X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=eb503d5858440a6954f8a4db74b040549fceb438;hb=c42fcf7bf5cfcf51e67dd0f683edb9ab6683d157;hp=485f9ec8e32a5d341c2e1cfa14542b86606dcd3b;hpb=87fd27f8449d6f4802d154072d9d6e876e22a846;p=jalview.git

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 485f9ec..eb503d5 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -22,7 +22,10 @@ import java.io.*;
 
 import java.util.*;
 
-import java.net.*;
+import org.apache.log4j.Logger;
+import org.apache.log4j.SimpleLayout;
+import org.apache.log4j.Level;
+import org.apache.log4j.ConsoleAppender;
 
 
 /**
@@ -30,6 +33,9 @@ import java.net.*;
  * <br><br>Current properties include:
  * <br>logs.Axis.Level - one of the stringified Levels for log4j controlling the logging level for axis (used for web services)
  * <br>logs.Castor.Level - one of the stringified Levels for log4j controlling the logging level for castor (used for serialization)
+ * <br>logs.Jalview.Level - Cache.log stringified level.
+ * <br>DISCOVERY_START - Boolean - controls if discovery services are queried on startup
+ * <br>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
  * <br>SCREEN_WIDTH,SCREEN_HEIGHT,SCREEN_Y=285,SCREEN_X=371,SHOW_FULLSCREEN
  * FONT_NAME,FONT_SIZE,FONT_STYLE,GAP_SYMBOL,LAST_DIRECTORY,USER_DEFINED_COLOUR
  * SHOW_FULL_ID,SHOW_IDENTITY,SHOW_QUALITY,SHOW_ANNOTATIONS,SHOW_CONSERVATION,
@@ -40,6 +46,10 @@ import java.net.*;
  */
 public class Cache
 {
+  /**
+   * Initialises the Apache Axis logger
+   */
+  public static Logger log;
 
     /** Jalview Properties */
     public static Properties applicationProperties = new Properties();
@@ -47,6 +57,38 @@ public class Cache
     /** Default file is  ~/.jalview_properties */
     static String propertiesFile;
 
+    public static void initLogger()
+    {
+      try
+      {
+        Logger laxis = Logger.getLogger("org.apache.axis");
+        Logger lcastor = Logger.getLogger("org.exolab.castor");
+        jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
+
+        laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level",
+            Level.INFO.toString())));
+        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())));
+        ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
+                                                 "System.err");
+        ap.setName("JalviewLogger");
+
+        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)
+      {
+      System.err.println("Problems initializing the log4j system\n");
+      }
+    }
+
+
     /** Called when Jalview is started */
     public static void loadProperties(String propsFile)
     {
@@ -114,6 +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 && (
@@ -121,7 +164,6 @@ public class Cache
              || System.getProperty("java.awt.headless").equals("false")))
         {
 
-
           class VersionChecker
               extends Thread
           {
@@ -161,10 +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);
     }
 
 
@@ -231,7 +280,7 @@ public class Cache
             out.close();
         }
         catch (Exception ex)
-        {    }
+        {   System.out.println("Error setting property: "+key+" "+obj+"\n"+ex);   }
         return obj;
     }
 
@@ -244,6 +293,6 @@ public class Cache
             out.close();
         }
         catch (Exception ex)
-        {    }
+        {  System.out.println("Error saving properties: "+ex);  }
     }
 }