<html>
-<title>Jalview Command Line Arguments
-</title>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<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.</div></td>
- </tr>
+ <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</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="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>
+ <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">-annotations FILE</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>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-nodisplay</div>
- <td>
- <div align="left">Run Jalview without User Interface</div>
- </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>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-tree FILE</div>
- <td>
- <div align="left">Load the given newick format tree file onto
- the alignment</div>
- </td>
- </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
- 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">-dasserver nickname=URL</div>
- <td>
- <div align="left">Add and enable a das server with given
- nickname (alphanumeric or underscores only) for retrieval of features
- for all alignments</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-fetchfrom nickname</div>
- <td>
- <div align="left">Query nickname for features for the alignments
- and display them</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>
+ </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">-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/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 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 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 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">-json FILE</div></td>
+ <td><div align="left">Create alignment file FILE in
+ JSON 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 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>
+ <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>
+ <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>
git://source.jalview.org / jalview.git / blobdiff