ModellerOutput set in preferences

[jalview.git] / src / jalview / bin / Cache.java

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index c6a517f..eb503d5 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -22,7 +22,6 @@ import java.io.*;
 \r
 import java.util.*;\r
 \r
-import java.net.*;\r
 import org.apache.log4j.Logger;\r
 import org.apache.log4j.SimpleLayout;\r
 import org.apache.log4j.Level;\r
@@ -73,7 +72,6 @@ public class Cache
         jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(\r
             "logs.Jalview.level",\r
             Level.INFO.toString())));\r
-\r
         ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),\r
                                                  "System.err");\r
         ap.setName("JalviewLogger");\r
@@ -81,6 +79,8 @@ public class Cache
         laxis.addAppender(ap);\r
         lcastor.addAppender(ap);\r
         jalview.bin.Cache.log.addAppender(ap);\r
+        // Tell the user that debug is enabled\r
+        jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");\r
       }\r
       catch (Exception ex)\r
       {\r
@@ -203,6 +203,9 @@ public class Cache
         }\r
         else\r
         {\r
+          if(jnlpVersion!=null)\r
+            setProperty("LATEST_VERSION", jnlpVersion);\r
+          else\r
           applicationProperties.remove("LATEST_VERSION");\r
         }\r
 \r
@@ -210,6 +213,7 @@ public class Cache
 \r
         //LOAD USERDEFINED COLOURS\r
         jalview.gui.UserDefinedColours.initUserColourSchemes( getProperty("USER_DEFINED_COLOURS"));\r
+        jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER", false);\r
     }\r
 \r
 \r