X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=ac8a183e6f68746608293153973e29a9322c5c6c;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=adfd206a14f34a588cb589d31eb1c500ffc656df;hpb=ec45a7f3c872496cc282806938e2b9d6e023f935;p=jalview.git

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index adfd206..ac8a183 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -171,6 +171,8 @@ 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>
@@ -198,8 +200,13 @@ 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>
@@ -801,11 +808,13 @@ public class Cache
         if (jalview.jbgui.GDesktop.class.getClassLoader()
                 .loadClass("uk.ac.vamsas.client.VorbaId") != null)
         {
-          Console.debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
+          Console.debug(
+                  "Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
           vamsasJarsArePresent = 1;
           JLoggerLog4j lvclient = JLoggerLog4j.getLogger("uk.ac.vamsas",
                   Console.getCachedLogLevel("logs.Vamsas.Level"));
-          JLoggerLog4j.addAppender(lvclient, Console.log, JALVIEW_LOGGER_NAME);
+          JLoggerLog4j.addAppender(lvclient, Console.log,
+                  JALVIEW_LOGGER_NAME);
           // Tell the user that debug is enabled
           lvclient.debug(ChannelProperties.getProperty("app_name")
                   + " Vamsas Client Debugging Output Follows.");
@@ -838,11 +847,13 @@ public class Cache
         if (Cache.class.getClassLoader()
                 .loadClass("groovy.lang.GroovyObject") != null)
         {
-          Console.debug("Found Groovy (groovy.lang.GroovyObject can be loaded)");
+          Console.debug(
+                  "Found Groovy (groovy.lang.GroovyObject can be loaded)");
           groovyJarsArePresent = 1;
           JLoggerLog4j lgclient = JLoggerLog4j.getLogger("groovy",
                   Console.getCachedLogLevel("logs.Groovy.Level"));
-          JLoggerLog4j.addAppender(lgclient, Console.log, JALVIEW_LOGGER_NAME);
+          JLoggerLog4j.addAppender(lgclient, Console.log,
+                  JALVIEW_LOGGER_NAME);
           // Tell the user that debug is enabled
           lgclient.debug(ChannelProperties.getProperty("app_name")
                   + " Groovy Client Debugging Output Follows.");
@@ -888,7 +899,8 @@ public class Cache
                   .loadClass("com.boxysystems.jgoogleanalytics.FocusPoint");
         } catch (Exception e)
         {
-          Console.debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
+          Console.debug(
+                  "com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
           tracker = null;
           jgoogleanalyticstracker = null;
           trackerfocus = null;
@@ -931,17 +943,22 @@ public class Cache
       {
         if (re != null)
         {
-          Console.debug("Caught runtime exception in googletracker init:", re);
+          Console.debug("Caught runtime exception in googletracker init:",
+                  re);
         }
         if (ex != null)
         {
-          Console.warn("Failed to initialise GoogleTracker for Jalview Desktop with version "
-                  + vrs, ex);
+          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);
+          Console.error(
+                  "Whilst initing GoogleTracker for Jalview Desktop version "
+                          + vrs,
+                  err);
         }
       }
       else
@@ -968,7 +985,8 @@ public class Cache
     Color col = ColorUtils.parseColourString(colprop);
     if (col == null)
     {
-      Console.warn("Couldn't parse '" + colprop + "' as a colour for " + property);
+      Console.warn("Couldn't parse '" + colprop + "' as a colour for "
+              + property);
     }
     return (col == null) ? defcolour : col;
   }
@@ -1348,8 +1366,10 @@ public class Cache
         char[] displayHttpPw = new char[httpPassword == null ? 0
                 : httpPassword.length];
         Arrays.fill(displayHttpPw, '*');
-        Console.debug("CACHE Proxy: setting new Authenticator with httpUser='"
-                + httpUser + "' httpPassword='" + displayHttpPw + "'");
+        Console.debug(
+                "CACHE Proxy: setting new Authenticator with httpUser='"
+                        + httpUser + "' httpPassword='" + displayHttpPw
+                        + "'");
         if (!Platform.isJS())
         /* *
          * java.net.Authenticator not implemented in SwingJS yet
@@ -1462,14 +1482,16 @@ public class Cache
        * 
        */
       {
-        Console.debug("AUTHENTICATOR setting default Authenticator to null");
+        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 + "\"");
+    Console.debug(
+            "AUTHENTICATOR setting property 'http.nonProxyHosts' to \""
+                    + nonProxyHosts + "\"");
     setOrClearSystemProperty("http.nonProxyHosts", nonProxyHosts);
   }