X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=370a2433c3d8b8bcd8683b89e500bf0581a9da5e;hb=53fe06e7ae7a8c00ec902413391cea15362bdbf2;hp=594046fc07976370f0650f290cc3f4e01f1ba965;hpb=9092d9f4c2231645b58968e964c858e010be14e2;p=jalview.git

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 594046f..370a243 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -42,24 +42,20 @@ import java.util.Locale;
 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.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;
@@ -174,6 +170,8 @@ import jalview.ws.sifts.SiftsSettings;
  * <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>
@@ -181,8 +179,8 @@ import jalview.ws.sifts.SiftsSettings;
  * 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>
@@ -201,7 +199,13 @@ 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>
@@ -274,7 +278,8 @@ 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 = {
@@ -309,6 +314,9 @@ 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;
 
@@ -316,54 +324,6 @@ public class Cache
 
   private final static String JS_PROPERTY_PREFIX = "jalview_";
 
-  public static void initLogger()
-  {
-    if (log != null)
-    {
-      return;
-    }
-    try
-    {
-      // TODO: redirect stdout and stderr here in order to grab the output of
-      // the log
-
-      ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
-              "System.err");
-      ap.setName("JalviewLogger");
-      org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
-      // log output
-      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);
-    }
-  }
-
   /**
    * Loads properties from the given properties file. Any existing properties
    * are first cleared.
@@ -371,10 +331,18 @@ 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 = ".jalview_properties";
       propertiesFile = System.getProperty("user.home") + File.separatorChar
-              + ".jalview_properties";
+              + channelPrefsFilename;
+      releasePropertiesFile = System.getProperty("user.home")
+              + File.separatorChar + releasePrefsFilename;
+      defaultProperties = true;
     }
     else
     {
@@ -394,20 +362,29 @@ public class Cache
         InputStream fis;
         try
         {
+          // props file provided as URL
           fis = new URL(propertiesFile).openStream();
           System.out.println(
                   "Loading jalview properties from : " + propertiesFile);
           System.out.println(
                   "Disabling Jalview writing to user's local properties file.");
           propsAreReadOnly = true;
-
         } catch (Exception ex)
         {
           fis = null;
         }
         if (fis == null)
         {
-          fis = new FileInputStream(propertiesFile);
+          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);
@@ -457,7 +434,7 @@ public class Cache
     default:
       String message = "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
               + proxyType;
-      Cache.warn(message);
+      Console.warn(message);
     }
 
     // LOAD THE AUTHORS FROM THE authors.props file
@@ -489,27 +466,27 @@ 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",
-            "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");
@@ -525,9 +502,13 @@ public class Cache
 
       class VersionChecker extends Thread
       {
+
         @Override
         public void run()
         {
+          String remoteBuildPropertiesUrl = Cache
+                  .getAppbaseBuildProperties();
+
           String orgtimeout = System
                   .getProperty("sun.net.client.defaultConnectTimeout");
           if (orgtimeout == null)
@@ -537,34 +518,29 @@ public class Cache
                     + 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)
-              {
-                continue;
-              }
+              System.setProperty("sun.net.client.defaultConnectTimeout",
+                      "5000");
+
+              URL url = new URL(remoteBuildPropertiesUrl);
+
+              BufferedReader in = new BufferedReader(
+                      new InputStreamReader(url.openStream()));
 
-              line = line.substring(line.indexOf("value=") + 7);
-              line = line.substring(0, line.lastIndexOf("\""));
-              remoteVersion = line;
-              break;
+              Properties remoteBuildProperties = new Properties();
+              remoteBuildProperties.load(in);
+              remoteVersion = remoteBuildProperties.getProperty("VERSION");
+            } catch (Exception ex)
+            {
+              System.out.println(
+                      "Non-fatal exception when checking version at "
+                              + remoteBuildPropertiesUrl + ":");
+              System.out.println(ex);
+              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);
@@ -637,8 +613,28 @@ 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);
@@ -661,8 +657,8 @@ 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);
     }
   }
 
@@ -820,21 +816,21 @@ 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);
@@ -859,25 +855,25 @@ 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);
@@ -911,7 +907,7 @@ public class Cache
                   .loadClass("com.boxysystems.jgoogleanalytics.FocusPoint");
         } catch (Exception e)
         {
-          log.debug(
+          Console.debug(
                   "com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
           tracker = null;
           jgoogleanalyticstracker = null;
@@ -930,10 +926,9 @@ public class Cache
                 .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")),
+                { ChannelProperties.getProperty("app_name") + " Desktop",
+                    (vrs = Cache.getProperty("VERSION") + "_"
+                            + Cache.getDefault("BUILD_DATE", "unknown")),
                     "UA-9060947-1" });
         jgoogleanalyticstracker
                 .getMethod("trackAsynchronously", new Class[]
@@ -954,57 +949,29 @@ public class Cache
       }
       if (re != null || ex != null || err != null)
       {
-        if (log != null)
+        if (re != 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);
-          }
+          Console.debug("Caught runtime exception in googletracker init:",
+                  re);
         }
-        else
+        if (ex != null)
         {
-          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.warn(
+                  "Failed to initialise GoogleTracker for Jalview Desktop with version "
+                          + vrs,
+                  ex);
+        }
+        if (err != null)
+        {
+          Console.error(
+                  "Whilst initing GoogleTracker for Jalview Desktop version "
+                          + vrs,
+                  err);
         }
       }
       else
       {
-        log.debug("Successfully initialised tracker.");
+        Console.debug("Successfully initialised tracker.");
       }
     }
   }
@@ -1026,7 +993,7 @@ 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;
@@ -1195,8 +1162,11 @@ 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);
   }
 
   /**
@@ -1206,14 +1176,16 @@ 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"));
@@ -1238,13 +1210,15 @@ 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")))
+    if (Console.isDebugEnabled()
+            || !"release".equals(ChannelProperties.getProperty("channel")))
     {
+      appendIfNotNull(sb, "Channel: ",
+              ChannelProperties.getProperty("channel"), "\n", null);
       appendIfNotNull(sb, "Getdown appdir: ",
-              System.getProperty("getdownappdir"), "\n", null);
+              System.getProperty("getdowninstanceappdir"), "\n", null);
+      appendIfNotNull(sb, "Getdown appbase: ",
+              System.getProperty("getdowninstanceappbase"), "\n", null);
       appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"),
               "\n", "unknown");
     }
@@ -1259,7 +1233,7 @@ 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)
@@ -1303,7 +1277,7 @@ public class Cache
                             ? " [" + startupProxyProperties[6] + "]"
                             : "");
 
-    Cache.debug(sb.toString());
+    Console.debug(sb.toString());
   }
 
   public static void setProxyPropertiesFromPreferences()
@@ -1329,7 +1303,7 @@ public class Cache
     case Cache.PROXYTYPE_NONE:
       if (!previousProxyType.equals(proxyType))
       {
-        Cache.log.info("Setting no proxy settings");
+        Console.info("Setting no proxy settings");
         Cache.setProxyProperties(null, null, null, null, null, null, null,
                 null, null);
       }
@@ -1337,7 +1311,7 @@ public class Cache
     case Cache.PROXYTYPE_CUSTOM:
       // always re-set a custom proxy -- it might have changed, particularly
       // password
-      Cache.log.info("Setting custom proxy settings");
+      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),
@@ -1351,7 +1325,7 @@ public class Cache
               proxyAuthSet ? Cache.proxyAuthPassword : null, "localhost");
       break;
     default: // system proxy settings by default
-      Cache.log.info("Setting system proxy settings");
+      Console.info("Setting system proxy settings");
       Cache.resetProxyProperties();
     }
   }
@@ -1403,90 +1377,105 @@ public class Cache
         char[] displayHttpPw = new char[httpPassword == null ? 0
                 : httpPassword.length];
         Arrays.fill(displayHttpPw, '*');
-        Cache.debug("CACHE Proxy: setting new Authenticator with httpUser='"
-                + httpUser + "' httpPassword='" + displayHttpPw + "'");
-        Authenticator.setDefault(new Authenticator()
+        Console.debug(
+                "CACHE Proxy: setting new Authenticator with httpUser='"
+                        + httpUser + "' httpPassword='" + displayHttpPw
+                        + "'");
+        if (!Platform.isJS())
+        /* *
+         * java.net.Authenticator not implemented in SwingJS yet
+         * 
+         * @j2sIgnore
+         * 
+         */
         {
-          @Override
-          protected PasswordAuthentication getPasswordAuthentication()
+          Authenticator.setDefault(new Authenticator()
           {
-            if (getRequestorType() == RequestorType.PROXY)
+            @Override
+            protected PasswordAuthentication getPasswordAuthentication()
             {
-              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))))
+              if (getRequestorType() == RequestorType.PROXY)
               {
-                // open Preferences -> Connections
-                String message = MessageManager
-                        .getString("label.proxy_password_required");
-                Preferences.openPreferences(Preferences.CONNECTIONS_TAB,
-                        message);
-                Preferences.getInstance().proxyAuthPasswordCheckHighlight(true);
-              }
-              else
-              {
-                try
+                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
                 {
-                  if (protocol.equalsIgnoreCase("http")
-                          && getRequestingHost().equalsIgnoreCase(httpHost)
-                          && getRequestingPort() == Integer
-                                  .valueOf(httpPort))
+                  try
                   {
-                    Cache.debug(
-                            "AUTHENTICATOR returning PasswordAuthentication(\""
-                                    + httpUser + "\", '"
-                                    + new String(displayHttpPw) + "')");
-                    return new PasswordAuthentication(httpUser,
-                            httpPassword);
-                  }
-                  if (protocol.equalsIgnoreCase("https")
-                          && getRequestingHost().equalsIgnoreCase(httpsHost)
-                          && getRequestingPort() == Integer
-                                  .valueOf(httpsPort))
+                    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)
                   {
-                    char[] displayHttpsPw = new char[httpPassword.length];
-                    Arrays.fill(displayHttpsPw, '*');
-                    Cache.debug(
-                            "AUTHENTICATOR returning PasswordAuthentication(\""
-                                    + httpsUser + "\", '" + displayHttpsPw
-                                    + "'");
-                    return new PasswordAuthentication(httpsUser,
-                            httpsPassword);
+                    Console.error("Problem with proxy port values [http:"
+                            + httpPort + ", https:" + httpsPort + "]");
                   }
-                } catch (NumberFormatException e)
-                {
-                  Cache.error("Problem with proxy port values [http:"
-                          + httpPort + ", https:" + httpsPort + "]");
+                  Console.debug(
+                          "AUTHENTICATOR after trying to get PasswordAuthentication");
                 }
-                Cache.debug(
-                        "AUTHENTICATOR after trying to get PasswordAuthentication");
               }
+              // non proxy request
+              Console.debug("AUTHENTICATOR returning null");
+              return null;
             }
-            // non proxy request
-            Cache.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)
-        Cache.debug(
+        Console.debug(
                 "AUTHENTICATOR setting property 'jdk.http.auth.tunneling.disabledSchemes' to \"\"");
         System.setProperty("jdk.http.auth.tunneling.disabledSchemes", "");
       } catch (SecurityException e)
       {
-        Cache.error("Could not set default Authenticator");
-        Cache.debug(getStackTraceString(e));
+        Console.error("Could not set default Authenticator");
+        Console.debug(getStackTraceString(e));
       }
     }
     else
@@ -1496,13 +1485,24 @@ public class Cache
       /* 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.
        */
-      Cache.debug("AUTHENTICATOR setting default Authenticator to null");
-      Authenticator.setDefault(null);
+      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
-    Cache.debug("AUTHENTICATOR setting property 'http.nonProxyHosts' to \""
-            + nonProxyHosts + "\"");
+    Console.debug(
+            "AUTHENTICATOR setting property 'http.nonProxyHosts' to \""
+                    + nonProxyHosts + "\"");
     setOrClearSystemProperty("http.nonProxyHosts", nonProxyHosts);
   }
 
@@ -1528,72 +1528,76 @@ public class Cache
     }
   }
 
-  public final static int TRACE = 10;
-
-  public final static int DEBUG = 20;
+  /**
+   * Getdown appbase methods
+   */
 
-  public final static int INFO = 30;
+  private static final String releaseAppbase;
 
-  public final static int WARN = 40;
+  private static String getdownAppbase;
 
-  public final static int ERROR = 50;
+  private static String getdownDistDir;
 
-  public static boolean println(int level, String message)
+  static
   {
-    if (Cache.log == null)
+    if (!Platform.isJS())
     {
-      if (level >= WARN)
-        System.err.println(message);
-      else if (level >= INFO)
-        System.out.println(message);
-      // not printing debug or trace messages
-      return false;
+      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 (level >= ERROR)
+    else
     {
-      Cache.log.error(message);
+      // 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";
     }
-    else if (level >= WARN)
+  }
+
+  // look for properties (passed in by getdown) otherwise default to release
+  private static void setGetdownAppbase()
+  {
+    if (getdownAppbase != null)
     {
-      Cache.log.warn(message);
+      return;
     }
-    else if (level >= INFO)
+    String appbase = System.getProperty("getdownappbase");
+    String distDir = System.getProperty("getdowndistdir");
+    if (appbase == null)
     {
-      Cache.log.info(message);
+      appbase = buildProperties.getProperty("GETDOWNAPPBASE");
+      distDir = buildProperties.getProperty("GETDOWNAPPDISTDIR");
     }
-    else if (level >= DEBUG)
+    if (appbase == null)
     {
-      Cache.log.debug(message);
+      appbase = releaseAppbase;
+      distDir = "release";
     }
-    else
+    if (appbase.endsWith("/"))
     {
-      Cache.log.trace(message);
+      appbase = appbase.substring(0, appbase.length() - 1);
     }
-    return true;
-  }
-
-  public static void trace(String message)
-  {
-    println(TRACE, message);
-  }
-
-  public static void debug(String message)
-  {
-    println(DEBUG, message);
-  }
-
-  public static void info(String message)
-  {
-    println(INFO, message);
+    if (distDir == null)
+    {
+      distDir = appbase.equals(releaseAppbase) ? "release" : "alt";
+    }
+    getdownAppbase = appbase;
+    getdownDistDir = distDir;
   }
 
-  public static void warn(String message)
+  public static String getGetdownAppbase()
   {
-    println(WARN, message);
+    setGetdownAppbase();
+    return getdownAppbase;
   }
 
-  public static void error(String message)
+  public static String getAppbaseBuildProperties()
   {
-    println(ERROR, message);
+    String appbase = getGetdownAppbase();
+    return appbase + "/" + getdownDistDir + "/build_properties";
   }
-}
\ No newline at end of file
+}