<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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
+ * 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/>.
+-->
<title>Jalview Command Line Arguments
</title>
<body>
<table width="100%" border="1" cellspacing="0" cellpadding="0">
<tr >
<td width="27%"><div align="center">-nodisplay</div></td>
- <td width="73%"><div align="left">Run Jalview without User Interface.</div></td>
+ <td width="73%"><div align="left">Run Jalview without User Interface. (automatically disables questionnaire, version and usage stats checks)</div></td>
</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>
- </tr>
- <tr>
- <td>
- <div align="center">-annotations FILE</div>
+ </div>
</td>
- <td>Add precalculated annotations to the alignment. See <a
- href="annotationsFormat.html" target="NEW">Annotation File</a>
- description.</td>
</tr>
<tr>
<td>
- <div align="center"></div>
- <td>
- <div align="left"></div>
+ <div align="center">-colour COLOURSCHEME</div>
</td>
- </tr>
- <tr>
- <td>
- <div align="center">-nodisplay</div>
- <td>
- <div align="left">Run Jalview without User Interface</div>
- </td>
- </tr>
+ <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">-props FILE</div>
- <td>
- <div align="left">Use the given Jalview properties file instead
- of users default</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>
+ description.</td>
</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">-features FILE</div>
- <td>
- <div align="left">Use the given file to mark features on the
- alignment</div>
- </td>
- </tr>
- <tr>
- <td>
<div align="center">-questionnaire URL</div>
<td>
<div align="left">Queries the given URL for information about
<div align="left">Turn off questionnaire check</div>
</td>
</tr>
+ <tr><td>
+ <div align="center">-nousagestats</div>
+ <td>
+ <div align="left">Turn off google analytics usage tracking</div>
+ </td>
+ </tr>
+ <tr><td>
+ <div align="center">-[no]sortbytree</div>
+ <td>
+ <div align="left">Enable or disable automatic sorting of associated view when a new tree is displayed</div>
+ </td>
+ </tr>
<tr>
<td>
<div align="center">-dasserver nickname=URL</div>
<td>
- <div align="left">Add and enable a das server with given
+ <div align="left">Add and enable a <a href="dassettings.html">DAS server</a> with given
nickname (alphanumeric or underscores only) for retrieval of features
for all alignments<br>
Sources that also support the sequence command may be specified by prepending the URL with 'sequence:'<br>
<td>
<div align="center">-fetchfrom nickname</div>
<td>
- <div align="left">Query nickname for features for the alignments
+ <div align="left">Query a <a href="dassettings.html">DAS source</a> called nickname for features for the alignments
and display them</div>
</td>
</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">-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">-vsess VAMSAS SESSION URL</div>
+ <td>
+ <div align="left">Join the given vamsas session<br>If a document was also specified, this will be imported first and then committed as new data from Jalview to the specified session (Experimental - not yet enabled!).<em>New in 2.5</em></div></div>
+ </td>
+ </tr>
+ <tr>
<td>
<div align="center">-fasta FILE</div>
</td>
git://source.jalview.org / jalview.git / blobdiff