X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=8412dabcc0bbd700627fdcb1189a00fa924fc774;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=621ded0d4f42532486646217536a3f60f579fe7a;hpb=743075ad19dc11ae8456491c51a0c8808b996dc1;p=jalview.git

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 621ded0..8412dab 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -1,28 +1,51 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.datamodel.PDBEntry;
+import jalview.structure.StructureImportSettings;
+import jalview.ws.dbsources.das.api.DasSourceRegistryI;
+import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
+import jalview.ws.sifts.SiftsSettings;
+
+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.Locale;
+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
@@ -40,9 +63,6 @@ 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>
@@ -59,6 +79,10 @@ import org.biojava.dasobert.dasregistry.Das1Source;
  * <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>
@@ -82,8 +106,8 @@ import org.biojava.dasobert.dasregistry.Das1Source;
  * service</li>
  * <li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire
  * service</li>
- * <li>USAGESTATS (false - user prompted) Enable google analytics tracker for collecting usage
- * statistics</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>
@@ -98,14 +122,15 @@ import org.biojava.dasobert.dasregistry.Das1Source;
  * <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>GROUP_LINKS list of name|URL[|&lt;separator&gt;] tuples - see jalview.utils.GroupURLLink for more info
- *  </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>VERSION_CHECK (true) check for the latest release version from www.jalview.org</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
@@ -114,13 +139,60 @@ import org.biojava.dasobert.dasregistry.Das1Source;
  * 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>
+ * <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></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 $Revision$
@@ -148,23 +220,65 @@ public class Cache
 
   public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
 
+  public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
+          .getProperty("user.home")
+          + File.separatorChar
+          + ".sifts_downloads" + File.separatorChar;
+
+  private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
+
+  private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
+
+  /**
+   * Allowed values are PDB or mmCIF
+   */
+  private final static String PDB_DOWNLOAD_FORMAT = PDBEntry.Type.MMCIF
+          .toString();
+
+  private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
+          .toString();
+
+  /*
+   * a date formatter using a fixed (rather than the user's) locale; 
+   * this ensures that date properties can be written and re-read successfully
+   * even if the user changes their locale setting
+   */
+  private static final DateFormat date_format = SimpleDateFormat
+          .getDateTimeInstance(SimpleDateFormat.MEDIUM,
+                  SimpleDateFormat.MEDIUM, Locale.UK);
+
   /**
    * Initialises the Jalview Application Log
    */
   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
-      
+      // 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");
@@ -207,13 +321,37 @@ 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)
     {
@@ -222,13 +360,34 @@ 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
@@ -237,8 +396,8 @@ 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);
 
@@ -253,26 +412,55 @@ 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 = "";
     }
+    else
+    {
+      codeInstallation = " (" + codeInstallation + ")";
+    }
+    new BuildDetails(codeVersion, null, codeInstallation);
+
+    SiftsSettings
+            .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
+
+    SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache.getDefault(
+            "sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
 
-    System.out.println("Jalview Version: " + codeVersion);
+    SiftsSettings.setFailSafePIDThreshold(jalview.bin.Cache.getDefault(
+            "sifts_fail_safe_pid_threshold",
+            DEFAULT_FAIL_SAFE_PID_THRESHOLD));
 
+    SiftsSettings.setCacheThresholdInDays(jalview.bin.Cache.getDefault(
+            "sifts_cache_threshold_in_days",
+            DEFAULT_CACHE_THRESHOLD_IN_DAYS));
+
+    System.out
+            .println("Jalview Version: " + codeVersion + codeInstallation);
+
+    StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
+            .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
+    StructureImportSettings
+            .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
+    // StructureImportSettings
+    // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
+    // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
     // 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)
+            && getDefault("VERSION_CHECK", true)
             && (System.getProperty("java.awt.headless") == null || System
                     .getProperty("java.awt.headless").equals("false")))
     {
 
       class VersionChecker extends Thread
       {
+        @Override
         public void run()
         {
           String orgtimeout = System
@@ -283,13 +471,14 @@ public class Cache
             System.out.println("# INFO: Setting default net timeout to "
                     + orgtimeout + " seconds.");
           }
-          String jnlpVersion = null;
+          String remoteVersion = null;
           try
           {
             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;
@@ -302,20 +491,20 @@ public class Cache
 
               line = line.substring(line.indexOf("value=") + 7);
               line = line.substring(0, line.lastIndexOf("\""));
-              jnlpVersion = line;
+              remoteVersion = line;
               break;
             }
           } catch (Exception ex)
           {
             System.out
-                    .println("Non-fatal exceptions when checking version at www.jalview.org :");
+                    .println("Non-fatal exception when checking version at www.jalview.org :");
             System.out.println(ex);
-            jnlpVersion = getProperty("VERSION");
+            remoteVersion = getProperty("VERSION");
           }
           System.setProperty("sun.net.client.defaultConnectTimeout",
                   orgtimeout);
 
-          setProperty("LATEST_VERSION", jnlpVersion);
+          setProperty("LATEST_VERSION", remoteVersion);
         }
       }
 
@@ -343,6 +532,17 @@ 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
@@ -400,12 +600,16 @@ public class Cache
    */
   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
@@ -413,8 +617,10 @@ public class Cache
     }
     return obj;
   }
+
   /**
    * remove the specified property from the jalview properties file
+   * 
    * @param string
    */
   public static void removeProperty(String string)
@@ -422,19 +628,23 @@ public class Cache
     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);
+      }
     }
   }
 
@@ -507,10 +717,11 @@ public class Cache
           // Tell the user that debug is enabled
           lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
         }
-      } catch (Error e) {
+      } catch (Error e)
+      {
         groovyJarsArePresent = 0;
-        jalview.bin.Cache.log.debug("Groovy Classes are not present",e);
-      }catch (Exception e)
+        jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
+      } catch (Exception e)
       {
         groovyJarsArePresent = 0;
         jalview.bin.Cache.log.debug("Groovy Classes are not present");
@@ -518,51 +729,15 @@ public class Cache
     }
     return (groovyJarsArePresent > 0);
   }
-  /**
-   * generate Das1Sources from the local das source list
-   * 
-   * @return Vector of Das1Sources
-   */
-  public static Vector getLocalDasSources()
-  {
-    Vector localSources = new Vector();
-    String local = jalview.bin.Cache.getProperty("DAS_LOCAL_SOURCE");
-    if (local != null)
-    {
-      StringTokenizer 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));
-        if (source.getUrl().startsWith("sequence:"))
-        {
-          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" });
-        }
-
-        source.setNickname(token.substring(0, bar));
-
-        localSources.addElement(source);
-      }
-    }
-    return localSources;
-  }
 
   /**
-   * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not enabled.
+   * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
+   * enabled.
    */
   protected static Object tracker = null;
+
   protected static Class trackerfocus = null;
+
   protected static Class jgoogleanalyticstracker = null;
 
   /**
@@ -572,20 +747,23 @@ public class Cache
   {
     if (tracker == null)
     {
-      if (jgoogleanalyticstracker==null)
+      if (jgoogleanalyticstracker == null)
       {
         // try to get the tracker class
-        try {
-          jgoogleanalyticstracker = Cache.class.getClassLoader().loadClass(
-          "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
+        try
+        {
+          jgoogleanalyticstracker = Cache.class
+                  .getClassLoader()
+                  .loadClass(
+                          "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
           trackerfocus = Cache.class.getClassLoader().loadClass(
-          "com.boxysystems.jgoogleanalytics.FocusPoint");
+                  "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;
+          jgoogleanalyticstracker = null;
+          trackerfocus = null;
           return;
         }
       }
@@ -596,14 +774,22 @@ public class Cache
       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." })});
+        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;
@@ -619,18 +805,21 @@ public class Cache
         if (log != null)
         {
           if (re != null)
-            log
-                    .debug(
-                            "Caught runtime exception in googletracker init:",
-                            re);
+          {
+            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
         {
@@ -665,4 +854,147 @@ public class Cache
     }
   }
 
+  /**
+   * 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));
+  }
+
+  /**
+   * Stores a formatted date in a jalview property, using a fixed locale.
+   * 
+   * @param propertyName
+   * @param date
+   * @return the formatted date string
+   */
+  public static String setDateProperty(String propertyName, Date date)
+  {
+    String formatted = date_format.format(date);
+    setProperty(propertyName, formatted);
+    return formatted;
+  }
+
+  /**
+   * Reads a date stored in a Jalview property, parses it (using a fixed locale
+   * format) and returns as a Date, or null if parsing fails
+   * 
+   * @param propertyName
+   * @return
+   * 
+   */
+  public static Date getDateProperty(String propertyName)
+  {
+    String val = getProperty(propertyName);
+    if (val != null)
+    {
+      try
+      {
+        return date_format.parse(val);
+      } catch (Exception ex)
+      {
+        System.err.println("Invalid or corrupt date in property '"
+                + propertyName + "' : value was '" + val + "'");
+      }
+    }
+    return null;
+  }
+
+  /**
+   * 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 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);
+    }
+  }
 }