documented the -colour command line argument.

diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html
index 9bca344..67fca9b 100644 (file)
--- a/help/html/features/clarguments.html
+++ b/help/html/features/clarguments.html
@@ -41,7 +41,17 @@
  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>

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 64ffd38..fc6d23e 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -94,6 +94,7 @@ public class Jalview
               .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"
+                      + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
                       + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
                       + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
                       + "-features FILE\tUse the given file to mark features on the alignment.\n"