X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=21d5205ebb719d98172708389d0958b278984f59;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=ec5ff08c67a92332b3f1d1cf8abb2dd11dba9b4f;hpb=83f6c6309e9705037a0853a26da74821c9d4fd12;p=jalview.git

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index ec5ff08..21d5205 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -1,94 +1,195 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
- *
- * 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 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 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 list entries are separated by '|' symbols unless otherwise stated
- * (|) clauses are alternative values for a tag.
- * <br><br>Current properties include:
- * <ul>
- * <br>logs.Axis.Level - one of the stringified Levels for log4j controlling the logging level for axis (used for web services)
- * <br>
- * </li><li>logs.Castor.Level - one of the stringified Levels for log4j controlling the logging level for castor (used for serialization)
+ * Stores and retrieves Jalview Application Properties Lists and fields within
+ * list entries are separated by '|' symbols unless otherwise stated (|) clauses
+ * are alternative values for a tag. <br>
  * <br>
- * </li><li>logs.Jalview.Level - Cache.log stringified level.
+ * Current properties include:
+ * <ul>
  * <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>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><li>PIR_MODELLER boolean indicating if PIR files are written with MODELLER 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><li>NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire 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><li>EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering 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><li> 
+ * logs.Axis.Level - one of the stringified Levels for log4j controlling the
+ * logging level for axis (used for web services) <br>
  * </li>
+ * <li>logs.Castor.Level - one of the stringified Levels for log4j controlling
+ * the logging level for castor (used for serialization) <br>
+ * </li>
+ * <li>logs.Jalview.Level - Cache.log stringified level. <br>
+ * </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>
+ * <li>LATEST_VERSION the latest jalview version advertised on the
+ * www.jalview.org</li>
+ * <li>PIR_MODELLER boolean indicating if PIR files are written with MODELLER
+ * 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>
+ * <li>NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire
+ * 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>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>
+ * <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>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 (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 $Revision$
  */
@@ -98,55 +199,82 @@ public class Cache
    * property giving log4j level for CASTOR loggers
    */
   public static final String CASTORLOGLEVEL = "logs.Castor.level";
+
   /**
    * property giving log4j level for AXIS loggers
    */
-  public static final String AXISLOGLEVEL = "logs.Castor.level";
+  public static final String AXISLOGLEVEL = "logs.Axis.level";
+
   /**
    * property giving log4j level for Jalview Log
    */
   public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
 
+  public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE";
+
+  public static final String DAS_REGISTRY_URL = "DAS_REGISTRY_URL";
+
+  public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
+
   /**
    * 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 */
+  /** 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");
+              "System.err");
       ap.setName("JalviewLogger");
-      org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for log output
+      org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
+      // 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");
 
       laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level",
-          Level.INFO.toString())));
+              Level.INFO.toString())));
       lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
-          Level.INFO.toString())));
+              Level.INFO.toString())));
       lcastor = Logger.getLogger("org.exolab.castor.xml");
       lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
               Level.INFO.toString())));
+      // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
+      // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
+      // Level.INFO.toString())));
       jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(
-          "logs.Jalview.level",
-          Level.INFO.toString())));
-      //laxis.addAppender(ap);
-      //lcastor.addAppender(ap);
-      //jalview.bin.Cache.log.addAppender(ap);
+              "logs.Jalview.level", Level.INFO.toString())));
+      // laxis.addAppender(ap);
+      // lcastor.addAppender(ap);
+      // jalview.bin.Cache.log.addAppender(ap);
       // Tell the user that debug is enabled
       jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       System.err.println("Problems initializing the log4j system\n");
       ex.printStackTrace(System.err);
@@ -159,29 +287,76 @@ public class Cache
     propertiesFile = propsFile;
     if (propsFile == null)
     {
-      propertiesFile = System.getProperty("user.home") + File.separatorChar +
-          ".jalview_properties";
+      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)
+    } catch (Exception ex)
     {
       System.out.println("Error reading properties file: " + ex);
     }
 
     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
@@ -189,20 +364,16 @@ public class Cache
     // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
     try
     {
-      String buildDetails = "jar:"
-          .concat(
-              Cache.class.getProtectionDomain().getCodeSource().getLocation().
-              toString()
-              .concat("!/.build_properties")
-          );
+      String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
+              .getCodeSource().getLocation().toString()
+              .concat("!/.build_properties"));
 
       java.net.URL localJarFileURL = new java.net.URL(buildDetails);
 
       InputStream in = localJarFileURL.openStream();
       applicationProperties.load(in);
       in.close();
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       System.out.println("Error reading build details: " + ex);
       applicationProperties.remove("VERSION");
@@ -210,37 +381,54 @@ 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 && (
-        System.getProperty("java.awt.headless") == null
-        || System.getProperty("java.awt.headless").equals("false")))
+    if (jnlpVersion == null
+            && getDefault("VERSION_CHECK", true)
+            && (System.getProperty("java.awt.headless") == null || System
+                    .getProperty("java.awt.headless").equals("false")))
     {
 
-      class VersionChecker
-          extends Thread
+      class VersionChecker extends Thread
       {
         public void run()
         {
+          String orgtimeout = System
+                  .getProperty("sun.net.client.defaultConnectTimeout");
+          if (orgtimeout == null)
+          {
+            orgtimeout = "30";
+            System.out.println("# INFO: Setting default net timeout to "
+                    + orgtimeout + " seconds.");
+          }
           String jnlpVersion = null;
           try
           {
-            java.net.URL url = new java.net.URL(
-                "http://www.jalview.org/webstart/jalview.jnlp");
-            BufferedReader in = new BufferedReader(new InputStreamReader(url.
-                openStream()));
+            System.setProperty("sun.net.client.defaultConnectTimeout",
+                    "5000");
+            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;
-            while ( (line = in.readLine()) != null)
+            while ((line = in.readLine()) != null)
             {
               if (line.indexOf("jalview.version") == -1)
               {
@@ -252,12 +440,15 @@ public class Cache
               jnlpVersion = line;
               break;
             }
-          }
-          catch (Exception ex)
+          } catch (Exception ex)
           {
+            System.out
+                    .println("Non-fatal exceptions when checking version at www.jalview.org :");
             System.out.println(ex);
             jnlpVersion = getProperty("VERSION");
           }
+          System.setProperty("sun.net.client.defaultConnectTimeout",
+                  orgtimeout);
 
           setProperty("LATEST_VERSION", jnlpVersion);
         }
@@ -280,18 +471,31 @@ public class Cache
 
     setProperty("VERSION", codeVersion);
 
-    //LOAD USERDEFINED COLOURS
-    jalview.gui.UserDefinedColours.initUserColourSchemes(getProperty(
-        "USER_DEFINED_COLOURS"));
-    jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER", false);
+    // LOAD USERDEFINED COLOURS
+    jalview.gui.UserDefinedColours
+            .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
+    jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
+            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
-   *
+   * Gets Jalview application property of given key. Returns null if key not
+   * found
+   * 
+   * @param key
+   *          Name of property
+   * 
    * @return Property value
    */
   public static String getProperty(String key)
@@ -299,8 +503,9 @@ public class Cache
     return applicationProperties.getProperty(key);
   }
 
-  /** These methods are used when checking if the saved preference
-   * is different to the default setting
+  /**
+   * These methods are used when checking if the saved preference is different
+   * to the default setting
    */
 
   public static boolean getDefault(String property, boolean def)
@@ -314,8 +519,9 @@ public class Cache
     return def;
   }
 
-  /** These methods are used when checking if the saved preference
-   * is different to the default setting
+  /**
+   * These methods are used when checking if the saved preference is different
+   * to the default setting
    */
   public static String getDefault(String property, String def)
   {
@@ -330,40 +536,61 @@ public class Cache
 
   /**
    * Stores property in the file "HOME_DIR/.jalview_properties"
-   *
-   * @param key Name of object
-   * @param obj String value of property
-   *
+   * 
+   * @param key
+   *          Name of object
+   * @param obj
+   *          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();
-    }
-    catch (Exception ex)
+      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 + "\n" +
-                         ex);
+      System.out.println("Error setting property: " + key + " " + obj
+              + "\n" + ex);
     }
     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);
+      }
     }
   }
 
@@ -371,8 +598,10 @@ public class Cache
    * internal vamsas class discovery state
    */
   private static int vamsasJarsArePresent = -1;
+
   /**
    * Searches for vamsas client classes on class path.
+   * 
    * @return true if vamsas client is present on classpath
    */
   public static boolean vamsasJarsPresent()
@@ -382,21 +611,20 @@ public class Cache
       try
       {
         if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass(
-            "uk.ac.vamsas.client.VorbaId") != null)
+                "uk.ac.vamsas.client.VorbaId") != null)
         {
-          jalview.bin.Cache.log.debug(
-              "Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
+          jalview.bin.Cache.log
+                  .debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
           vamsasJarsArePresent = 1;
           Logger lvclient = Logger.getLogger("uk.ac.vamsas");
-          lvclient.setLevel(Level.toLevel(Cache.getDefault("logs.Vamsas.Level",
-              Level.INFO.toString())));
+          lvclient.setLevel(Level.toLevel(Cache.getDefault(
+                  "logs.Vamsas.Level", Level.INFO.toString())));
 
           lvclient.addAppender(log.getAppender("JalviewLogger"));
           // Tell the user that debug is enabled
           lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
         }
-      }
-      catch (Exception e)
+      } catch (Exception e)
       {
         vamsasJarsArePresent = 0;
         jalview.bin.Cache.log.debug("Vamsas Classes are not present");
@@ -404,12 +632,15 @@ public class Cache
     }
     return (vamsasJarsArePresent > 0);
   }
+
   /**
    * internal vamsas class discovery state
    */
   private static int groovyJarsArePresent = -1;
+
   /**
    * Searches for vamsas client classes on class path.
+   * 
    * @return true if vamsas client is present on classpath
    */
   public static boolean groovyJarsPresent()
@@ -419,21 +650,24 @@ public class Cache
       try
       {
         if (Cache.class.getClassLoader().loadClass(
-            "groovy.lang.GroovyObject") != null)
+                "groovy.lang.GroovyObject") != null)
         {
-          jalview.bin.Cache.log.debug(
-              "Found Groovy (groovy.lang.GroovyObject can be loaded)");
+          jalview.bin.Cache.log
+                  .debug("Found Groovy (groovy.lang.GroovyObject can be loaded)");
           groovyJarsArePresent = 1;
           Logger lgclient = Logger.getLogger("groovy");
-          lgclient.setLevel(Level.toLevel(Cache.getDefault("logs.Groovy.Level",
-              Level.INFO.toString())));
+          lgclient.setLevel(Level.toLevel(Cache.getDefault(
+                  "logs.Groovy.Level", Level.INFO.toString())));
 
           lgclient.addAppender(log.getAppender("JalviewLogger"));
           // Tell the user that debug is enabled
           lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
         }
-      }
-      catch (Exception e)
+      } catch (Error e)
+      {
+        groovyJarsArePresent = 0;
+        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");
@@ -442,4 +676,270 @@ public class Cache
     return (groovyJarsArePresent > 0);
   }
 
+  /**
+   * 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;
+
+  /**
+   * Initialise the google tracker if it is not done already.
+   */
+  public static void initGoogleTracker()
+  {
+    if (tracker == null)
+    {
+      if (jgoogleanalyticstracker == null)
+      {
+        // try to get the tracker class
+        try
+        {
+          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));
+  }
+
+  /**
+   * 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;
+  }
+
+  /**
+   * 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);
+    }
+  }
 }