From: amwaterhouse Date: Mon, 5 Dec 2005 16:29:55 +0000 (+0000) Subject: New instructions for making groups file X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=41d5f49ca6079ce78d64765382053e185e434c88;p=jalview.git New instructions for making groups file --- 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" - +"TEXTSEQUENCE_IDSEQUENCE_INDEXSTART_RESIDUEEND_RESIDUECOLOUR\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. " + +"\nGROUPNAMEGROUPCOLOUR\n" + +"TEXTSEQUENCE_IDSEQUENCE_INDEXSTART_RESIDUEEND_RESIDUEGROUPNAME\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"