X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=0744cd9e18b854c37a0f837e297a3794b83ab99c;hb=ab92d7c2f18178bc4ab6584c8dfe657a68e70693;hp=ec5ff08c67a92332b3f1d1cf8abb2dd11dba9b4f;hpb=83f6c6309e9705037a0853a26da74821c9d4fd12;p=jalview.git

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index ec5ff08..0744cd9 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -53,6 +53,7 @@ import org.apache.log4j.*;
  * </li><li>SHOW_QUALITY show alignment quality annotation
  * </li><li>SHOW_ANNOTATIONS show alignment annotation rows
  * </li><li>SHOW_CONSERVATION show alignment conservation annotation
+ * </li><li>CENTRE_COLUMN_LABELS centre the labels at each column in a displayed annotation row 
  * </li><li>DEFAULT_COLOUR default colour scheme to apply for a new alignment
  * </li><li>DEFAULT_FILE_FORMAT file format used to save 
  * </li><li>STARTUP_FILE file loaded on startup (may be a fully qualified url)
@@ -84,6 +85,7 @@ import org.apache.log4j.*;
  * </li><li>DAS_REGISTRY_URL the registry to query
  * </li><li>DEFAULT_BROWSER for unix
  * </li><li>DAS_ACTIVE_SOURCE list of active sources
+ * </li><li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop (false) 
  * </li><li> 
  * </li>
  * 
@@ -101,11 +103,12 @@ public class Cache
   /**
    * property giving log4j level for AXIS loggers
    */
-  public static final String AXISLOGLEVEL = "logs.Castor.level";
+  public static final String AXISLOGLEVEL = "logs.Axis.level";
   /**
    * property giving log4j level for Jalview Log
    */
   public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
+  public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE";
 
   /**
    * Initialises the Jalview Application Log
@@ -137,6 +140,9 @@ public class Cache
       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())));
@@ -232,9 +238,16 @@ public class Cache
       {
         public void run()
         {
+          String orgtimeout = System.getProperty("sun.net.client.defaultConnectTimeout");
+          if (orgtimeout==null)
+          {
+            orgtimeout="30";
+            System.out.println("# INFO: Setting default net timeout to "+orgtimeout+" seconds.");
+          }
           String jnlpVersion = null;
           try
           {
+            System.setProperty("sun.net.client.defaultConnectTimeout", "5000");
             java.net.URL url = new java.net.URL(
                 "http://www.jalview.org/webstart/jalview.jnlp");
             BufferedReader in = new BufferedReader(new InputStreamReader(url.
@@ -255,9 +268,11 @@ public class Cache
           }
           catch (Exception ex)
           {
+            System.out.println("Non-fatal exceptions when checking version at www.jalview.org :");
             System.out.println(ex);
             jnlpVersion = getProperty("VERSION");
           }
+          System.setProperty("sun.net.client.defaultConnectTimeout", orgtimeout);
 
           setProperty("LATEST_VERSION", jnlpVersion);
         }