X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=0ec0e7892fe8a4e4bb659efa1f273da280aa8190;hb=5a0f398fd4bab96dd3cba085ffe77b010cfe24eb;hp=751461f2c6e9ff5b29d320e59310482b8a6afd7f;hpb=6312cb6f6a715162cccd42b952c4801ee39715be;p=jalview.git

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 751461f..0ec0e78 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -27,8 +27,14 @@ import java.io.FileInputStream;
 import java.io.FileOutputStream;
 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.Arrays;
 import java.util.Collections;
 import java.util.Date;
 import java.util.Enumeration;
@@ -36,24 +42,23 @@ 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;
 import jalview.ws.sifts.SiftsSettings;
 
 /**
@@ -165,6 +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>
@@ -172,8 +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>
@@ -192,7 +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>
@@ -265,7 +278,30 @@ 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;
 
   /** Jalview Properties */
   public static Properties applicationProperties = new Properties()
@@ -278,54 +314,15 @@ 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 boolean propsAreReadOnly = Platform.isJS();
 
-  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())));
-      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);
-    }
-  }
+  private final static String JS_PROPERTY_PREFIX = "jalview_";
 
   /**
    * Loads properties from the given properties file. Any existing properties
@@ -334,10 +331,18 @@ 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 = ".jalview_properties";
       propertiesFile = System.getProperty("user.home") + File.separatorChar
-              + ".jalview_properties";
+              + channelPrefsFilename;
+      releasePropertiesFile = System.getProperty("user.home")
+              + File.separatorChar + releasePrefsFilename;
+      defaultProperties = true;
     }
     else
     {
@@ -345,65 +350,112 @@ 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();
+          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)
+        {
+          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 (fis == null)
-      {
-        fis = new FileInputStream(propertiesFile);
+        System.out.println("Error reading properties file: " + ex);
       }
-      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);
+      authorDetails = null;
+    }
+    if (authorDetails == null)
+    {
       applicationProperties.remove("AUTHORS");
       applicationProperties.remove("AUTHORFNAMES");
       applicationProperties.remove("YEAR");
@@ -414,34 +466,33 @@ public class Cache
     SiftsSettings
             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 
-    SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache
+    SiftsSettings.setSiftDownloadDirectory(Cache
             .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
 
     SiftsSettings.setFailSafePIDThreshold(
-            jalview.bin.Cache.getDefault("sifts_fail_safe_pid_threshold",
+            Cache.getDefault("sifts_fail_safe_pid_threshold",
                     DEFAULT_FAIL_SAFE_PID_THRESHOLD));
 
     SiftsSettings.setCacheThresholdInDays(
-            jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days",
+            Cache.getDefault("sifts_cache_threshold_in_days",
                     DEFAULT_CACHE_THRESHOLD_IN_DAYS));
 
     IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
-            "http://www.jalview.org/services/identifiers"));
+            "https://www.jalview.org/services/identifiers"));
     IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
 
-    StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
-            .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
+    StructureImportSettings.setDefaultStructureFileFormat(
+            Cache.getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
     StructureImportSettings
             .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
     // StructureImportSettings
-    // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
+    // .setDefaultPDBFileParser(Cache.getDefault(
     // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
 
     String jnlpVersion = System.getProperty("jalview.version");
 
     // jnlpVersion will be null if a latest version check for the channel needs
-    // to
-    // be done
+    // to be done
     // Dont do this check if running in headless mode
 
     if (jnlpVersion == null && getDefault("VERSION_CHECK", true)
@@ -451,9 +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)
@@ -463,34 +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);
 
-              line = line.substring(line.indexOf("value=") + 7);
-              line = line.substring(0, line.lastIndexOf("\""));
-              remoteVersion = line;
-              break;
+              BufferedReader in = new BufferedReader(
+                      new InputStreamReader(url.openStream()));
+
+              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);
@@ -515,29 +565,71 @@ 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)
+      {
+        System.err.println("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"));
+      }
     } catch (Exception ex)
     {
       System.out.println("Error reading build details: " + ex);
@@ -558,10 +650,10 @@ public class Cache
     }
     setProperty("VERSION", codeVersion);
     new BuildDetails(codeVersion, null, codeInstallation);
-    if (printV && reportVersion)
+    if (printVersion && reportVersion)
     {
-      System.out.println(
-              "Jalview Version: " + codeVersion + codeInstallation);
+      System.out.println(ChannelProperties.getProperty("app_name")
+              + " Version: " + codeVersion + codeInstallation);
     }
   }
 
@@ -587,7 +679,13 @@ public class Cache
    */
   public static String getProperty(String key)
   {
-    return applicationProperties.getProperty(key);
+    String prop = applicationProperties.getProperty(key);
+    if (prop == null && Platform.isJS())
+    {
+      prop = applicationProperties.getProperty(Platform.getUniqueAppletID()
+              + "_" + JS_PROPERTY_PREFIX + key);
+    }
+    return prop;
   }
 
   /**
@@ -625,18 +723,13 @@ public class Cache
   }
 
   /**
-   * These methods are used when checking if the saved preference is different
-   * to the default setting
+   * 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 string = getProperty(property);
-    if (string != null)
-    {
-      return string;
-    }
-
-    return def;
+    String value = getProperty(property);
+    return value == null ? def : value;
   }
 
   /**
@@ -718,21 +811,21 @@ 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);
@@ -757,25 +850,25 @@ 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);
@@ -809,7 +902,7 @@ 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;
@@ -828,10 +921,9 @@ 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[]
@@ -852,57 +944,29 @@ 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.");
       }
     }
   }
@@ -924,7 +988,7 @@ 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;
@@ -1093,8 +1157,11 @@ 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);
   }
 
   /**
@@ -1104,20 +1171,25 @@ public class Cache
   public static String getVersionDetailsForConsole()
   {
     StringBuilder sb = new StringBuilder();
-    sb.append("Jalview Version: "
-            + 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: "
-            + 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: "
-            + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
+    sb.append("Build Date: ");
+    sb.append(Cache.getDefault("BUILD_DATE", "unknown"));
     sb.append("\n");
-    sb.append("Java version: " + System.getProperty("java.version"));
+    sb.append("Java version: ");
+    sb.append(System.getProperty("java.version"));
     sb.append("\n");
-    sb.append(System.getProperty("os.arch") + " "
-            + System.getProperty("os.name") + " "
-            + System.getProperty("os.version"));
+    sb.append(System.getProperty("os.arch"));
+    sb.append(" ");
+    sb.append(System.getProperty("os.name"));
+    sb.append(" ");
+    sb.append(System.getProperty("os.version"));
     sb.append("\n");
     appendIfNotNull(sb, "Install4j version: ",
             System.getProperty("sys.install4jVersion"), "\n", null);
@@ -1126,13 +1198,22 @@ public class Cache
     appendIfNotNull(sb, "Launcher version: ",
             System.getProperty("launcher_version"), "\n", null);
     LookAndFeel laf = UIManager.getLookAndFeel();
-    String lafName = laf == null?"Not obtained":laf.getName();
-    String lafClass = laf == null?"unknown":laf.getClass().getName();
-    appendIfNotNull(sb, "LookAndFeel: ", lafName+" ("+lafClass+")", "\n", null);
-    // 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"))) {
+    String lafName = laf == null ? "Not obtained" : laf.getName();
+    String lafClass = laf == null ? "unknown" : laf.getClass().getName();
+    sb.append("LookAndFeel: ");
+    sb.append(lafName);
+    sb.append(" (");
+    sb.append(lafClass);
+    sb.append(")\n");
+    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");
     }
@@ -1147,6 +1228,371 @@ public class Cache
   {
     // consider returning more human friendly info
     // eg 'built from Source' or update channel
-    return jalview.bin.Cache.getDefault("INSTALLATION", "unknown");
+    return Cache.getDefault("INSTALLATION", "unknown");
+  }
+
+  public static String getStackTraceString(Throwable t)
+  {
+    StringWriter sw = new StringWriter();
+    PrintWriter pw = new PrintWriter(sw);
+    t.printStackTrace(pw);
+    return sw.toString();
+  }
+
+  // proxy properties methods
+  public static void clearProxyProperties()
+  {
+    setProxyProperties(null, null, null, null, null, null, null, null,
+            null);
+  }
+
+  public static void resetProxyProperties()
+  {
+    setProxyProperties(startupProxyProperties[0], startupProxyProperties[1],
+            startupProxyProperties[2], startupProxyProperties[3],
+            startupProxyProperties[4],
+            startupProxyProperties[5] == null ? null
+                    : startupProxyProperties[5].toCharArray(),
+            startupProxyProperties[6],
+            startupProxyProperties[7] == null ? null
+                    : startupProxyProperties[7].toCharArray(),
+            startupProxyProperties[8]);
+    StringBuilder sb = new StringBuilder();
+    sb.append("Setting proxy properties to: http.proxyHost=")
+            .append(startupProxyProperties[0]).append(", http.proxyPort=")
+            .append(startupProxyProperties[1])
+            .append(startupProxyProperties[4] != null
+                    && !startupProxyProperties[4].isEmpty()
+                            ? " [" + startupProxyProperties[4] + "]"
+                            : "")
+            .append(", https.proxyHost=").append(startupProxyProperties[2])
+            .append(", https.proxyPort=").append(startupProxyProperties[3])
+            .append(startupProxyProperties[6] != null
+                    && !startupProxyProperties[6].isEmpty()
+                            ? " [" + startupProxyProperties[6] + "]"
+                            : "");
+
+    Console.debug(sb.toString());
+  }
+
+  public static void setProxyPropertiesFromPreferences()
+  {
+    setProxyPropertiesFromPreferences(Cache.PROXYTYPE_SYSTEM);
+  }
+
+  public static void setProxyPropertiesFromPreferences(
+          String previousProxyType)
+  {
+    String proxyType = Cache.getDefault("USE_PROXY",
+            Cache.PROXYTYPE_SYSTEM);
+    if (previousProxyType != null
+            && !proxyType.equals(Cache.PROXYTYPE_CUSTOM) // always apply
+                                                         // customProxy
+            && proxyType.equals(previousProxyType))
+    {
+      // no change
+      return;
+    }
+    switch (proxyType)
+    {
+    case Cache.PROXYTYPE_NONE:
+      if (!previousProxyType.equals(proxyType))
+      {
+        Console.info("Setting no proxy settings");
+        Cache.setProxyProperties(null, null, null, null, null, null, null,
+                null, null);
+      }
+      break;
+    case Cache.PROXYTYPE_CUSTOM:
+      // always re-set a custom proxy -- it might have changed, particularly
+      // password
+      Console.info("Setting custom proxy settings");
+      boolean proxyAuthSet = Cache.getDefault("PROXY_AUTH", false);
+      Cache.setProxyProperties(Cache.getDefault("PROXY_SERVER", null),
+              Cache.getDefault("PROXY_PORT", null),
+              Cache.getDefault("PROXY_SERVER_HTTPS", null),
+              Cache.getDefault("PROXY_PORT_HTTPS", null),
+              proxyAuthSet ? Cache.getDefault("PROXY_AUTH_USERNAME", "")
+                      : null,
+              proxyAuthSet ? Cache.proxyAuthPassword : null,
+              proxyAuthSet ? Cache.getDefault("PROXY_AUTH_USERNAME", "")
+                      : null,
+              proxyAuthSet ? Cache.proxyAuthPassword : null, "localhost");
+      break;
+    default: // system proxy settings by default
+      Console.info("Setting system proxy settings");
+      Cache.resetProxyProperties();
+    }
+  }
+
+  public static void setProxyProperties(String httpHost, String httpPort,
+          String httpsHost, String httpsPort, String httpUser,
+          char[] httpPassword, String httpsUser, char[] httpsPassword,
+          String nonProxyHosts)
+  {
+    setOrClearSystemProperty("http.proxyHost", httpHost);
+    setOrClearSystemProperty("http.proxyPort", httpPort);
+    setOrClearSystemProperty("https.proxyHost", httpsHost);
+    setOrClearSystemProperty("https.proxyPort", httpsPort);
+    setOrClearSystemProperty("http.proxyUser", httpUser);
+    setOrClearSystemProperty("https.proxyUser", httpsUser);
+    // note: passwords for http.proxyPassword and https.proxyPassword are sent
+    // via the Authenticator, properties do not need to be set
+
+    // are we using a custom proxy (password prompt might be required)?
+    boolean customProxySet = getDefault("USE_PROXY", PROXYTYPE_SYSTEM)
+            .equals(PROXYTYPE_CUSTOM);
+
+    /*
+     * A bug in Java means the AuthCache does not get reset, so once it has working credentials,
+     * it never asks for more, so changing the Authenticator has no effect (as getPasswordAuthentication()
+     * is not re-called).
+     * This could lead to password leak to a hostile proxy server, so I'm putting in a hack to clear
+     * the AuthCache.
+     * see https://www.generacodice.com/en/articolo/154918/Reset-the-Authenticator-credentials
+     * ...
+     * Turns out this is only accessible in Java 8, and not in Java 9 onwards, so commenting out
+     */
+    /*
+    try
+    {
+      sun.net.www.protocol.http.AuthCacheValue
+              .setAuthCache(new sun.net.www.protocol.http.AuthCacheImpl());
+    } catch (Throwable t)
+    {
+      Cache.error(t.getMessage());
+      Cache.debug(getStackTraceString(t));
+    }
+    */
+
+    if (httpUser != null || httpsUser != null)
+    {
+      try
+      {
+        char[] displayHttpPw = new char[httpPassword == null ? 0
+                : httpPassword.length];
+        Arrays.fill(displayHttpPw, '*');
+        Console.debug(
+                "CACHE Proxy: setting new Authenticator with httpUser='"
+                        + httpUser + "' httpPassword='" + displayHttpPw
+                        + "'");
+        if (!Platform.isJS())
+        /* *
+         * java.net.Authenticator not implemented in SwingJS yet
+         * 
+         * @j2sIgnore
+         * 
+         */
+        {
+          Authenticator.setDefault(new Authenticator()
+          {
+            @Override
+            protected PasswordAuthentication getPasswordAuthentication()
+            {
+              if (getRequestorType() == RequestorType.PROXY)
+              {
+                String protocol = getRequestingProtocol();
+                boolean needProxyPasswordSet = false;
+                if (customProxySet &&
+                // we have a username but no password for the scheme being
+                // requested
+                (protocol.equalsIgnoreCase("http")
+                        && (httpUser != null && httpUser.length() > 0
+                                && (httpPassword == null
+                                        || httpPassword.length == 0)))
+                        || (protocol.equalsIgnoreCase("https")
+                                && (httpsUser != null
+                                        && httpsUser.length() > 0
+                                        && (httpsPassword == null
+                                                || httpsPassword.length == 0))))
+                {
+                  // open Preferences -> Connections
+                  String message = MessageManager
+                          .getString("label.proxy_password_required");
+                  Preferences.openPreferences(
+                          Preferences.TabRef.CONNECTIONS_TAB, message);
+                  Preferences.getInstance()
+                          .proxyAuthPasswordCheckHighlight(true, true);
+                }
+                else
+                {
+                  try
+                  {
+                    if (protocol.equalsIgnoreCase("http")
+                            && getRequestingHost()
+                                    .equalsIgnoreCase(httpHost)
+                            && getRequestingPort() == Integer
+                                    .valueOf(httpPort))
+                    {
+                      Console.debug(
+                              "AUTHENTICATOR returning PasswordAuthentication(\""
+                                      + httpUser + "\", '"
+                                      + new String(displayHttpPw) + "')");
+                      return new PasswordAuthentication(httpUser,
+                              httpPassword);
+                    }
+                    if (protocol.equalsIgnoreCase("https")
+                            && getRequestingHost()
+                                    .equalsIgnoreCase(httpsHost)
+                            && getRequestingPort() == Integer
+                                    .valueOf(httpsPort))
+                    {
+                      char[] displayHttpsPw = new char[httpPassword.length];
+                      Arrays.fill(displayHttpsPw, '*');
+                      Console.debug(
+                              "AUTHENTICATOR returning PasswordAuthentication(\""
+                                      + httpsUser + "\", '" + displayHttpsPw
+                                      + "'");
+                      return new PasswordAuthentication(httpsUser,
+                              httpsPassword);
+                    }
+                  } catch (NumberFormatException e)
+                  {
+                    Console.error("Problem with proxy port values [http:"
+                            + httpPort + ", https:" + httpsPort + "]");
+                  }
+                  Console.debug(
+                          "AUTHENTICATOR after trying to get PasswordAuthentication");
+                }
+              }
+              // non proxy request
+              Console.debug("AUTHENTICATOR returning null");
+              return null;
+            }
+          });
+        } // end of j2sIgnore for java.net.Authenticator
+
+        // required to re-enable basic authentication (should be okay for a
+        // local proxy)
+        Console.debug(
+                "AUTHENTICATOR setting property 'jdk.http.auth.tunneling.disabledSchemes' to \"\"");
+        System.setProperty("jdk.http.auth.tunneling.disabledSchemes", "");
+      } catch (SecurityException e)
+      {
+        Console.error("Could not set default Authenticator");
+        Console.debug(getStackTraceString(e));
+      }
+    }
+    else
+    {
+      // reset the Authenticator to protect http.proxyUser and
+      // http.proxyPassword Just In Case
+      /* as noted above, due to bug in java this doesn't work if the sun.net.www.protocol.http.AuthCache
+       * has working credentials. No workaround for Java 11.
+       */
+      if (!Platform.isJS())
+      /* *
+       * java.net.Authenticator not implemented in SwingJS yet
+       * 
+       * @j2sIgnore
+       * 
+       */
+      {
+        Console.debug(
+                "AUTHENTICATOR setting default Authenticator to null");
+        Authenticator.setDefault(null);
+      }
+    }
+
+    // nonProxyHosts not currently configurable in Preferences
+    Console.debug(
+            "AUTHENTICATOR setting property 'http.nonProxyHosts' to \""
+                    + nonProxyHosts + "\"");
+    setOrClearSystemProperty("http.nonProxyHosts", nonProxyHosts);
+  }
+
+  public static void setOrClearSystemProperty(String key, char[] value)
+  {
+    setOrClearSystemProperty(key,
+            (value == null) ? null : new String(value));
+  }
+
+  public static void setOrClearSystemProperty(String key, String value)
+  {
+    if (key == null)
+    {
+      return;
+    }
+    if (value == null)
+    {
+      System.clearProperty(key);
+    }
+    else
+    {
+      System.setProperty(key, value);
+    }
+  }
+
+  /**
+   * Getdown appbase methods
+   */
+
+  private static final String releaseAppbase;
+
+  private static String getdownAppbase;
+
+  private static String getdownDistDir;
+
+  static
+  {
+    if (!Platform.isJS())
+    {
+      Float specversion = Float
+              .parseFloat(System.getProperty("java.specification.version"));
+      releaseAppbase = (specversion < 9)
+              ? "https://www.jalview.org/getdown/release/1.8"
+              : "https://www.jalview.org/getdown/release/11";
+    }
+    else
+    {
+      // this value currenly made up, can be changed to URL that will be
+      // "https://www.jalview.org/jalview-js/swingjs/j2s/build_properties"
+      releaseAppbase = "https://www.jalview.org/jalview-js";
+      getdownAppbase = releaseAppbase;
+      getdownDistDir = "/swingjs/j2s";
+    }
+  }
+
+  // look for properties (passed in by getdown) otherwise default to release
+  private static void setGetdownAppbase()
+  {
+    if (getdownAppbase != null)
+    {
+      return;
+    }
+    String appbase = System.getProperty("getdownappbase");
+    String distDir = System.getProperty("getdowndistdir");
+    if (appbase == null)
+    {
+      appbase = buildProperties.getProperty("GETDOWNAPPBASE");
+      distDir = buildProperties.getProperty("GETDOWNAPPDISTDIR");
+    }
+    if (appbase == null)
+    {
+      appbase = releaseAppbase;
+      distDir = "release";
+    }
+    if (appbase.endsWith("/"))
+    {
+      appbase = appbase.substring(0, appbase.length() - 1);
+    }
+    if (distDir == null)
+    {
+      distDir = appbase.equals(releaseAppbase) ? "release" : "alt";
+    }
+    getdownAppbase = appbase;
+    getdownDistDir = distDir;
+  }
+
+  public static String getGetdownAppbase()
+  {
+    setGetdownAppbase();
+    return getdownAppbase;
+  }
+
+  public static String getAppbaseBuildProperties()
+  {
+    String appbase = getGetdownAppbase();
+    return appbase + "/" + getdownDistDir + "/build_properties";
   }
 }