X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=483b1fcd263874feacf94c2340ef423758d42339;hb=c1e71094304dcd2b975c485416ec5e25cca30815;hp=366911784f0d1ccbc06844511b5904cf317c0d63;hpb=8dadf27423ca69874dc6a3c9d416974ba5ae767f;p=jalview.git

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 3669117..483b1fc 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -24,38 +24,51 @@ 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.List;
 import java.util.Locale;
+import java.util.Map;
 import java.util.Properties;
 import java.util.StringTokenizer;
 import java.util.TreeSet;
-import java.util.regex.Pattern;
 
 import javax.swing.LookAndFeel;
 import javax.swing.UIManager;
 
-import org.apache.log4j.ConsoleAppender;
-import org.apache.log4j.Level;
-import org.apache.log4j.Logger;
-import org.apache.log4j.SimpleLayout;
-
+import jalview.analytics.Plausible;
+import jalview.bin.argparser.Arg;
+import jalview.bin.argparser.ArgParser;
 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;
 
 /**
@@ -118,7 +131,7 @@ import jalview.ws.sifts.SiftsSettings;
  * service</li>
  * <li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire
  * service</li>
- * <li>USAGESTATS (false - user prompted) Enable google analytics tracker for
+ * <li>USAGESTATS (false - user prompted) Enable analytics tracker for
  * collecting usage statistics</li>
  * <li>SHOW_OVERVIEW boolean for overview window display</li>
  * <li>ANTI_ALIAS boolean for smooth fonts</li>
@@ -130,6 +143,10 @@ import jalview.ws.sifts.SiftsSettings;
  * <li>WRAP_ALIGNMENT</li>
  * <li>EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering
  * style check</li>
+ * <li>BITMAP_SCALE - scale factor for PNG export - default 0.0 - native
+ * resolution</li>
+ * <li>BITMAP_HEIGHT - height bound for PNG export or 0 for unbound</li>
+ * <li>BITMAP_WIDTH - width bound for PNG export or 0 for unbound</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>
@@ -196,8 +213,13 @@ import jalview.ws.sifts.SiftsSettings;
  * <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>
@@ -232,6 +254,9 @@ public class Cache
    */
   public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
 
+  // for tests
+  public static final String BOOTSTRAP_TEST = "BOOTSTRAP_TEST";
+
   /**
    * Sifts settings
    */
@@ -270,7 +295,48 @@ 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()
@@ -283,59 +349,28 @@ 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 boolean propsAreReadOnly = false;
+  private static final String fallbackPropertiesFile = ".jalview_properties";
 
-  public static void initLogger()
+  private static boolean propsAreReadOnly = Platform.isJS();
+
+  public static boolean isPropsAreReadOnly()
   {
-    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())));
-      // we shouldn't need to do this
-      org.apache.log4j.Logger.getRootLogger()
-              .setLevel(org.apache.log4j.Level.INFO);
-
-      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);
-    }
+    return propsAreReadOnly;
+  }
+
+  public static void setPropsAreReadOnly(boolean propsAreReadOnly)
+  {
+    Cache.propsAreReadOnly = propsAreReadOnly;
   }
 
+  private final static String JS_PROPERTY_PREFIX = "jalview_";
+
   /**
    * Loads properties from the given properties file. Any existing properties
    * are first cleared.
@@ -343,10 +378,18 @@ public class Cache
   public static void loadProperties(String propsFile)
   {
     propertiesFile = propsFile;
-    if (propsFile == null)
+    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
     {
@@ -354,65 +397,119 @@ public class Cache
       propsAreReadOnly = true;
     }
 
-    try
+    if (propertiesFile == null)
+    { // BH 2019
+      Platform.readInfoProperties(JS_PROPERTY_PREFIX,
+              applicationProperties);
+    }
+    else
     {
-      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;
+        InputStream fis;
+        try
+        {
+          // props file provided as URL
+          fis = new URL(propertiesFile).openStream();
+          if (!Jalview.quiet())
+          {
+            jalview.bin.Console.outPrintln(
+                    "Loading jalview properties from : " + propertiesFile);
+            jalview.bin.Console.outPrintln(
+                    "Disabling Jalview writing to user's local properties file.");
+          }
+          propsAreReadOnly = true;
+        } catch (Exception ex)
+        {
+          fis = null;
+        }
+        if (fis == null)
+        {
+          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);
+
+        // remove any old build properties
 
+        deleteBuildProperties();
+        fis.close();
       } catch (Exception ex)
       {
-        fis = null;
+        if (!Jalview.quiet())
+          jalview.bin.Console
+                  .outPrintln("Error reading properties file: " + ex);
       }
-      if (fis == null)
-      {
-        fis = new FileInputStream(propertiesFile);
-      }
-      applicationProperties.clear();
-      applicationProperties.load(fis);
-
-      // remove any old build properties
-
-      deleteBuildProperties();
-      fis.close();
-    } catch (Exception ex)
-    {
-      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
+    String authorDetails = resolveResourceURLFor("/authors.props");
+
     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();
+      if (authorDetails != null)
+      {
+        URL localJarFileURL = new URL(authorDetails);
+        InputStream in = localJarFileURL.openStream();
+        applicationProperties.load(in);
+        in.close();
+      }
     } catch (Exception ex)
     {
-      System.out.println("Error reading author details: " + ex);
+      if (!Jalview.quiet())
+        jalview.bin.Console
+                .outPrintln("Error reading author details: " + ex);
+      authorDetails = null;
+    }
+    if (authorDetails == null)
+    {
       applicationProperties.remove("AUTHORS");
       applicationProperties.remove("AUTHORFNAMES");
       applicationProperties.remove("YEAR");
@@ -423,27 +520,27 @@ 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",
             "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");
@@ -463,36 +560,44 @@ public class Cache
         @Override
         public void run()
         {
-          String buildPropertiesUrl = Cache.getAppbaseBuildProperties();
+          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
-          {
-            System.setProperty("sun.net.client.defaultConnectTimeout",
-                    "5000");
-            java.net.URL url = new java.net.URL(buildPropertiesUrl);
-
-            BufferedReader in = new BufferedReader(
-                    new InputStreamReader(url.openStream()));
-
-            Properties remoteBuildProperties = new Properties();
-            remoteBuildProperties.load(in);
-            remoteVersion = remoteBuildProperties.getProperty("VERSION");
-          } catch (Exception ex)
+          if (remoteBuildPropertiesUrl.startsWith("http"))
           {
-            System.out
-                    .println("Non-fatal exception when checking version at "
-                            + buildPropertiesUrl + ":");
-            System.out.println(ex);
-            remoteVersion = getProperty("VERSION");
+            try
+            {
+              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())
+              {
+                jalview.bin.Console.errPrintln(
+                        "Non-fatal exception when checking version at "
+                                + remoteBuildPropertiesUrl + ":");
+                jalview.bin.Console.printStackTrace(ex);
+              }
+              remoteVersion = getProperty("VERSION");
+            }
           }
           System.setProperty("sun.net.client.defaultConnectTimeout",
                   orgtimeout);
@@ -517,32 +622,81 @@ public class Cache
     }
 
     // LOAD USERDEFINED COLOURS
-    jalview.bin.Cache
-            .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
+    Cache.initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
     jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
             false);
   }
 
+  /**
+   * construct a resource URL for the given absolute resource pathname
+   * 
+   * @param resourcePath
+   * @return
+   */
+  private static String resolveResourceURLFor(String resourcePath)
+  {
+    String url = null;
+    if (Platform.isJS() || !Cache.class.getProtectionDomain()
+            .getCodeSource().getLocation().toString().endsWith(".jar"))
+    {
+      try
+      {
+        url = Cache.class.getResource(resourcePath).toString();
+      } catch (Exception ex)
+      {
+        jalview.bin.Console.errPrintln("Failed to resolve resource "
+                + resourcePath + ": " + ex.getMessage());
+      }
+    }
+    else
+    {
+      url = "jar:".concat(Cache.class.getProtectionDomain().getCodeSource()
+              .getLocation().toString().concat("!" + resourcePath));
+    }
+    return url;
+  }
+
   public static void loadBuildProperties(boolean reportVersion)
   {
     String codeInstallation = getProperty("INSTALLATION");
-    boolean printV = codeInstallation == null;
+    boolean printVersion = codeInstallation == null;
 
-    // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
+    /*
+     * read build properties - from the Jalview jar for a Java distribution,
+     * or from codebase file in test or JalviewJS context
+     */
     try
     {
-      String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
-              .getCodeSource().getLocation().toString()
-              .concat("!/.build_properties"));
-
-      java.net.URL localJarFileURL = new java.net.URL(buildDetails);
-
+      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())
+        jalview.bin.Console
+                .outPrintln("Error reading build details: " + ex);
       applicationProperties.remove("VERSION");
     }
     String codeVersion = getProperty("VERSION");
@@ -560,10 +714,11 @@ public class Cache
     }
     setProperty("VERSION", codeVersion);
     new BuildDetails(codeVersion, null, codeInstallation);
-    if (printV && reportVersion)
+    if (printVersion && reportVersion)
     {
-      System.out.println(
-              "Jalview Version: " + codeVersion + codeInstallation);
+      jalview.bin.Console
+              .outPrintln(ChannelProperties.getProperty("app_name")
+                      + " version: " + codeVersion + codeInstallation);
     }
   }
 
@@ -589,7 +744,27 @@ public class Cache
    */
   public static String getProperty(String key)
   {
-    return 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()
+              + "_" + JS_PROPERTY_PREFIX + key);
+    }
+    return prop;
   }
 
   /**
@@ -618,30 +793,45 @@ public class Cache
         def = Integer.parseInt(string);
       } catch (NumberFormatException e)
       {
-        System.out.println("Error parsing int property '" + property
-                + "' with value '" + string + "'");
+        if (!Jalview.quiet())
+          jalview.bin.Console.errPrintln("Error parsing int property '"
+                  + property + "' with value '" + string + "'");
       }
     }
 
     return def;
   }
 
-  /**
-   * These methods are used when checking if the saved preference is different
-   * to the default setting
-   */
-  public static String getDefault(String property, String def)
+  public static float getDefault(String property, float def)
   {
     String string = getProperty(property);
     if (string != null)
     {
-      return string;
+      try
+      {
+        def = Float.parseFloat(string);
+      } catch (NumberFormatException e)
+      {
+        if (!Jalview.quiet())
+          jalview.bin.Console.errPrintln("Error parsing float property '"
+                  + property + "' with value '" + string + "'");
+      }
     }
 
     return def;
   }
 
   /**
+   * Answers the value of the given property, or the supplied default value if
+   * the property is not set
+   */
+  public static String getDefault(String property, String def)
+  {
+    String value = getProperty(property);
+    return value == null ? def : value;
+  }
+
+  /**
    * Stores property in the file "HOME_DIR/.jalview_properties"
    * 
    * @param key
@@ -657,16 +847,25 @@ 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())
+        jalview.bin.Console.errPrintln(
+                "Error setting property: " + key + " " + obj + "\n" + ex);
     }
     return oldValue;
   }
@@ -696,7 +895,8 @@ public class Cache
         out.close();
       } catch (Exception ex)
       {
-        System.out.println("Error saving properties: " + ex);
+        if (!Jalview.quiet())
+          jalview.bin.Console.errPrintln("Error saving properties: " + ex);
       }
     }
   }
@@ -720,21 +920,21 @@ 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);
@@ -759,156 +959,67 @@ 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);
   }
 
   /**
-   * 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.
+   * Initialise the tracker if it is not done already.
    */
-  public static void initGoogleTracker()
+  public static void initAnalytics()
   {
-    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();
-          }
+    Plausible.setEnabled(true);
 
-          if (err != null)
-          {
-            System.err.println(
-                    "ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
-                            + vrs);
-            err.printStackTrace();
-          }
-        }
-      }
-      else
-      {
-        log.debug("Successfully initialised tracker.");
-      }
+    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)
+    {
+    */
+    List<String> pathParts = new ArrayList<>();
+    pathParts.add(appName);
+    pathParts.add(version);
+    pathParts.add(APPLICATION_STARTED);
+    path = ("/" + String.join("/", pathParts)).replace(' ', '+');
+    /*
     }
+    */
+    Plausible plausible = Plausible.getInstance();
+
+    // This will send a new "application_launch" event with parameters
+    // including the old-style "path", the channel name and version
+    plausible.sendEvent("application_launch", path, true);
   }
 
+  private static final String APPLICATION_STARTED = "Application Started";
+
   /**
    * get the user's default colour if available
    * 
@@ -926,7 +1037,7 @@ 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;
@@ -975,8 +1086,9 @@ public class Cache
         return date_format.parse(val);
       } catch (Exception ex)
       {
-        System.err.println("Invalid or corrupt date in property '"
-                + propertyName + "' : value was '" + val + "'");
+        jalview.bin.Console
+                .errPrintln("Invalid or corrupt date in property '"
+                        + propertyName + "' : value was '" + val + "'");
       }
     }
     return null;
@@ -999,8 +1111,8 @@ public class Cache
         return Integer.valueOf(val);
       } catch (NumberFormatException x)
       {
-        System.err.println("Invalid integer in property '" + property
-                + "' (value was '" + val + "')");
+        jalview.bin.Console.errPrintln("Invalid integer in property '"
+                + property + "' (value was '" + val + "')");
       }
     }
     return null;
@@ -1063,7 +1175,9 @@ public class Cache
         }
       } catch (Exception ex)
       {
-        System.out.println("Error loading User ColourFile\n" + ex);
+        if (!Jalview.quiet())
+          jalview.bin.Console
+                  .outPrintln("Error loading User ColourFile\n" + ex);
       }
     }
     if (!files.equals(coloursFound.toString()))
@@ -1095,8 +1209,11 @@ public class Cache
     {
       return;
     }
-    String line = prefix + (value != null ? value : defaultValue) + suffix;
-    sb.append(line);
+    if (prefix != null)
+      sb.append(prefix);
+    sb.append(value == null ? defaultValue : value);
+    if (suffix != null)
+      sb.append(suffix);
   }
 
   /**
@@ -1106,18 +1223,21 @@ public class Cache
   public static String getVersionDetailsForConsole()
   {
     StringBuilder sb = new StringBuilder();
-    sb.append("Jalview Version: ");
-    sb.append(jalview.bin.Cache.getDefault("VERSION", "TEST"));
+    sb.append(ChannelProperties.getProperty("app_name"))
+            .append(" Version: ");
+    sb.append(Cache.getDefault("VERSION", "TEST"));
     sb.append("\n");
-    sb.append("Jalview Installation: ");
-    sb.append(jalview.bin.Cache.getDefault("INSTALLATION", "unknown"));
+    sb.append(ChannelProperties.getProperty("app_name"))
+            .append(" Installation: ");
+    sb.append(Cache.getDefault("INSTALLATION", "unknown"));
     sb.append("\n");
     sb.append("Build Date: ");
-    sb.append(jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
+    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"));
@@ -1138,17 +1258,19 @@ public class Cache
     sb.append(" (");
     sb.append(lafClass);
     sb.append(")\n");
-    // Not displayed in release version ( determined by possible version number
-    // regex 9[9.]*9[.-_a9]* )
-    if (Pattern.matches("^\\d[\\d\\.]*\\d[\\.\\-\\w]*$",
-            jalview.bin.Cache.getDefault("VERSION", "TEST")))
+    appendIfNotNull(sb, "Channel: ",
+            ChannelProperties.getProperty("channel"), "\n", null);
+    if (Console.isDebugEnabled()
+            || !"release".equals(ChannelProperties.getProperty("channel")))
     {
       appendIfNotNull(sb, "Getdown appdir: ",
-              System.getProperty("getdownappdir"), "\n", null);
+              System.getProperty("getdowninstanceappdir"), "\n", null);
       appendIfNotNull(sb, "Getdown appbase: ",
-              System.getProperty("getdownappbase"), "\n", null);
+              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();
   }
@@ -1161,7 +1283,7 @@ 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)
@@ -1172,6 +1294,291 @@ public class Cache
     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
    */
@@ -1184,11 +1591,22 @@ public class Cache
 
   static
   {
-    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";
+    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
@@ -1202,6 +1620,11 @@ public class Cache
     String distDir = System.getProperty("getdowndistdir");
     if (appbase == null)
     {
+      appbase = buildProperties.getProperty("GETDOWNAPPBASE");
+      distDir = buildProperties.getProperty("GETDOWNAPPDISTDIR");
+    }
+    if (appbase == null)
+    {
       appbase = releaseAppbase;
       distDir = "release";
     }
@@ -1228,4 +1651,93 @@ public class Cache
     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())
+    {
+      if (file != null)
+      {
+        jalview.bin.Console
+                .errPrintln("Could not load bootstrap preferences file '"
+                        + file.getPath() + "'");
+      }
+      String channelPrefsFilename = ChannelProperties
+              .getProperty("preferences.filename");
+      String propertiesFilename = System.getProperty("user.home")
+              + File.separatorChar + channelPrefsFilename;
+      jalview.bin.Console.errPrintln(
+              "Using default properties file '" + propertiesFilename + "'");
+      file = new File(propertiesFilename);
+    }
+    if (file == null || !file.exists())
+
+    {
+      String releasePrefsFilename = fallbackPropertiesFile;
+      String releasePropertiesFilename = System.getProperty("user.home")
+              + File.separatorChar + releasePrefsFilename;
+      jalview.bin.Console.errPrintln("Falling back to properties file '"
+              + releasePropertiesFilename + "'");
+      file = new File(releasePropertiesFilename);
+    }
+
+    if (!file.exists())
+    {
+      jalview.bin.Console
+              .errPrintln("Could not load bootstrap preferences file '"
+                      + file.getPath() + "'");
+      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)
+    {
+      jalview.bin.Console
+              .errPrintln("Could not find bootstrap preferences file '"
+                      + file.getAbsolutePath() + "'");
+    } catch (IOException e)
+    {
+      jalview.bin.Console.errPrintln(
+              "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);
+  }
+
+  public static boolean getArgCacheDefault(Arg a, String pref, boolean def)
+  {
+    ArgParser ap = Jalview.getInstance().getArgParser();
+    return ap.isSet(a) ? ap.getBoolean(a) : getDefault(pref, def);
+  }
 }