From 41d5f49ca6079ce78d64765382053e185e434c88 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 5 Dec 2005 16:29:55 +0000
Subject: [PATCH] New instructions for making groups file

---
 src/jalview/bin/Jalview.java |    7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 2899abb..1a67c05 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"
-- 
1.7.10.2