<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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
*
* 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>
+ <p><strong>The Jalview Executable's Command Line
+ Arguments</strong></p>
+ See <a href="commandline.html">running Jalview from the command
+ line</a> for more information.<br>
+ <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. (automatically disables questionnaire, version and usage stats checks)</div></td>
+ </tr>
+
+ <tr>
+ <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/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">-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/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/URL</div>
+ <td>
+ <div align="left">Load the given newick format tree file onto
+ the alignment</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-questionnaire URL</div>
+ <td>
+ <div align="left">Queries the given URL for information about
+ any Jalview user questionnaires</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-noquestionnaire</div>
+ <td>
+ <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 <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>
+ <em>e.g.</em> sequence:http://localdas.somewhere.org/das/source</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-fetchfrom nickname</div>
+ <td>
+ <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/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>
+
+ <td>
+ <div align="left">Create alignment file FILE in Fasta format.</div>
+ </td>
+ </tr>
+ <tr>
+ <td><div align="center">-clustal FILE</div></td>
+ <td><div align="left">Create alignment file FILE in Clustal format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-msf FILE</div></td>
+
+ <td><div align="left">Create alignment file FILE in MSF format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-pileup FILE</div></td>
+ <td><div align="left">Create alignment file FILE in Pileup format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-pir FILE</div></td>
+
+ <td><div align="left">Create alignment file FILE in PIR format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-pfam FILE</div></td>
+ <td><div align="left">Create alignment file FILE in PFAM format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-blc FILE</div></td>
+ <td><div align="left">Create alignment file FILE in BLC format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-jalview FILE</div></td>
+
+ <td><div align="left">Create alignment file FILE in Jalview format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-png FILE</div></td>
+ <td><div align="left">Create PNG image FILE from alignment.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-imgMap FILE</div></td>
+
+ <td><div align="left">Create HTML file FILE with image map of PNG
+ image.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-eps FILE</div></td>
+ <td><div align="left">Create EPS file FILE from alignment.</div></td>
+ </tr>
+ </table>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff