X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbin%2FCache.java;h=48837ff99f68878911d9f01f9bb7535b3317bd83;hb=98637eee5027a7d57c71a38a3d4062220bb94f9c;hp=cebb50414d00c84864a3e39439865d0010bc716e;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index cebb504..48837ff 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -124,6 +124,11 @@ import org.biojava.dasobert.dasregistry.Das1Source;
  * histogram.</li>
  * <li>SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
  * logo.</li>
+ * <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_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
+ * warning dialog box is displayed.</li>
  * 
  * <li></li>
  * 
@@ -170,6 +175,10 @@ public class Cache
 
   public static void initLogger()
   {
+    if (log != null)
+    {
+      return;
+    }
     try
     {
       // TODO: redirect stdout and stderr here in order to grab the output of
@@ -235,9 +244,7 @@ public class Cache
       System.out.println("Using proxyServer: "
               + getDefault("PROXY_SERVER", null) + " proxyPort: "
               + getDefault("PROXY_PORT", null));
-      System
-              .setProperty("http.proxyHost", getDefault("PROXY_SERVER",
-                      null));
+      System.setProperty("http.proxyHost", getDefault("PROXY_SERVER", null));
       System.setProperty("http.proxyPort", getDefault("PROXY_PORT", null));
     }
 
@@ -247,8 +254,8 @@ public class Cache
     try
     {
       String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
-              .getCodeSource().getLocation().toString().concat(
-                      "!/.build_properties"));
+              .getCodeSource().getLocation().toString()
+              .concat("!/.build_properties"));
 
       java.net.URL localJarFileURL = new java.net.URL(buildDetails);
 
@@ -603,8 +610,7 @@ public class Cache
                   "com.boxysystems.jgoogleanalytics.FocusPoint");
         } catch (Exception e)
         {
-          log
-                  .debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
+          log.debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
           tracker = null;
           jgoogleanalyticstracker = null;
           trackerfocus = null;
@@ -648,10 +654,7 @@ public class Cache
         if (log != null)
         {
           if (re != null)
-            log
-                    .debug(
-                            "Caught runtime exception in googletracker init:",
-                            re);
+            log.debug("Caught runtime exception in googletracker init:", re);
           if (ex != null)
             log.warn(
                     "Failed to initialise GoogleTracker for Jalview Desktop with version "