X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=fc9dddab4dd49cbaeebffb9f33dfd1738c114d53;hb=refs%2Fheads%2Fpatch%2FJAL-4196_structure_viewer_synchronising;hp=94a1825c72d345315fddf2673cc6bececbd7f319;hpb=5757f3c3ee60e52a2446ab111f35452cf4435ab2;p=jalview.git

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 94a1825..fc9ddda 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -20,39 +20,53 @@
  */
 package jalview.bin;
 
-import jalview.datamodel.PDBEntry;
-import jalview.gui.UserDefinedColours;
-import jalview.schemes.ColourSchemeLoader;
-import jalview.schemes.ColourSchemes;
-import jalview.schemes.UserColourScheme;
-import jalview.structure.StructureImportSettings;
-import jalview.urls.IdOrgSettings;
-import jalview.util.ColorUtils;
-import jalview.util.Platform;
-import jalview.ws.sifts.SiftsSettings;
-
 import java.awt.Color;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileInputStream;
+import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
+import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
+import java.io.PrintWriter;
+import java.io.StringWriter;
+import java.net.Authenticator;
+import java.net.PasswordAuthentication;
 import java.net.URL;
 import java.text.DateFormat;
 import java.text.SimpleDateFormat;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
 import java.util.Collections;
 import java.util.Date;
 import java.util.Enumeration;
+import java.util.HashMap;
 import java.util.Locale;
+import java.util.Map;
 import java.util.Properties;
 import java.util.StringTokenizer;
 import java.util.TreeSet;
 
-import org.apache.log4j.ConsoleAppender;
-import org.apache.log4j.Level;
-import org.apache.log4j.Logger;
-import org.apache.log4j.SimpleLayout;
+import javax.swing.LookAndFeel;
+import javax.swing.UIManager;
+
+import jalview.analytics.GoogleAnalytics4;
+import jalview.datamodel.PDBEntry;
+import jalview.gui.Preferences;
+import jalview.gui.UserDefinedColours;
+import jalview.log.JLoggerLog4j;
+import jalview.schemes.ColourSchemeLoader;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.UserColourScheme;
+import jalview.structure.StructureImportSettings;
+import jalview.urls.IdOrgSettings;
+import jalview.util.ChannelProperties;
+import jalview.util.ColorUtils;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.sifts.SiftsSettings;
 
 /**
  * Stores and retrieves Jalview Application Properties Lists and fields within
@@ -163,6 +177,8 @@ import org.apache.log4j.SimpleLayout;
  * <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
  * respond to selections made in other alignments containing the same sequences.
  * </li>
+ * <li>SHOW_JWS2_SERVICES (true) when set to false, jalview will not
+ * auto-discover JABAWS services</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>
@@ -170,8 +186,8 @@ import org.apache.log4j.SimpleLayout;
  * 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>www.jalview.org (https://www.jalview.org) a property enabling all HTTP
+ * requests to be redirected to a mirror of https://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>
@@ -190,7 +206,13 @@ import org.apache.log4j.SimpleLayout;
  * <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>
  * <li>ID_ORG_HOSTURL location of jalview service providing identifiers.org urls
  * </li>
- * 
+ * <li>NONEWS - when set disables Jalview News from automatically appearing</li>
+ * <li>NOHTMLTEMPLATES - when set, the
+ * https://github.com/jalview/exporter-templates/tree/master/biojs repository is
+ * not downloaded automatically</li>
+ * <li>NOIDENTIFIERSSERVICE - when set, jalview won't automatically download
+ * available URL linkouts via www.jalview.org/services/identifiers</li>
+ * <li>
  * </ul>
  * Deprecated settings:
  * <ul>
@@ -225,6 +247,9 @@ public class Cache
    */
   public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
 
+  // for tests
+  public static final String BOOTSTRAP_TEST = "BOOTSTRAP_TEST";
+
   /**
    * Sifts settings
    */
@@ -263,7 +288,48 @@ public class Cache
   /**
    * Initialises the Jalview Application Log
    */
-  public static Logger log;
+
+  public final static String JALVIEW_LOGGER_NAME = "JalviewLogger";
+
+  // save the proxy properties set at startup
+  public final static String[] startupProxyProperties = {
+      System.getProperty("http.proxyHost"),
+      System.getProperty("http.proxyPort"),
+      System.getProperty("https.proxyHost"),
+      System.getProperty("https.proxyPort"),
+      System.getProperty("http.proxyUser"),
+      System.getProperty("http.proxyPassword"),
+      System.getProperty("https.proxyUser"),
+      System.getProperty("https.proxyPassword"),
+      System.getProperty("http.nonProxyHosts") };
+
+  public final static String PROXYTYPE_NONE = "none";
+
+  // "false" and "true" for backward compatibility
+  public final static String PROXYTYPE_SYSTEM = "false";
+
+  public final static String PROXYTYPE_CUSTOM = "true";
+
+  // in-memory only storage of proxy password, safer to use char array
+  public static char[] proxyAuthPassword = null;
+
+  /**
+   * Session properties, set by command line, try not to affect stored
+   * properties!
+   */
+  private static Map<String, String> sessionProperties = new HashMap<>();
+
+  private static boolean bypassSessionProperties = false;
+
+  public static void enableSessionProperties()
+  {
+    bypassSessionProperties = false;
+  }
+
+  public static void disableSessionProperties()
+  {
+    bypassSessionProperties = true;
+  }
 
   /** Jalview Properties */
   public static Properties applicationProperties = new Properties()
@@ -276,57 +342,28 @@ public class Cache
     }
   };
 
+  /* build Properties (not all saved to .jalview_properties) */
+  public static Properties buildProperties = new Properties();
+
   /** Default file is ~/.jalview_properties */
   static String propertiesFile;
 
+  private static final String fallbackPropertiesFile = ".jalview_properties";
+
   private static boolean propsAreReadOnly = Platform.isJS();
 
-  private final static String JS_PROPERTY_PREFIX = "jalview_";
+  public static boolean isPropsAreReadOnly()
+  {
+    return propsAreReadOnly;
+  }
 
-  public static void initLogger()
+  public static void setPropsAreReadOnly(boolean propsAreReadOnly)
   {
-    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
-      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())));
-      lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
-              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);
-      // Tell the user that debug is enabled
-      jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
-    } catch (Exception ex)
-    {
-      System.err.println("Problems initializing the log4j system\n");
-      ex.printStackTrace(System.err);
-    }
+    Cache.propsAreReadOnly = propsAreReadOnly;
   }
 
+  private final static String JS_PROPERTY_PREFIX = "jalview_";
+
   /**
    * Loads properties from the given properties file. Any existing properties
    * are first cleared.
@@ -334,10 +371,18 @@ public class Cache
   public static void loadProperties(String propsFile)
   {
     propertiesFile = propsFile;
+    String releasePropertiesFile = null;
+    boolean defaultProperties = false;
     if (propsFile == null && !propsAreReadOnly)
     {
+      String channelPrefsFilename = ChannelProperties
+              .getProperty("preferences.filename");
+      String releasePrefsFilename = fallbackPropertiesFile;
       propertiesFile = System.getProperty("user.home") + File.separatorChar
-              + ".jalview_properties";
+              + channelPrefsFilename;
+      releasePropertiesFile = System.getProperty("user.home")
+              + File.separatorChar + releasePrefsFilename;
+      defaultProperties = true;
     }
     else
     {
@@ -357,20 +402,32 @@ public class Cache
         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.");
+          // props file provided as URL
+          fis = new URL(propertiesFile).openStream();
+          if (!Jalview.quiet())
+          {
+            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);
+          String readPropertiesFile = propertiesFile;
+          // if we're using the usual properties file and the channel properties
+          // file doesn't exist, read .jalview_properties
+          // (but we'll still save to the channel properties file).
+          if (defaultProperties && (!new File(propertiesFile).exists())
+                  && (new File(releasePropertiesFile).exists()))
+          {
+            readPropertiesFile = releasePropertiesFile;
+          }
+          fis = new FileInputStream(readPropertiesFile);
         }
         applicationProperties.clear();
         applicationProperties.load(fis);
@@ -381,19 +438,47 @@ public class Cache
         fis.close();
       } catch (Exception ex)
       {
-        System.out.println("Error reading properties file: " + ex);
+        if (!Jalview.quiet())
+          System.out.println("Error reading properties file: " + ex);
       }
     }
+
+    /* TO BE REPLACED WITH PROXY_TYPE SETTINGS 
     if (getDefault("USE_PROXY", false))
     {
       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);
+    // PROXY TYPE settings (now three options "none", "false", "true", but using
+    // backward compatible strings)
+    String proxyType = getDefault("USE_PROXY", PROXYTYPE_SYSTEM);
+    // default to upgrading old settings
+    switch (proxyType)
+    {
+    case PROXYTYPE_NONE:
+      clearProxyProperties();
+      break;
+    case PROXYTYPE_SYSTEM: // use system settings
+      resetProxyProperties();
+      break;
+    case PROXYTYPE_CUSTOM: // use specified proxy settings
+      String httpHost = getDefault("PROXY_SERVER", "");
+      String httpPort = getDefault("PROXY_PORT", "8080");
+      String httpsHost = getDefault("PROXY_SERVER_HTTPS", httpHost);
+      String httpsPort = getDefault("PROXY_PORT_HTTPS", httpPort);
+      String httpUser = getDefault("PROXY_AUTH_USER", null);
+      // https.proxyUser and https.proxyPassword are not able to be
+      // independently set in Preferences yet (or http.nonProxyHosts)
+      String httpsUser = getDefault("PROXY_AUTH_USER_HTTPS", httpUser);
+      setProxyProperties(httpHost, httpPort, httpsHost, httpsPort, httpUser,
+              proxyAuthPassword, httpsUser, proxyAuthPassword, "localhost");
+      break;
+    default:
+      String message = "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
+              + proxyType;
+      Console.warn(message);
     }
 
     // LOAD THE AUTHORS FROM THE authors.props file
@@ -410,14 +495,15 @@ public class Cache
       }
     } catch (Exception ex)
     {
-      System.out.println("Error reading author details: " + ex);
+      if (!Jalview.quiet())
+        System.out.println("Error reading author details: " + ex);
       authorDetails = null;
     }
     if (authorDetails == null)
     {
-        applicationProperties.remove("AUTHORS");
-        applicationProperties.remove("AUTHORFNAMES");
-        applicationProperties.remove("YEAR");
+      applicationProperties.remove("AUTHORS");
+      applicationProperties.remove("AUTHORFNAMES");
+      applicationProperties.remove("YEAR");
     }
 
     loadBuildProperties(false);
@@ -425,88 +511,94 @@ public class Cache
     SiftsSettings
             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 
-    SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache
+    SiftsSettings.setSiftDownloadDirectory(Cache
             .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
 
     SiftsSettings.setFailSafePIDThreshold(
-            jalview.bin.Cache.getDefault("sifts_fail_safe_pid_threshold",
+            Cache.getDefault("sifts_fail_safe_pid_threshold",
                     DEFAULT_FAIL_SAFE_PID_THRESHOLD));
 
     SiftsSettings.setCacheThresholdInDays(
-            jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days",
+            Cache.getDefault("sifts_cache_threshold_in_days",
                     DEFAULT_CACHE_THRESHOLD_IN_DAYS));
 
     IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
-            "http://www.jalview.org/services/identifiers"));
+            "https://www.jalview.org/services/identifiers"));
     IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
 
-    StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
-            .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
+    StructureImportSettings.setDefaultStructureFileFormat(
+            Cache.getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
     StructureImportSettings
             .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
     // StructureImportSettings
-    // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
+    // .setDefaultPDBFileParser(Cache.getDefault(
     // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
 
     String jnlpVersion = System.getProperty("jalview.version");
 
-    // jnlpVersion will be null if a latest version check for the channel needs to
-    // be done
+    // jnlpVersion will be null if a latest version check for the channel needs
+    // to be done
     // 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")))
     {
-      new Thread()
+
+      class VersionChecker extends Thread
       {
+
         @Override
         public void run()
         {
+          String remoteBuildPropertiesUrl = Cache
+                  .getAppbaseBuildProperties();
+
           String orgtimeout = System
                   .getProperty("sun.net.client.defaultConnectTimeout");
           if (orgtimeout == null)
           {
             orgtimeout = "30";
-            System.out.println("# INFO: Setting default net timeout to "
-                    + orgtimeout + " seconds.");
+            Console.debug("Setting default net timeout to " + orgtimeout
+                    + " seconds.");
           }
           String remoteVersion = null;
-          try
+          if (remoteBuildPropertiesUrl.startsWith("http"))
           {
-            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)
+            try
             {
-              if (line.indexOf("jalview.version") == -1)
+              System.setProperty("sun.net.client.defaultConnectTimeout",
+                      "5000");
+
+              URL url = new URL(remoteBuildPropertiesUrl);
+
+              BufferedReader in = new BufferedReader(
+                      new InputStreamReader(url.openStream()));
+
+              Properties remoteBuildProperties = new Properties();
+              remoteBuildProperties.load(in);
+              remoteVersion = remoteBuildProperties.getProperty("VERSION");
+            } catch (Exception ex)
+            {
+              if (!Jalview.quiet())
               {
-                continue;
+                System.out.println(
+                        "Non-fatal exception when checking version at "
+                                + remoteBuildPropertiesUrl + ":");
+                System.out.println(ex);
               }
-
-              line = line.substring(line.indexOf("value=") + 7);
-              line = line.substring(0, line.lastIndexOf("\""));
-              remoteVersion = line;
-              break;
+              remoteVersion = getProperty("VERSION");
             }
-          } catch (Exception ex)
-          {
-            System.out.println(
-                    "Non-fatal exception when checking version at www.jalview.org :");
-            System.out.println(ex);
-            remoteVersion = getProperty("VERSION");
           }
           System.setProperty("sun.net.client.defaultConnectTimeout",
                   orgtimeout);
 
           setProperty("LATEST_VERSION", remoteVersion);
         }
-      }.start();
+      }
+
+      VersionChecker vc = new VersionChecker();
+      vc.start();
     }
     else
     {
@@ -543,8 +635,8 @@ public class Cache
         url = Cache.class.getResource(resourcePath).toString();
       } catch (Exception ex)
       {
-        System.err.println("Failed to resolve resource " + resourcePath + ": "
-                + ex.getMessage());
+        System.err.println("Failed to resolve resource " + resourcePath
+                + ": " + ex.getMessage());
       }
     }
     else
@@ -569,11 +661,32 @@ public class Cache
       String buildDetails = resolveResourceURLFor("/.build_properties");
       URL localJarFileURL = new URL(buildDetails);
       InputStream in = localJarFileURL.openStream();
-      applicationProperties.load(in);
+      buildProperties.load(in);
       in.close();
+      if (buildProperties.getProperty("BUILD_DATE", null) != null)
+      {
+        applicationProperties.put("BUILD_DATE",
+                buildProperties.getProperty("BUILD_DATE"));
+      }
+      if (buildProperties.getProperty("INSTALLATION", null) != null)
+      {
+        applicationProperties.put("INSTALLATION",
+                buildProperties.getProperty("INSTALLATION"));
+      }
+      if (buildProperties.getProperty("VERSION", null) != null)
+      {
+        applicationProperties.put("VERSION",
+                buildProperties.getProperty("VERSION"));
+      }
+      if (buildProperties.getProperty("JAVA_COMPILE_VERSION", null) != null)
+      {
+        applicationProperties.put("JAVA_COMPILE_VERSION",
+                buildProperties.getProperty("JAVA_COMPILE_VERSION"));
+      }
     } catch (Exception ex)
     {
-      System.out.println("Error reading build details: " + ex);
+      if (!Jalview.quiet())
+        System.out.println("Error reading build details: " + ex);
       applicationProperties.remove("VERSION");
     }
     String codeVersion = getProperty("VERSION");
@@ -593,8 +706,8 @@ public class Cache
     new BuildDetails(codeVersion, null, codeInstallation);
     if (printVersion && reportVersion)
     {
-      System.out
-            .println("Jalview Version: " + codeVersion + codeInstallation);
+      System.out.println(ChannelProperties.getProperty("app_name")
+              + " version: " + codeVersion + codeInstallation);
     }
   }
 
@@ -620,7 +733,21 @@ public class Cache
    */
   public static String getProperty(String key)
   {
-    String prop = applicationProperties.getProperty(key);
+    return getProperty(key, false);
+  }
+
+  public static String getProperty(String key,
+          boolean skipSessionProperties)
+  {
+    String prop = null;
+    if (!(skipSessionProperties || bypassSessionProperties))
+    {
+      prop = getSessionProperty(key);
+    }
+    if (prop == null)
+    {
+      prop = applicationProperties.getProperty(key);
+    }
     if (prop == null && Platform.isJS())
     {
       prop = applicationProperties.getProperty(Platform.getUniqueAppletID()
@@ -655,8 +782,9 @@ public class Cache
         def = Integer.parseInt(string);
       } catch (NumberFormatException e)
       {
-        System.out.println("Error parsing int property '" + property
-                + "' with value '" + string + "'");
+        if (!Jalview.quiet())
+          System.out.println("Error parsing int property '" + property
+                  + "' with value '" + string + "'");
       }
     }
 
@@ -689,16 +817,25 @@ public class Cache
     try
     {
       oldValue = applicationProperties.setProperty(key, obj);
-      if (propertiesFile != null && !propsAreReadOnly)
+      if (propertiesFile != null && !propsAreReadOnly
+      // don't rewrite if new value is same as old value
+              && !((obj == null && oldValue == null)
+                      || (obj != null && obj.equals(oldValue))))
       {
+        // reset the session property too
+        if (sessionProperties.containsKey(key))
+        {
+          sessionProperties.remove(key);
+        }
         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);
+      if (!Jalview.quiet())
+        System.out.println(
+                "Error setting property: " + key + " " + obj + "\n" + ex);
     }
     return oldValue;
   }
@@ -728,7 +865,8 @@ public class Cache
         out.close();
       } catch (Exception ex)
       {
-        System.out.println("Error saving properties: " + ex);
+        if (!Jalview.quiet())
+          System.out.println("Error saving properties: " + ex);
       }
     }
   }
@@ -752,21 +890,21 @@ public class Cache
         if (jalview.jbgui.GDesktop.class.getClassLoader()
                 .loadClass("uk.ac.vamsas.client.VorbaId") != null)
         {
-          jalview.bin.Cache.log.debug(
+          Console.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.addAppender(log.getAppender("JalviewLogger"));
+          JLoggerLog4j lvclient = JLoggerLog4j.getLogger("uk.ac.vamsas",
+                  Console.getCachedLogLevel("logs.Vamsas.Level"));
+          JLoggerLog4j.addAppender(lvclient, Console.log,
+                  JALVIEW_LOGGER_NAME);
           // Tell the user that debug is enabled
-          lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
+          lvclient.debug(ChannelProperties.getProperty("app_name")
+                  + " Vamsas Client Debugging Output Follows.");
         }
       } catch (Exception e)
       {
         vamsasJarsArePresent = 0;
-        jalview.bin.Cache.log.debug("Vamsas Classes are not present");
+        Console.debug("Vamsas Classes are not present");
       }
     }
     return (vamsasJarsArePresent > 0);
@@ -791,25 +929,25 @@ public class Cache
         if (Cache.class.getClassLoader()
                 .loadClass("groovy.lang.GroovyObject") != null)
         {
-          jalview.bin.Cache.log.debug(
+          Console.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.addAppender(log.getAppender("JalviewLogger"));
+          JLoggerLog4j lgclient = JLoggerLog4j.getLogger("groovy",
+                  Console.getCachedLogLevel("logs.Groovy.Level"));
+          JLoggerLog4j.addAppender(lgclient, Console.log,
+                  JALVIEW_LOGGER_NAME);
           // Tell the user that debug is enabled
-          lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
+          lgclient.debug(ChannelProperties.getProperty("app_name")
+                  + " Groovy Client Debugging Output Follows.");
         }
       } catch (Error e)
       {
         groovyJarsArePresent = 0;
-        jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
+        Console.debug("Groovy Classes are not present", e);
       } catch (Exception e)
       {
         groovyJarsArePresent = 0;
-        jalview.bin.Cache.log.debug("Groovy Classes are not present");
+        Console.debug("Groovy Classes are not present");
       }
     }
     return (groovyJarsArePresent > 0);
@@ -825,84 +963,123 @@ public class Cache
 
   protected static Class jgoogleanalyticstracker = null;
 
+  private static boolean useGA4 = true;
+
   /**
    * Initialise the google tracker if it is not done already.
    */
   public static void initGoogleTracker()
   {
-    if (tracker == null)
+    if (useGA4)
+    {
+      GoogleAnalytics4.setEnabled(true);
+
+      String appName = ChannelProperties.getProperty("app_name")
+              + " Desktop";
+      String version = Cache.getProperty("VERSION") + "_"
+              + Cache.getDefault("BUILD_DATE", "unknown");
+      String path;
+      /* we don't want to encode ':' as "%3A" for backward compatibility with the UA setup
+      try
+      {
+        path = "/" + String.join("/", URLEncoder.encode(appName, "UTF-8"),
+                URLEncoder.encode(version, "UTF-8"),
+                URLEncoder.encode(APPLICATION_STARTED, "UTF-8"));
+      } catch (UnsupportedEncodingException e)
+      {
+      */
+      path = ("/" + String.join("/", appName, version, APPLICATION_STARTED))
+              .replace(' ', '+');
+      /*
+      }
+      */
+      GoogleAnalytics4 ga4 = GoogleAnalytics4.getInstance();
+
+      // This will add a page_view similar to the old UA analytics.
+      // We probably want to get rid of this once the application_launch event
+      // is being processed properly.
+      ga4.sendAnalytics("page_view", "page_location", path, "page_title",
+              APPLICATION_STARTED);
+
+      // This will send a new "application_launch" event with parameters
+      // including the old-style "path", the channel name and version
+      ga4.sendAnalytics("application_launch", true, "page_location", path);
+    }
+    else
     {
-      if (jgoogleanalyticstracker == null)
+      if (tracker == null)
       {
-        // try to get the tracker class
+        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)
+          {
+            Console.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
         {
-          jgoogleanalyticstracker = Cache.class.getClassLoader().loadClass(
-                  "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
-          trackerfocus = Cache.class.getClassLoader()
-                  .loadClass("com.boxysystems.jgoogleanalytics.FocusPoint");
+          // Google analytics tracking code for Library Finder
+          tracker = jgoogleanalyticstracker
+                  .getConstructor(new Class[]
+                  { String.class, String.class, String.class })
+                  .newInstance(new Object[]
+                  { ChannelProperties.getProperty("app_name") + " Desktop",
+                      (vrs = Cache.getProperty("VERSION") + "_"
+                              + 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)
         {
-          log.debug(
-                  "com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
-          tracker = null;
-          jgoogleanalyticstracker = null;
-          trackerfocus = null;
-          return;
+          ex = e;
+        } catch (Error e)
+        {
+          err = e;
         }
-      }
-      // 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 || ex != null || err != null)
         {
           if (re != null)
           {
-            log.debug("Caught runtime exception in googletracker init:",
+            Console.debug("Caught runtime exception in googletracker init:",
                     re);
           }
           if (ex != null)
           {
-            log.warn(
+            Console.warn(
                     "Failed to initialise GoogleTracker for Jalview Desktop with version "
                             + vrs,
                     ex);
           }
           if (err != null)
           {
-            log.error(
+            Console.error(
                     "Whilst initing GoogleTracker for Jalview Desktop version "
                             + vrs,
                     err);
@@ -910,37 +1087,14 @@ public class Cache
         }
         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();
-          }
+          Console.debug("Successfully initialised tracker.");
         }
       }
-      else
-      {
-        log.debug("Successfully initialised tracker.");
-      }
     }
   }
 
+  private static final String APPLICATION_STARTED = "Application Started.";
+
   /**
    * get the user's default colour if available
    * 
@@ -958,7 +1112,7 @@ public class Cache
     Color col = ColorUtils.parseColourString(colprop);
     if (col == null)
     {
-      log.warn("Couldn't parse '" + colprop + "' as a colour for "
+      Console.warn("Couldn't parse '" + colprop + "' as a colour for "
               + property);
     }
     return (col == null) ? defcolour : col;
@@ -1095,7 +1249,8 @@ public class Cache
         }
       } catch (Exception ex)
       {
-        System.out.println("Error loading User ColourFile\n" + ex);
+        if (!Jalview.quiet())
+          System.out.println("Error loading User ColourFile\n" + ex);
       }
     }
     if (!files.equals(coloursFound.toString()))
@@ -1114,31 +1269,83 @@ public class Cache
   }
 
   /**
+   * Initial logging information helper for various versions output
+   * 
+   * @param prefix
+   * @param value
+   * @param defaultValue
+   */
+  private static void appendIfNotNull(StringBuilder sb, String prefix,
+          String value, String suffix, String defaultValue)
+  {
+    if (value == null && defaultValue == null)
+    {
+      return;
+    }
+    if (prefix != null)
+      sb.append(prefix);
+    sb.append(value == null ? defaultValue : value);
+    if (suffix != null)
+      sb.append(suffix);
+  }
+
+  /**
    * 
    * @return Jalview version, build details and JVM platform version for console
    */
   public static String getVersionDetailsForConsole()
   {
-    return "Jalview Version: "
-            + jalview.bin.Cache.getDefault("VERSION", "TEST")
-            + "\n" + "Jalview Installation: "
-            + jalview.bin.Cache.getDefault("INSTALLATION",
-                    "unknown")
-            + "\n" + "Build Date: "
-            + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
-            + "\n" + "Java version: "
-            + System.getProperty("java.version") + "\n"
-            + System.getProperty("os.arch") + " "
-            + System.getProperty("os.name") + " "
-            + System.getProperty("os.version")
-            + (jalview.bin.Cache.getDefault("VERSION", "TEST")
-                    .equals("DEVELOPMENT")
-								? "\nGetdown appdir: " + System.getProperty("getdownappdir") + "\nJava path: "
-                                    + System.getProperty(
-                                            "java.home")
-                                    + File.separator + "bin"
-                                    + File.separator + "java"
-								: "");
+    StringBuilder sb = new StringBuilder();
+    sb.append(ChannelProperties.getProperty("app_name"))
+            .append(" Version: ");
+    sb.append(Cache.getDefault("VERSION", "TEST"));
+    sb.append("\n");
+    sb.append(ChannelProperties.getProperty("app_name"))
+            .append(" Installation: ");
+    sb.append(Cache.getDefault("INSTALLATION", "unknown"));
+    sb.append("\n");
+    sb.append("Build Date: ");
+    sb.append(Cache.getDefault("BUILD_DATE", "unknown"));
+    sb.append("\n");
+    sb.append("Java version: ");
+    sb.append(System.getProperty("java.version"));
+    sb.append("\n");
+    sb.append("Java platform: ");
+    sb.append(System.getProperty("os.arch"));
+    sb.append(" ");
+    sb.append(System.getProperty("os.name"));
+    sb.append(" ");
+    sb.append(System.getProperty("os.version"));
+    sb.append("\n");
+    appendIfNotNull(sb, "Install4j version: ",
+            System.getProperty("sys.install4jVersion"), "\n", null);
+    appendIfNotNull(sb, "Install4j template version: ",
+            System.getProperty("installer_template_version"), "\n", null);
+    appendIfNotNull(sb, "Launcher version: ",
+            System.getProperty("launcher_version"), "\n", null);
+    LookAndFeel laf = UIManager.getLookAndFeel();
+    String lafName = laf == null ? "Not obtained" : laf.getName();
+    String lafClass = laf == null ? "unknown" : laf.getClass().getName();
+    sb.append("LookAndFeel: ");
+    sb.append(lafName);
+    sb.append(" (");
+    sb.append(lafClass);
+    sb.append(")\n");
+    appendIfNotNull(sb, "Channel: ",
+            ChannelProperties.getProperty("channel"), "\n", null);
+    if (Console.isDebugEnabled()
+            || !"release".equals(ChannelProperties.getProperty("channel")))
+    {
+      appendIfNotNull(sb, "Getdown appdir: ",
+              System.getProperty("getdowninstanceappdir"), "\n", null);
+      appendIfNotNull(sb, "Getdown appbase: ",
+              System.getProperty("getdowninstanceappbase"), "\n", null);
+      appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"),
+              "\n", "unknown");
+      appendIfNotNull(sb, "Preferences file: ", propertiesFile, "\n",
+              "unknown");
+    }
+    return sb.toString();
   }
 
   /**
@@ -1149,6 +1356,444 @@ public class Cache
   {
     // consider returning more human friendly info
     // eg 'built from Source' or update channel
-    return jalview.bin.Cache.getDefault("INSTALLATION", "unknown");
+    return Cache.getDefault("INSTALLATION", "unknown");
+  }
+
+  public static String getStackTraceString(Throwable t)
+  {
+    StringWriter sw = new StringWriter();
+    PrintWriter pw = new PrintWriter(sw);
+    t.printStackTrace(pw);
+    return sw.toString();
+  }
+
+  // proxy properties methods
+  public static void clearProxyProperties()
+  {
+    setProxyProperties(null, null, null, null, null, null, null, null,
+            null);
+  }
+
+  public static void resetProxyProperties()
+  {
+    setProxyProperties(startupProxyProperties[0], startupProxyProperties[1],
+            startupProxyProperties[2], startupProxyProperties[3],
+            startupProxyProperties[4],
+            startupProxyProperties[5] == null ? null
+                    : startupProxyProperties[5].toCharArray(),
+            startupProxyProperties[6],
+            startupProxyProperties[7] == null ? null
+                    : startupProxyProperties[7].toCharArray(),
+            startupProxyProperties[8]);
+    StringBuilder sb = new StringBuilder();
+    sb.append("Setting proxy properties to: http.proxyHost=")
+            .append(startupProxyProperties[0]).append(", http.proxyPort=")
+            .append(startupProxyProperties[1])
+            .append(startupProxyProperties[4] != null
+                    && !startupProxyProperties[4].isEmpty()
+                            ? " [" + startupProxyProperties[4] + "]"
+                            : "")
+            .append(", https.proxyHost=").append(startupProxyProperties[2])
+            .append(", https.proxyPort=").append(startupProxyProperties[3])
+            .append(startupProxyProperties[6] != null
+                    && !startupProxyProperties[6].isEmpty()
+                            ? " [" + startupProxyProperties[6] + "]"
+                            : "");
+
+    Console.debug(sb.toString());
+  }
+
+  public static void setProxyPropertiesFromPreferences()
+  {
+    setProxyPropertiesFromPreferences(Cache.PROXYTYPE_SYSTEM);
+  }
+
+  public static void setProxyPropertiesFromPreferences(
+          String previousProxyType)
+  {
+    String proxyType = Cache.getDefault("USE_PROXY",
+            Cache.PROXYTYPE_SYSTEM);
+    if (previousProxyType != null
+            && !proxyType.equals(Cache.PROXYTYPE_CUSTOM) // always apply
+                                                         // customProxy
+            && proxyType.equals(previousProxyType))
+    {
+      // no change
+      return;
+    }
+    switch (proxyType)
+    {
+    case Cache.PROXYTYPE_NONE:
+      if (!previousProxyType.equals(proxyType))
+      {
+        Console.info("Setting no proxy settings");
+        Cache.setProxyProperties(null, null, null, null, null, null, null,
+                null, null);
+      }
+      break;
+    case Cache.PROXYTYPE_CUSTOM:
+      // always re-set a custom proxy -- it might have changed, particularly
+      // password
+      Console.info("Setting custom proxy settings");
+      boolean proxyAuthSet = Cache.getDefault("PROXY_AUTH", false);
+      Cache.setProxyProperties(Cache.getDefault("PROXY_SERVER", null),
+              Cache.getDefault("PROXY_PORT", null),
+              Cache.getDefault("PROXY_SERVER_HTTPS", null),
+              Cache.getDefault("PROXY_PORT_HTTPS", null),
+              proxyAuthSet ? Cache.getDefault("PROXY_AUTH_USERNAME", "")
+                      : null,
+              proxyAuthSet ? Cache.proxyAuthPassword : null,
+              proxyAuthSet ? Cache.getDefault("PROXY_AUTH_USERNAME", "")
+                      : null,
+              proxyAuthSet ? Cache.proxyAuthPassword : null, "localhost");
+      break;
+    default: // system proxy settings by default
+      Console.info("Setting system proxy settings");
+      Cache.resetProxyProperties();
+    }
+  }
+
+  public static void setProxyProperties(String httpHost, String httpPort,
+          String httpsHost, String httpsPort, String httpUser,
+          char[] httpPassword, String httpsUser, char[] httpsPassword,
+          String nonProxyHosts)
+  {
+    setOrClearSystemProperty("http.proxyHost", httpHost);
+    setOrClearSystemProperty("http.proxyPort", httpPort);
+    setOrClearSystemProperty("https.proxyHost", httpsHost);
+    setOrClearSystemProperty("https.proxyPort", httpsPort);
+    setOrClearSystemProperty("http.proxyUser", httpUser);
+    setOrClearSystemProperty("https.proxyUser", httpsUser);
+    // note: passwords for http.proxyPassword and https.proxyPassword are sent
+    // via the Authenticator, properties do not need to be set
+
+    // are we using a custom proxy (password prompt might be required)?
+    boolean customProxySet = getDefault("USE_PROXY", PROXYTYPE_SYSTEM)
+            .equals(PROXYTYPE_CUSTOM);
+
+    /*
+     * A bug in Java means the AuthCache does not get reset, so once it has working credentials,
+     * it never asks for more, so changing the Authenticator has no effect (as getPasswordAuthentication()
+     * is not re-called).
+     * This could lead to password leak to a hostile proxy server, so I'm putting in a hack to clear
+     * the AuthCache.
+     * see https://www.generacodice.com/en/articolo/154918/Reset-the-Authenticator-credentials
+     * ...
+     * Turns out this is only accessible in Java 8, and not in Java 9 onwards, so commenting out
+     */
+    /*
+    try
+    {
+      sun.net.www.protocol.http.AuthCacheValue
+              .setAuthCache(new sun.net.www.protocol.http.AuthCacheImpl());
+    } catch (Throwable t)
+    {
+      Cache.error(t.getMessage());
+      Cache.debug(getStackTraceString(t));
+    }
+    */
+
+    if (httpUser != null || httpsUser != null)
+    {
+      try
+      {
+        char[] displayHttpPw = new char[httpPassword == null ? 0
+                : httpPassword.length];
+        Arrays.fill(displayHttpPw, '*');
+        Console.debug(
+                "CACHE Proxy: setting new Authenticator with httpUser='"
+                        + httpUser + "' httpPassword='" + displayHttpPw
+                        + "'");
+        if (!Platform.isJS())
+        /* *
+         * java.net.Authenticator not implemented in SwingJS yet
+         * 
+         * @j2sIgnore
+         * 
+         */
+        {
+          Authenticator.setDefault(new Authenticator()
+          {
+            @Override
+            protected PasswordAuthentication getPasswordAuthentication()
+            {
+              if (getRequestorType() == RequestorType.PROXY)
+              {
+                String protocol = getRequestingProtocol();
+                boolean needProxyPasswordSet = false;
+                if (customProxySet &&
+                // we have a username but no password for the scheme being
+                // requested
+                        (protocol.equalsIgnoreCase("http")
+                                && (httpUser != null
+                                        && httpUser.length() > 0
+                                        && (httpPassword == null
+                                                || httpPassword.length == 0)))
+                        || (protocol.equalsIgnoreCase("https")
+                                && (httpsUser != null
+                                        && httpsUser.length() > 0
+                                        && (httpsPassword == null
+                                                || httpsPassword.length == 0))))
+                {
+                  // open Preferences -> Connections
+                  String message = MessageManager
+                          .getString("label.proxy_password_required");
+                  Preferences.openPreferences(
+                          Preferences.TabRef.CONNECTIONS_TAB, message);
+                  Preferences.getInstance()
+                          .proxyAuthPasswordCheckHighlight(true, true);
+                }
+                else
+                {
+                  try
+                  {
+                    if (protocol.equalsIgnoreCase("http")
+                            && getRequestingHost()
+                                    .equalsIgnoreCase(httpHost)
+                            && getRequestingPort() == Integer
+                                    .valueOf(httpPort))
+                    {
+                      Console.debug(
+                              "AUTHENTICATOR returning PasswordAuthentication(\""
+                                      + httpUser + "\", '"
+                                      + new String(displayHttpPw) + "')");
+                      return new PasswordAuthentication(httpUser,
+                              httpPassword);
+                    }
+                    if (protocol.equalsIgnoreCase("https")
+                            && getRequestingHost()
+                                    .equalsIgnoreCase(httpsHost)
+                            && getRequestingPort() == Integer
+                                    .valueOf(httpsPort))
+                    {
+                      char[] displayHttpsPw = new char[httpPassword.length];
+                      Arrays.fill(displayHttpsPw, '*');
+                      Console.debug(
+                              "AUTHENTICATOR returning PasswordAuthentication(\""
+                                      + httpsUser + "\", '" + displayHttpsPw
+                                      + "'");
+                      return new PasswordAuthentication(httpsUser,
+                              httpsPassword);
+                    }
+                  } catch (NumberFormatException e)
+                  {
+                    Console.error("Problem with proxy port values [http:"
+                            + httpPort + ", https:" + httpsPort + "]");
+                  }
+                  Console.debug(
+                          "AUTHENTICATOR after trying to get PasswordAuthentication");
+                }
+              }
+              // non proxy request
+              Console.debug("AUTHENTICATOR returning null");
+              return null;
+            }
+          });
+        } // end of j2sIgnore for java.net.Authenticator
+
+        // required to re-enable basic authentication (should be okay for a
+        // local proxy)
+        Console.debug(
+                "AUTHENTICATOR setting property 'jdk.http.auth.tunneling.disabledSchemes' to \"\"");
+        System.setProperty("jdk.http.auth.tunneling.disabledSchemes", "");
+      } catch (SecurityException e)
+      {
+        Console.error("Could not set default Authenticator");
+        Console.debug(getStackTraceString(e));
+      }
+    }
+    else
+    {
+      // reset the Authenticator to protect http.proxyUser and
+      // http.proxyPassword Just In Case
+      /* as noted above, due to bug in java this doesn't work if the sun.net.www.protocol.http.AuthCache
+       * has working credentials. No workaround for Java 11.
+       */
+      if (!Platform.isJS())
+      /* *
+       * java.net.Authenticator not implemented in SwingJS yet
+       * 
+       * @j2sIgnore
+       * 
+       */
+      {
+        Console.debug(
+                "AUTHENTICATOR setting default Authenticator to null");
+        Authenticator.setDefault(null);
+      }
+    }
+
+    // nonProxyHosts not currently configurable in Preferences
+    Console.debug(
+            "AUTHENTICATOR setting property 'http.nonProxyHosts' to \""
+                    + nonProxyHosts + "\"");
+    setOrClearSystemProperty("http.nonProxyHosts", nonProxyHosts);
+  }
+
+  public static void setOrClearSystemProperty(String key, char[] value)
+  {
+    setOrClearSystemProperty(key,
+            (value == null) ? null : new String(value));
+  }
+
+  public static void setOrClearSystemProperty(String key, String value)
+  {
+    if (key == null)
+    {
+      return;
+    }
+    if (value == null)
+    {
+      System.clearProperty(key);
+    }
+    else
+    {
+      System.setProperty(key, value);
+    }
+  }
+
+  /**
+   * Getdown appbase methods
+   */
+
+  private static final String releaseAppbase;
+
+  private static String getdownAppbase;
+
+  private static String getdownDistDir;
+
+  static
+  {
+    if (!Platform.isJS())
+    {
+      Float specversion = Float
+              .parseFloat(System.getProperty("java.specification.version"));
+      releaseAppbase = (specversion < 9)
+              ? "https://www.jalview.org/getdown/release/1.8"
+              : "https://www.jalview.org/getdown/release/11";
+    }
+    else
+    {
+      // this value currenly made up, can be changed to URL that will be
+      // "https://www.jalview.org/jalview-js/swingjs/j2s/build_properties"
+      releaseAppbase = "https://www.jalview.org/jalview-js";
+      getdownAppbase = releaseAppbase;
+      getdownDistDir = "/swingjs/j2s";
+    }
+  }
+
+  // look for properties (passed in by getdown) otherwise default to release
+  private static void setGetdownAppbase()
+  {
+    if (getdownAppbase != null)
+    {
+      return;
+    }
+    String appbase = System.getProperty("getdownappbase");
+    String distDir = System.getProperty("getdowndistdir");
+    if (appbase == null)
+    {
+      appbase = buildProperties.getProperty("GETDOWNAPPBASE");
+      distDir = buildProperties.getProperty("GETDOWNAPPDISTDIR");
+    }
+    if (appbase == null)
+    {
+      appbase = releaseAppbase;
+      distDir = "release";
+    }
+    if (appbase.endsWith("/"))
+    {
+      appbase = appbase.substring(0, appbase.length() - 1);
+    }
+    if (distDir == null)
+    {
+      distDir = appbase.equals(releaseAppbase) ? "release" : "alt";
+    }
+    getdownAppbase = appbase;
+    getdownDistDir = distDir;
+  }
+
+  public static String getGetdownAppbase()
+  {
+    setGetdownAppbase();
+    return getdownAppbase;
+  }
+
+  public static String getAppbaseBuildProperties()
+  {
+    String appbase = getGetdownAppbase();
+    return appbase + "/" + getdownDistDir + "/build_properties";
+  }
+
+  private static final Collection<String> bootstrapProperties = new ArrayList<>(
+          Arrays.asList(JALVIEWLOGLEVEL, BOOTSTRAP_TEST));
+
+  public static Properties bootstrapProperties(String filename)
+  {
+    Properties bootstrapProps = new Properties();
+    File file = null;
+    if (filename != null)
+    {
+      file = new File(filename);
+    }
+    if (file == null || !file.exists())
+    {
+      String channelPrefsFilename = ChannelProperties
+              .getProperty("preferences.filename");
+      String propertiesFilename = System.getProperty("user.home")
+              + File.separatorChar + channelPrefsFilename;
+      file = new File(propertiesFilename);
+    }
+    if (file == null || !file.exists())
+    {
+      String releasePrefsFilename = fallbackPropertiesFile;
+      String releasePropertiesFilename = System.getProperty("user.home")
+              + File.separatorChar + releasePrefsFilename;
+      file = new File(releasePropertiesFilename);
+    }
+
+    if (filename == null)
+      return null;
+    if (!file.exists())
+    {
+      System.err.println("Could not load bootstrap preferences file '"
+              + filename + "'");
+      return null;
+    }
+
+    try
+    {
+      FileInputStream in = new FileInputStream(file.getAbsoluteFile());
+      Properties props = new Properties();
+      props.load(in);
+      for (String prop : bootstrapProperties)
+      {
+        if (props.containsKey(prop))
+          bootstrapProps.put(prop, props.getProperty(prop));
+      }
+    } catch (FileNotFoundException e)
+    {
+      System.err.println("Could not find bootstrap preferences file '"
+              + file.getAbsolutePath() + "'");
+    } catch (IOException e)
+    {
+      System.err.println(
+              "IOException when loading bootstrap preferences file '"
+                      + file.getAbsolutePath() + "'");
+    }
+    return bootstrapProps;
+  }
+
+  public static void setSessionProperty(String key, String val)
+  {
+    if (key != null)
+    {
+      sessionProperties.put(key, val);
+    }
+  }
+
+  public static String getSessionProperty(String key)
+  {
+    return key == null ? null : sessionProperties.get(key);
   }
 }