3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
4 * Copyright (C) 2014 The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
22 <title>Jalview Command Line Arguments
25 <p><strong>The Jalview Executable's Command Line
26 Arguments</strong></p>
27 See <a href="commandline.html">running Jalview from the command
28 line</a> for more information.<br>
29 <table width="100%" border="1" cellspacing="0" cellpadding="0">
31 <td width="27%"><div align="center">-nodisplay</div></td>
32 <td width="73%"><div align="left">Run Jalview without User Interface. (automatically disables questionnaire, version and usage stats checks)</div></td>
36 <td><div align="center">-props FILE/URL</div></td>
37 <td><div align="left">Use the given Jalview properties file instead
38 of users default.</div></td>
41 <td><div align="center">-features FILE/URL</div></td>
42 <td><div align="left">
43 <p>Use the given file to add sequence features to an alignment.
44 See <a href="featuresFormat.html" target="NEW">Features
45 File</a> (Known as Groups file prior to 2.08) description. </p>
52 <div align="center">-colour COLOURSCHEME</div>
54 <td>Set the colourscheme for the alignment. This can be any of
55 the built-in colourschemes, a name of a predefined colourscheme
56 (defined in the Jalview properties file), or an 'inline' colourscheme
57 (see the applet's colour parameter for more information).</td>
61 <div align="center">-annotations FILE/URL</div>
63 <td>Add precalculated annotations to the alignment. See <a
64 href="annotationsFormat.html" target="NEW">Annotation File</a>
69 <div align="center">-tree FILE/URL</div>
71 <div align="left">Load the given newick format tree file onto
77 <div align="center">-questionnaire URL</div>
79 <div align="left">Queries the given URL for information about
80 any Jalview user questionnaires</div>
85 <div align="center">-noquestionnaire</div>
87 <div align="left">Turn off questionnaire check</div>
91 <div align="center">-nousagestats</div>
93 <div align="left">Turn off google analytics usage tracking</div>
97 <div align="center">-[no]sortbytree</div>
99 <div align="left">Enable or disable automatic sorting of associated view when a new tree is displayed</div>
104 <div align="center">-dasserver nickname=URL</div>
106 <div align="left">Add and enable a <a href="dassettings.html">DAS server</a> with given
107 nickname (alphanumeric or underscores only) for retrieval of features
108 for all alignments<br>
109 Sources that also support the sequence command may be specified by prepending the URL with 'sequence:'<br>
110 <em>e.g.</em> sequence:http://localdas.somewhere.org/das/source</div>
115 <div align="center">-fetchfrom nickname</div>
117 <div align="left">Query a <a href="dassettings.html">DAS source</a> called nickname for features for the alignments
118 and display them</div>
123 <div align="center">-groovy FILE/URL</div>
125 <div align="left">Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other
126 arguments have been processed</div>
131 <div align="center">-jabaws URL</div>
133 <div align="left">Specify the URL of the preferred JABAWS server</div>
138 <div align="center">-vdoc VAMSAS DOCUMENT FILE/URL</div>
140 <div align="left">Import the given vamsas document into a new session.<br><em>New in 2.5</em></div>
145 <div align="center">-vsess VAMSAS SESSION URL</div>
147 <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>
152 <div align="center">-fasta FILE</div>
156 <div align="left">Create alignment file FILE in Fasta format.</div>
160 <td><div align="center">-clustal FILE</div></td>
161 <td><div align="left">Create alignment file FILE in Clustal format.</div></td>
164 <td><div align="center">-msf FILE</div></td>
166 <td><div align="left">Create alignment file FILE in MSF format.</div></td>
169 <td><div align="center">-pileup FILE</div></td>
170 <td><div align="left">Create alignment file FILE in Pileup format.</div></td>
173 <td><div align="center">-pir FILE</div></td>
175 <td><div align="left">Create alignment file FILE in PIR format.</div></td>
178 <td><div align="center">-pfam FILE</div></td>
179 <td><div align="left">Create alignment file FILE in PFAM format.</div></td>
182 <td><div align="center">-blc FILE</div></td>
183 <td><div align="left">Create alignment file FILE in BLC format.</div></td>
186 <td><div align="center">-jalview FILE</div></td>
188 <td><div align="left">Create alignment file FILE in Jalview format.</div></td>
191 <td><div align="center">-png FILE</div></td>
192 <td><div align="left">Create PNG image FILE from alignment.</div></td>
195 <td><div align="center">-imgMap FILE</div></td>
197 <td><div align="left">Create HTML file FILE with image map of PNG
201 <td><div align="center">-eps FILE</div></td>
202 <td><div align="left">Create EPS file FILE from alignment.</div></td>
205 <td><div align="center">-svg FILE</div></td>
206 <td><div align="left">Create Scalable Vector Graphics file FILE from alignment.</div></td>