.org</li>
  * <li>PIR_MODELLER boolean indicating if PIR files are written with MODELLER
- * descriptions </li>
+ * descriptions</li>
  * <li>(FASTA,MSF,PILEUP,CLUSTAL,BLC,PIR,PFAM)_JVSUFFIX boolean for adding jv
- * suffix to file </li>
- * <li>RECENT_URL list of recently retrieved URLs </li>
- * <li>RECENT_FILE list of recently opened files </li>
- * <li>USE_PROXY flag for whether a http proxy is to be used </li>
- * <li>PROXY_SERVER the proxy </li>
- * <li>PROXY_PORT </li>
+ * suffix to file</li>
+ * <li>RECENT_URL list of recently retrieved URLs</li>
+ * <li>RECENT_FILE list of recently opened files</li>
+ * <li>USE_PROXY flag for whether a http proxy is to be used</li>
+ * <li>PROXY_SERVER the proxy</li>
+ * <li>PROXY_PORT</li>
  * <li>NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire
- * service </li>
+ * service</li>
  * <li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire
- * service </li>
- * <li>DAS_LOCAL_SOURCE list of local das sources </li>
- * <li>SHOW_OVERVIEW boolean for overview window display </li>
- * <li>ANTI_ALIAS boolean for smooth fonts </li>
- * <li>RIGHT_ALIGN_IDS boolean </li>
- * <li>AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus
- * </li>
- * <li>PAD_GAPS boolean </li>
- * <li>ID_ITALICS boolean </li>
- * <li>SHOW_JV_SUFFIX </li>
- * <li>WRAP_ALIGNMENT </li>
+ * service</li>
+ * <li>USAGESTATS (false - user prompted) Enable google analytics tracker for
+ * collecting usage statistics</li>
+ * <li>DAS_LOCAL_SOURCE list of local das sources</li>
+ * <li>SHOW_OVERVIEW boolean for overview window display</li>
+ * <li>ANTI_ALIAS boolean for smooth fonts</li>
+ * <li>RIGHT_ALIGN_IDS boolean</li>
+ * <li>AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus</li>
+ * <li>PAD_GAPS boolean</li>
+ * <li>ID_ITALICS boolean</li>
+ * <li>SHOW_JV_SUFFIX</li>
+ * <li>WRAP_ALIGNMENT</li>
  * <li>EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering
- * style check </li>
- * <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity) </li>
+ * style check</li>
+ * <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity)</li>
  * <li>SEQUENCE_LINKS list of name|URL pairs for opening a url with
- * $SEQUENCE_ID$ </li>
- * <li>DAS_REGISTRY_URL the registry to query </li>
- * <li>DEFAULT_BROWSER for unix </li>
- * <li>DAS_ACTIVE_SOURCE list of active sources </li>
+ * $SEQUENCE_ID$</li>
+ * <li>GROUP_LINKS list of name|URL[|&lt;separator&gt;] tuples - see
+ * jalview.utils.GroupURLLink for more info</li>
+ * <li>DAS_REGISTRY_URL the registry to query</li>
+ * <li>DEFAULT_BROWSER for unix</li>
+ * <li>DAS_ACTIVE_SOURCE list of active sources</li>
  * <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
- * (false) </li>
- * <li>SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence ID tooltip</li>
- * <li>SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence ID tooltip</li>
- * <li> </li>
+ * (false)</li>
+ * <li>VERSION_CHECK (true) check for the latest release version from
+ * www.jalview.org (or the alias given by the www.jalview.org property)</li>
+ * <li>SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence
+ * ID tooltip</li>
+ * <li>SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence
+ * ID tooltip</li>
+ * <li>SHOW_UNCONSERVED (false) only render unconserved residues - conserved
+ * displayed as '.'</li>
+ * <li>SORT_BY_TREE (false) sort the current alignment view according to the
+ * order of a newly displayed tree</li>
+ * <li>DBFETCH_USEPICR (false) use PICR to recover valid DB references from
+ * sequence ID strings before attempting retrieval from any datasource</li>
+ * <li>SHOW_GROUP_CONSENSUS (false) Show consensus annotation for groups in the
+ * alignment.</li>
+ * <li>SHOW_GROUP_CONSERVATION (false) Show conservation annotation for groups
+ * in the alignment.</li>
+ * <li>SHOW_CONSENSUS_HISTOGRAM (false) Show consensus annotation row's
+ * histogram.</li>
+ * <li>SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
+ * logo.</li>
+ * <li>NORMALISE_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
+ * logo normalised to row height rather than histogram height.</li>
+ * <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
+ * respond to selections made in other alignments containing the same sequences.
+ * </li>
+ * <li>JWS2HOSTURLS comma-separated list of URLs to try for JABAWS services</li>
+ * <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
+ * warning dialog box is displayed.</li>
+ * <li>ANNOTATIONCOLOUR_MIN (orange) Shade used for minimum value of annotation
+ * when shading by annotation</li>
+ * <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
+ * when shading by annotation</li>
+ * <li>www.jalview.org (http://www.jalview.org) a property enabling all HTTP
+ * requests to be redirected to a mirror of http://www.jalview.org</li>
+ * <li>FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
+ * alignment figure to accommodate even the longest sequence ID or annotation
+ * label.</li>
+ * <li>FIGURE_FIXEDIDWIDTH Specifies the width to use for the left-hand column
+ * when exporting an alignment as a figure (setting FIGURE_AUTOIDWIDTH to true
+ * will override this).</li>
+ * <li>STRUCT_FROM_PDB (false) derive secondary structure annotation from PDB
+ * record</li>
+ * <li>USE_RNAVIEW (false) use RNAViewer to derive secondary structure</li>
+ * <li>ADD_SS_ANN (false) add secondary structure annotation to alignment
+ * display</li>
+ * <li>ADD_TEMPFACT_ANN (false) add Temperature Factor annotation to alignment
+ * display</li>
+ * <li>STRUCTURE_DISPLAY choose from JMOL (default) or CHIMERA for 3D structure
+ * display</li>
+ * <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>
  * 
  * </ul>
+ * Deprecated settings:
+ * <ul>
+ * *
+ * <li>DISCOVERY_START - Boolean - controls if discovery services are queried on
+ * startup (JWS1 services only)</li>
+ * <li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
+ * (JWS1 services only)</li>
+ * <li>SHOW_JWS1_SERVICES (true) enable or disable the original Jalview 2
+ * services in the desktop GUI</li>
+ * <li>ENABLE_RSBS_EDITOR (false for 2.7 release) enable or disable RSBS editing
+ * panel in web service preferences</li>
+ * </ul>
  * 
  * @author $author$
  * @version $Revision$
@@ -142,20 +222,37 @@ public class Cache
   public static Logger log;
 
   /** Jalview Properties */
-  public static Properties applicationProperties = new Properties();
+  public static Properties applicationProperties = new Properties()
+  {
+    // override results in properties output in alphabetical order
+    @Override
+    public synchronized Enumeration<Object> keys()
+    {
+      return Collections.enumeration(new TreeSet<Object>(super.keySet()));
+    }
+  };
 
   /** Default file is ~/.jalview_properties */
   static String propertiesFile;
 
+  private static boolean propsAreReadOnly = false;
+
   public static void initLogger()
   {
+    if (log != null)
+    {
+      return;
+    }
     try
     {
+      // TODO: redirect stdout and stderr here in order to grab the output of
+      // the log
+
       ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
               "System.err");
       ap.setName("JalviewLogger");
       org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
-                                                                // log output
+      // log output
       Logger laxis = Logger.getLogger("org.apache.axis");
       Logger lcastor = Logger.getLogger("org.exolab.castor");
       jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
@@ -193,13 +290,37 @@ public class Cache
       propertiesFile = System.getProperty("user.home") + File.separatorChar
               + ".jalview_properties";
     }
+    else
+    {
+      // don't corrupt the file we've been given.
+      propsAreReadOnly = true;
+    }
 
     try
     {
-      FileInputStream fis = new FileInputStream(propertiesFile);
+      InputStream fis;
+      try
+      {
+        fis = new java.net.URL(propertiesFile).openStream();
+        System.out.println("Loading jalview properties from : "
+                + propertiesFile);
+        System.out
+                .println("Disabling Jalview writing to user's local properties file.");
+        propsAreReadOnly = true;
+
+      } catch (Exception ex)
+      {
+        fis = null;
+      }
+      if (fis == null)
+      {
+        fis = new FileInputStream(propertiesFile);
+      }
       applicationProperties.load(fis);
-      applicationProperties.remove("LATEST_VERSION");
-      applicationProperties.remove("VERSION");
+
+      // remove any old build properties
+
+      deleteBuildProperties();
       fis.close();
     } catch (Exception ex)
     {
@@ -208,13 +329,34 @@ public class Cache
 
     if (getDefault("USE_PROXY", false))
     {
-      System.out.println("Using proxyServer: "
-              + getDefault("PROXY_SERVER", null) + " proxyPort: "
-              + getDefault("PROXY_PORT", null));
-      System
-              .setProperty("http.proxyHost", getDefault("PROXY_SERVER",
-                      null));
-      System.setProperty("http.proxyPort", getDefault("PROXY_PORT", null));
+      String proxyServer = getDefault("PROXY_SERVER", ""), proxyPort = getDefault(
+              "PROXY_PORT", "8080");
+
+      System.out.println("Using proxyServer: " + proxyServer
+              + " proxyPort: " + proxyPort);
+
+      System.setProperty("http.proxyHost", proxyServer);
+      System.setProperty("http.proxyPort", proxyPort);
+    }
+
+    // LOAD THE AUTHORS FROM THE authors.props file
+    try
+    {
+      String authorDetails = "jar:".concat(Cache.class
+              .getProtectionDomain().getCodeSource().getLocation()
+              .toString().concat("!/authors.props"));
+
+      java.net.URL localJarFileURL = new java.net.URL(authorDetails);
+
+      InputStream in = localJarFileURL.openStream();
+      applicationProperties.load(in);
+      in.close();
+    } catch (Exception ex)
+    {
+      System.out.println("Error reading author details: " + ex);
+      applicationProperties.remove("AUTHORS");
+      applicationProperties.remove("AUTHORFNAMES");
+      applicationProperties.remove("YEAR");
     }
 
     // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
@@ -223,8 +365,8 @@ public class Cache
     try
     {
       String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
-              .getCodeSource().getLocation().toString().concat(
-                      "!/.build_properties"));
+              .getCodeSource().getLocation().toString()
+              .concat("!/.build_properties"));
 
       java.net.URL localJarFileURL = new java.net.URL(buildDetails);
 
@@ -239,19 +381,26 @@ public class Cache
 
     String jnlpVersion = System.getProperty("jalview.version");
     String codeVersion = getProperty("VERSION");
-
+    String codeInstallation = getProperty("INSTALLATION");
     if (codeVersion == null)
     {
       // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
       codeVersion = "Test";
       jnlpVersion = "Test";
+      codeInstallation = "";
     }
-
-    System.out.println("Jalview Version: " + codeVersion);
+    else
+    {
+      codeInstallation = " (" + codeInstallation + ")";
+    }
+    new BuildDetails(codeVersion, null, codeInstallation);
+    System.out
+            .println("Jalview Version: " + codeVersion + codeInstallation);
 
     // jnlpVersion will be null if we're using InstallAnywhere
     // Dont do this check if running in headless mode
     if (jnlpVersion == null
+            && getDefault("VERSION_CHECK", true)
             && (System.getProperty("java.awt.headless") == null || System
                     .getProperty("java.awt.headless").equals("false")))
     {
@@ -273,8 +422,9 @@ public class Cache
           {
             System.setProperty("sun.net.client.defaultConnectTimeout",
                     "5000");
-            java.net.URL url = new java.net.URL(
-                    "http://www.jalview.org/webstart/jalview.jnlp");
+            java.net.URL url = new java.net.URL(Cache.getDefault(
+                    "www.jalview.org", "http://www.jalview.org")
+                    + "/webstart/jalview.jnlp");
             BufferedReader in = new BufferedReader(new InputStreamReader(
                     url.openStream()));
             String line = null;
@@ -328,12 +478,23 @@ public class Cache
             false);
   }
 
+  private static void deleteBuildProperties()
+  {
+    applicationProperties.remove("LATEST_VERSION");
+    applicationProperties.remove("VERSION");
+    applicationProperties.remove("AUTHORS");
+    applicationProperties.remove("AUTHORFNAMES");
+    applicationProperties.remove("YEAR");
+    applicationProperties.remove("BUILD_DATE");
+    applicationProperties.remove("INSTALLATION");
+  }
+
   /**
    * Gets Jalview application property of given key. Returns null if key not
    * found
    * 
    * @param key
-   *                Name of property
+   *          Name of property
    * 
    * @return Property value
    */
@@ -377,20 +538,24 @@ public class Cache
    * Stores property in the file "HOME_DIR/.jalview_properties"
    * 
    * @param key
-   *                Name of object
+   *          Name of object
    * @param obj
-   *                String value of property
+   *          String value of property
    * 
    * @return String value of property
    */
   public static String setProperty(String key, String obj)
   {
+
     try
     {
-      FileOutputStream out = new FileOutputStream(propertiesFile);
       applicationProperties.setProperty(key, obj);
-      applicationProperties.store(out, "---JalviewX Properties File---");
-      out.close();
+      if (!propsAreReadOnly)
+      {
+        FileOutputStream out = new FileOutputStream(propertiesFile);
+        applicationProperties.store(out, "---JalviewX Properties File---");
+        out.close();
+      }
     } catch (Exception ex)
     {
       System.out.println("Error setting property: " + key + " " + obj
@@ -399,16 +564,33 @@ public class Cache
     return obj;
   }
 
+  /**
+   * remove the specified property from the jalview properties file
+   * 
+   * @param string
+   */
+  public static void removeProperty(String string)
+  {
+    applicationProperties.remove(string);
+    saveProperties();
+  }
+
+  /**
+   * save the properties to the jalview properties path
+   */
   public static void saveProperties()
   {
-    try
-    {
-      FileOutputStream out = new FileOutputStream(propertiesFile);
-      applicationProperties.store(out, "---JalviewX Properties File---");
-      out.close();
-    } catch (Exception ex)
+    if (!propsAreReadOnly)
     {
-      System.out.println("Error saving properties: " + ex);
+      try
+      {
+        FileOutputStream out = new FileOutputStream(propertiesFile);
+        applicationProperties.store(out, "---JalviewX Properties File---");
+        out.close();
+      } catch (Exception ex)
+      {
+        System.out.println("Error saving properties: " + ex);
+      }
     }
   }
 
@@ -481,6 +663,10 @@ public class Cache
           // Tell the user that debug is enabled
           lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
         }
+      } catch (Error e)
+      {
+        groovyJarsArePresent = 0;
+        jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
       } catch (Exception e)
       {
         groovyJarsArePresent = 0;
@@ -491,38 +677,269 @@ public class Cache
   }
 
   /**
-   * generate Das1Sources from the local das source list
-   * @return Vector of Das1Sources
+   * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
+   * enabled.
    */
-  public static Vector getLocalDasSources()
+  protected static Object tracker = null;
+
+  protected static Class trackerfocus = null;
+
+  protected static Class jgoogleanalyticstracker = null;
+
+  /**
+   * Initialise the google tracker if it is not done already.
+   */
+  public static void initGoogleTracker()
   {
-    Vector localSources = new Vector();
-    String local = jalview.bin.Cache.getProperty("DAS_LOCAL_SOURCE");
-    if (local != null)
+    if (tracker == null)
     {
-      StringTokenizer st = new StringTokenizer(local, "\t");
-      while (st.hasMoreTokens())
+      if (jgoogleanalyticstracker == null)
       {
-        String token = st.nextToken();
-        int bar = token.indexOf("|");
-        Das1Source source = new Das1Source();
-        source.setUrl(token.substring(bar + 1));
-        if (source.getUrl().startsWith("sequence:"))
+        // try to get the tracker class
+        try
         {
-          source.setUrl(source.getUrl().substring(9));
-          // this source also serves sequences as well as features
-          source.setCapabilities(new String[] { "sequence", "features"});
-        } else {
-          // default is that all user added sources serve features
-          source.setCapabilities(new String[] { "features"}); 
+          jgoogleanalyticstracker = Cache.class
+                  .getClassLoader()
+                  .loadClass(
+                          "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
+          trackerfocus = Cache.class.getClassLoader().loadClass(
+                  "com.boxysystems.jgoogleanalytics.FocusPoint");
+        } catch (Exception e)
+        {
+          log.debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
+          tracker = null;
+          jgoogleanalyticstracker = null;
+          trackerfocus = null;
+          return;
         }
+      }
+      // now initialise tracker
+      Exception re = null, ex = null;
+      Error err = null;
+      String vrs = "No Version Accessible";
+      try
+      {
+        // Google analytics tracking code for Library Finder
+        tracker = jgoogleanalyticstracker.getConstructor(
+                new Class[] { String.class, String.class, String.class })
+                .newInstance(
+                        new Object[] {
+                            "Jalview Desktop",
+                            (vrs = jalview.bin.Cache.getProperty("VERSION")
+                                    + "_"
+                                    + jalview.bin.Cache.getDefault(
+                                            "BUILD_DATE", "unknown")),
+                            "UA-9060947-1" });
+        jgoogleanalyticstracker.getMethod("trackAsynchronously",
+                new Class[] { trackerfocus }).invoke(
+                tracker,
+                new Object[] { trackerfocus.getConstructor(
+                        new Class[] { String.class }).newInstance(
+                        new Object[] { "Application Started." }) });
+      } catch (RuntimeException e)
+      {
+        re = e;
+      } catch (Exception e)
+      {
+        ex = e;
+      } catch (Error e)
+      {
+        err = e;
+      }
+      if (re != null || ex != null || err != null)
+      {
+        if (log != null)
+        {
+          if (re != null)
+          {
+            log.debug("Caught runtime exception in googletracker init:", re);
+          }
+          if (ex != null)
+          {
+            log.warn(
+                    "Failed to initialise GoogleTracker for Jalview Desktop with version "
+                            + vrs, ex);
+          }
+          if (err != null)
+          {
+            log.error(
+                    "Whilst initing GoogleTracker for Jalview Desktop version "
+                            + vrs, err);
+          }
+        }
+        else
+        {
+          if (re != null)
+          {
+            System.err
+                    .println("Debug: Caught runtime exception in googletracker init:"
+                            + vrs);
+            re.printStackTrace();
+          }
+          if (ex != null)
+          {
+            System.err
+                    .println("Warning:  Failed to initialise GoogleTracker for Jalview Desktop with version "
+                            + vrs);
+            ex.printStackTrace();
+          }
+
+          if (err != null)
+          {
+            System.err
+                    .println("ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
+                            + vrs);
+            err.printStackTrace();
+          }
+        }
+      }
+      else
+      {
+        log.debug("Successfully initialised tracker.");
+      }
+    }
+  }
+
+  /**
+   * get the user's default colour if available
+   * 
+   * @param property
+   * @param defcolour
+   * @return
+   */
+  public static Color getDefaultColour(String property, Color defcolour)
+  {
+    String colprop = getProperty(property);
+    if (colprop == null)
+    {
+      return defcolour;
+    }
+    Color col = jalview.schemes.ColourSchemeProperty
+            .getAWTColorFromName(colprop);
+    if (col == null)
+    {
+      try
+      {
+        col = new jalview.schemes.UserColourScheme(colprop).findColour('A');
+      } catch (Exception ex)
+      {
+        log.warn("Couldn't parse '" + colprop + "' as a colour for "
+                + property);
+        col = null;
+      }
+    }
+    return (col == null) ? defcolour : col;
+  }
+
+  /**
+   * store a colour as a Jalview user default property
+   * 
+   * @param property
+   * @param colour
+   */
+  public static void setColourProperty(String property, Color colour)
+  {
+    setProperty(property, jalview.util.Format.getHexString(colour));
+  }
+
+  public static final DateFormat date_format = SimpleDateFormat
+          .getDateTimeInstance();
+
+  /**
+   * store a date in a jalview property
+   * 
+   * @param string
+   * @param time
+   */
+  public static void setDateProperty(String property, Date time)
+  {
+    setProperty(property, date_format.format(time));
+  }
 
-        source.setNickname(token.substring(0, bar));
+  /**
+   * read a date stored in a jalview property
+   * 
+   * @param property
+   * @return valid date as stored by setDateProperty, or null
+   * 
+   */
+  public static Date getDateProperty(String property)
+  {
+    String val = getProperty(property);
+    if (val != null)
+    {
+      try
+      {
+        return date_format.parse(val);
+      } catch (Exception ex)
+      {
+        System.err.println("Invalid or corrupt date in property '"
+                + property + "' : value was '" + val + "'");
+      }
+    }
+    return null;
+  }
 
-        localSources.addElement(source);
+  /**
+   * get and parse a property as an integer. send any parsing problems to
+   * System.err
+   * 
+   * @param property
+   * @return null or Integer
+   */
+  public static Integer getIntegerProperty(String property)
+  {
+    String val = getProperty(property);
+    if (val != null && (val = val.trim()).length() > 0)
+    {
+      try
+      {
+        return Integer.valueOf(val);
+      } catch (NumberFormatException x)
+      {
+        System.err.println("Invalid integer in property '" + property
+                + "' (value was '" + val + "')");
       }
     }
-    return localSources;
+    return null;
   }
 
+  private static DasSourceRegistryI sourceRegistry = null;
+
+  /**
+   * initialise and ..
+   * 
+   * @return instance of the das source registry
+   */
+  public static DasSourceRegistryI getDasSourceRegistry()
+  {
+    if (sourceRegistry == null)
+    {
+      sourceRegistry = new DasSourceRegistry();
+    }
+    return sourceRegistry;
+  }
+
+  /**
+   * Set the specified value, or remove it if null or empty. Does not save the
+   * properties file.
+   * 
+   * @param propName
+   * @param value
+   */
+  public static void setOrRemove(String propName, String value)
+  {
+    if (propName == null)
+    {
+      return;
+    }
+    if (value == null || value.trim().length() < 1)
+    {
+      Cache.applicationProperties.remove(propName);
+    }
+    else
+    {
+      Cache.applicationProperties.setProperty(propName, value);
+    }
+  }
 }