X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fclarguments.html;h=90707f7ea35f22b072cee62d38ad2d7c4f0d1571;hb=e66bdc1c0086ab56c56979d9dc6635e81503eb84;hp=9bca34431f6cdb9a4caed932c9951f339bfffe64;hpb=c53aeee9a688f68d64106a968876e542f701fbc6;p=jalview.git

diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html
index 9bca344..90707f7 100644
--- a/help/html/features/clarguments.html
+++ b/help/html/features/clarguments.html
@@ -1,14 +1,14 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -30,22 +30,32 @@
  </tr>
 
  <tr> 
- <td><div align="center">-props FILE</div></td>
+ <td><div align="center">-props FILE/URL</div></td>
  <td><div align="left">Use the given Jalview properties file instead 
  of users default.</div></td>
  </tr>
  <tr> 
- <td><div align="center">-features FILE</div></td>
+ <td><div align="center">-features FILE/URL</div></td>
  <td><div align="left"> 
  <p>Use the given file to add sequence features to an alignment. 
  See <a href="featuresFormat.html" target="NEW">Features 
  File</a> (Known as Groups file prior to 2.08) description. </p>
 
- </div></td>
+		</div>
+		</td>
+	</tr>
+	<tr>
+		<td>
+		<div align="center">-colour COLOURSCHEME</div>
+		</td>
+		<td>Set the colourscheme for the alignment. This can be any of
+		the built-in colourschemes, a name of a predefined colourscheme
+		(defined in the jalview properties file), or an 'inline' colourscheme
+		(see the applet's colour parameter for more information).</td>
  </tr>
 	<tr>
 		<td>
-		<div align="center">-annotations FILE</div>
+		<div align="center">-annotations FILE/URL</div>
 		</td>
 		<td>Add precalculated annotations to the alignment. See <a
 			href="annotationsFormat.html" target="NEW">Annotation File</a>
@@ -53,7 +63,7 @@
 	</tr>
 	<tr>
 		<td>
-		<div align="center">-tree FILE</div>
+		<div align="center">-tree FILE/URL</div>
 		<td>
 		<div align="left">Load the given newick format tree file onto
 		the alignment</div>
@@ -107,7 +117,7 @@
 	</tr>
 	<tr>
 		<td>
-		<div align="center">-groovy FILE</div>
+		<div align="center">-groovy FILE/URL</div>
 		<td>
 		<div align="left">Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other
 		arguments have been processed</div>
@@ -115,7 +125,7 @@
 	</tr>
 	<tr>
 	<td>
-		<div align="center">-vdoc VAMSAS DOCUMENT FILE or URL</div>
+		<div align="center">-vdoc VAMSAS DOCUMENT FILE/URL</div>
 		<td>
 		<div align="left">Import the given vamsas document into a new session.<br><em>New in 2.5</em></div>
 		</td>
@@ -129,14 +139,6 @@
 	</tr>
 	<tr>
 		<td>
-		<div align="center">-groovy FILE</div>
-		<td>
-		<div align="left">Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other
-		arguments have been processed</div>
-		</td>
-	</tr>
-	<tr>
-		<td>
 		<div align="center">-fasta FILE</div>
 		</td>
 
