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 0013c63..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
@@ -156,6 +156,7 @@ public class Cache
 \r
         System.out.println("Jalview Version: "+codeVersion);\r
 \r
+\r
         // jnlpVersion will be null if we're using InstallAnywhere\r
         // Dont do this check if running in headless mode\r
         if(jnlpVersion==null && (\r
@@ -163,7 +164,6 @@ public class Cache
              || System.getProperty("java.awt.headless").equals("false")))\r
         {\r
 \r
-\r
           class VersionChecker\r
               extends Thread\r
           {\r
@@ -203,13 +203,17 @@ public class Cache
         }\r
         else\r
         {\r
-          setProperty("LATEST_VERSION", jnlpVersion);\r
+          if(jnlpVersion!=null)\r
+            setProperty("LATEST_VERSION", jnlpVersion);\r
+          else\r
+          applicationProperties.remove("LATEST_VERSION");\r
         }\r
 \r
         setProperty("VERSION", codeVersion);\r
 \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