X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=02727518c85add9911220527b1ef0cf97fddca5f;hb=a87f4c6fd568ccf29aaf3af0ad528da442ea921d;hp=e8e66d8250bfd01bf7fe397d25998eaa6a982e03;hpb=a02c010dd9c92b25f13974038329b541d424dc77;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index e8e66d8..0272751 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,8 +20,6 @@ package jalview.bin;
 
 import jalview.gui.*;
 
-import org.apache.log4j.*;
-
 import javax.swing.*;
 
 import java.util.Vector;
@@ -37,33 +35,6 @@ import java.util.Vector;
  */
 public class Jalview
 {
-    /**
-     * Initialises the Apache Axis logger
-     */
-    private static void initLogger()
-    {
-        Logger laxis = Logger.getLogger("org.apache.axis");
-        Logger lcastor = Logger.getLogger("org.exolab.castor");
-
-        if (Cache.getProperty("logs.Axis.Level") == null)
-        {
-            Cache.setProperty("logs.Axis.Level", Level.INFO.toString());
-        }
-
-        if (Cache.getProperty("logs.Castor.Level") == null)
-        {
-            Cache.setProperty("logs.Castor.Level", Level.INFO.toString());
-        }
-
-        laxis.setLevel(Level.toLevel(Cache.getProperty("logs.Axis.Level")));
-        lcastor.setLevel(Level.toLevel(Cache.getProperty("logs.Castor.Level")));
-
-        ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
-                "System.err");
-        ap.setName("JalviewLogger");
-        laxis.addAppender(ap);
-        lcastor.addAppender(ap);
-    }
 
     /**
      * main class for Jalview application
@@ -86,8 +57,11 @@ public class Jalview
         System.out.println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
                            +"-nodisplay\tRun Jalview without User Interface.\n"
                            +"-props FILE\tUse the given Jalview properties file instead of users default.\n"
-                           +"-groups FILE\tUse the given file to mark groups on the alignment. \nGroups file is in the following tab delimited format\n"
-                           +"TEXT<tab>SEQUENCE_ID<tab>SEQUENCE_INDEX<tab>START_RESIDUE<tab>END_RESIDUE<tab>COLOUR\n"
+                           +"-groups FILE\tUse the given file to mark groups on the alignment."
+                           +"\nThe first lines of the groups file lists the GroupName and GroupColours"
+                           +" to be used in the alignment. Use the GROUPNAME label for each of your sequences. "
+                           +"\nGROUPNAME<tab>GROUPCOLOUR\n"
+                           +"TEXT<tab>SEQUENCE_ID<tab>SEQUENCE_INDEX<tab>START_RESIDUE<tab>END_RESIDUE<tab>GROUPNAME\n"
                            +"SequenceID is used in preference to SequenceIndex if both are provided.\n"
                            +"Enter ID_NOT_SPECIFIED for SEQUENCE_ID or -1 for SEQUENCE_INDEX if unknown.\n"
                            +"COLOUR can be hexadecimal RGB or 'red', 'blue' etc.\n\n"
@@ -105,27 +79,30 @@ public class Jalview
         System.exit(0);
           }
 
+          Cache.loadProperties(aparser.getValue("props")); // must do this before anything else!
 
           if (aparser.contains("nodisplay"))
+          {
             System.setProperty("java.awt.headless", "true");
-
+          }
           if (System.getProperty("java.awt.headless") != null
               && System.getProperty("java.awt.headless").equals("true"))
           {
             headless = true;
           }
 
-        Cache.loadProperties(aparser.getValue("props"));
-
-        try
-        {
-          initLogger();
-        }
-        catch (Exception e)
-        {
-          System.err.println("Problems initializing the log4j system\n");
-        }
-
+          try
+          {
+            Cache.initLogger();
+          }
+          catch (java.lang.NoClassDefFoundError error)
+          {
+            error.printStackTrace();
+            System.out.println(
+                "\nEssential logging libraries not found."
+                +"\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");
+            System.exit(0);
+          }
 
         Desktop desktop = null;
         if( !headless )
@@ -148,6 +125,7 @@ public class Jalview
 
           desktop = new Desktop();
           desktop.setVisible(true);
+          desktop.discoverer.start();
         }
 
 
@@ -170,7 +148,8 @@ public class Jalview
               if (! (new java.io.File(file)).exists())
               {
                 System.out.println("Can't find " + file);
-                System.exit(1);
+                if(headless)
+                  System.exit(1);
               }
             }
 
@@ -241,9 +220,7 @@ public class Jalview
         //////////////////////
           if (
               !headless &&
-              jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true) &&
-              jalview.bin.Cache.getDefault("STARTUP_FILE",
-                                         "http://www.jalview.org/examples/exampleFile.jar")!= null)
+              jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
           {
 
             file = jalview.bin.Cache.getDefault("STARTUP_FILE",
@@ -265,10 +242,6 @@ public class Jalview
               desktop.LoadFile(file, protocol, format);
             }
           }
-
-
-          if (desktop==null)
-            System.exit(0);
     }
 }