X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=a73405424d5743516bd7ae0325cadfdb209a439e;hb=0125a426aecc7065538a13f48236dc1e8d268044;hp=910c94720665a082c0180d8244e051112e57bbc6;hpb=f24dacb1da56fccf05d684e2f4899facec2aecf7;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 910c947..a734054 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -57,8 +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"
@@ -76,10 +79,12 @@ 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"))
           {
@@ -99,8 +104,6 @@ public class Jalview
             System.exit(0);
           }
 
-        Cache.loadProperties(aparser.getValue("props"));
-
         Desktop desktop = null;
         if( !headless )
         {
@@ -145,7 +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);
               }
             }
 
@@ -159,7 +163,7 @@ public class Jalview
             if (file.endsWith(".jar"))
               format = "Jalview";
             else
-              format = jalview.io.IdentifyFile.Identify(file, protocol);
+              format = new jalview.io.IdentifyFile().Identify(file, protocol);
 
             System.out.println("Opening: " + format + " file " + file);
 
@@ -234,14 +238,10 @@ public class Jalview
             }
             else
             {
-              format = jalview.io.IdentifyFile.Identify(file, protocol);
+              format = new jalview.io.IdentifyFile().Identify(file, protocol);
               desktop.LoadFile(file, protocol, format);
             }
           }
-
-
-          if (desktop==null)
-            System.exit(0);
     }
 }