X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=eb503d5858440a6954f8a4db74b040549fceb438;hb=38299bef6dfd4b713f615781e631dcb66e1155f2;hp=38661403f3c5c44c60adbdffd92df387993eaf92;hpb=acbb69521cbe230ab33b922f45329d21a95dc410;p=jalview.git

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 3866140..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)
       {
@@ -213,6 +213,7 @@ public class Cache
 
         //LOAD USERDEFINED COLOURS
         jalview.gui.UserDefinedColours.initUserColourSchemes( getProperty("USER_DEFINED_COLOURS"));
+        jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER", false);
     }