<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 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* 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.
- *
+ * 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
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
--->
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
<title>Jalview Command Line Arguments
</title>
<body>
</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>
</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>
</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>
</td>
</tr>
+ <tr>
+ <td>
+ <div align="center">-jabaws URL</div>
+ <td>
+ <div align="left">Specify the URL of the preferred JABAWS server</div>
+ </td>
+ </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>
</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>
<td><div align="center">-eps FILE</div></td>
<td><div align="left">Create EPS file FILE from alignment.</div></td>
</tr>
+ <tr>
+ <td><div align="center">-svg FILE</div></td>
+ <td><div align="left">Create Scalable Vector Graphics file FILE from alignment.</div></td>
+ </tr>
</table>
</body>
</html>