X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=eb503d5858440a6954f8a4db74b040549fceb438;hb=521ce3c96d5977a9bd941894eda7a13dd09deea9;hp=0013c63b7156ce91a5ce344197434788be4835b3;hpb=d16f364a9df0e2abe0d41889eb4b696bbeb3ca31;p=jalview.git

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 0013c63..eb503d5 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -22,7 +22,6 @@ import java.io.*;
 
 import java.util.*;
 
-import java.net.*;
 import org.apache.log4j.Logger;
 import org.apache.log4j.SimpleLayout;
 import org.apache.log4j.Level;
@@ -73,7 +72,6 @@ public class Cache
         jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(
             "logs.Jalview.level",
             Level.INFO.toString())));
-
         ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
                                                  "System.err");
         ap.setName("JalviewLogger");
@@ -81,6 +79,8 @@ public class Cache
         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)
       {
@@ -156,6 +156,7 @@ public class Cache
 
         System.out.println("Jalview Version: "+codeVersion);
 
+
         // jnlpVersion will be null if we're using InstallAnywhere
         // Dont do this check if running in headless mode
         if(jnlpVersion==null && (
@@ -163,7 +164,6 @@ public class Cache
              || System.getProperty("java.awt.headless").equals("false")))
         {
 
-
           class VersionChecker
               extends Thread
           {
@@ -203,13 +203,17 @@ public class Cache
         }
         else
         {
-          setProperty("LATEST_VERSION", jnlpVersion);
+          if(jnlpVersion!=null)
+            setProperty("LATEST_VERSION", jnlpVersion);
+          else
+          applicationProperties.remove("LATEST_VERSION");
         }
 
         setProperty("VERSION", codeVersion);
 
         //LOAD USERDEFINED COLOURS
         jalview.gui.UserDefinedColours.initUserColourSchemes( getProperty("USER_DEFINED_COLOURS"));
+        jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER", false);
     }