3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
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 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 * The Jalview Authors are detailed in the 'AUTHORS' file.
20 <title>Jalview Command Line Arguments
23 <p><strong>The Jalview Executable's Command Line
24 Arguments</strong></p>
25 See <a href="commandline.html">running Jalview from the command
26 line</a> for more information.<br>
27 <table width="100%" border="1" cellspacing="0" cellpadding="0">
29 <td width="27%"><div align="center">-nodisplay</div></td>
30 <td width="73%"><div align="left">Run Jalview without User Interface. (automatically disables questionnaire, version and usage stats checks)</div></td>
34 <td><div align="center">-props FILE/URL</div></td>
35 <td><div align="left">Use the given Jalview properties file instead
36 of users default.</div></td>
39 <td><div align="center">-features FILE/URL</div></td>
40 <td><div align="left">
41 <p>Use the given file to add sequence features to an alignment.
42 See <a href="featuresFormat.html" target="NEW">Features
43 File</a> (Known as Groups file prior to 2.08) description. </p>
50 <div align="center">-colour COLOURSCHEME</div>
52 <td>Set the colourscheme for the alignment. This can be any of
53 the built-in colourschemes, a name of a predefined colourscheme
54 (defined in the jalview properties file), or an 'inline' colourscheme
55 (see the applet's colour parameter for more information).</td>
59 <div align="center">-annotations FILE/URL</div>
61 <td>Add precalculated annotations to the alignment. See <a
62 href="annotationsFormat.html" target="NEW">Annotation File</a>
67 <div align="center">-tree FILE/URL</div>
69 <div align="left">Load the given newick format tree file onto
75 <div align="center">-questionnaire URL</div>
77 <div align="left">Queries the given URL for information about
78 any Jalview user questionnaires</div>
83 <div align="center">-noquestionnaire</div>
85 <div align="left">Turn off questionnaire check</div>
89 <div align="center">-nousagestats</div>
91 <div align="left">Turn off google analytics usage tracking</div>
95 <div align="center">-[no]sortbytree</div>
97 <div align="left">Enable or disable automatic sorting of associated view when a new tree is displayed</div>
102 <div align="center">-dasserver nickname=URL</div>
104 <div align="left">Add and enable a <a href="dassettings.html">DAS server</a> with given
105 nickname (alphanumeric or underscores only) for retrieval of features
106 for all alignments<br>
107 Sources that also support the sequence command may be specified by prepending the URL with 'sequence:'<br>
108 <em>e.g.</em> sequence:http://localdas.somewhere.org/das/source</div>
113 <div align="center">-fetchfrom nickname</div>
115 <div align="left">Query a <a href="dassettings.html">DAS source</a> called nickname for features for the alignments
116 and display them</div>
121 <div align="center">-groovy FILE/URL</div>
123 <div align="left">Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other
124 arguments have been processed</div>
129 <div align="center">-vdoc VAMSAS DOCUMENT FILE/URL</div>
131 <div align="left">Import the given vamsas document into a new session.<br><em>New in 2.5</em></div>
136 <div align="center">-vsess VAMSAS SESSION URL</div>
138 <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>
143 <div align="center">-fasta FILE</div>
147 <div align="left">Create alignment file FILE in Fasta format.</div>
151 <td><div align="center">-clustal FILE</div></td>
152 <td><div align="left">Create alignment file FILE in Clustal format.</div></td>
155 <td><div align="center">-msf FILE</div></td>
157 <td><div align="left">Create alignment file FILE in MSF format.</div></td>
160 <td><div align="center">-pileup FILE</div></td>
161 <td><div align="left">Create alignment file FILE in Pileup format.</div></td>
164 <td><div align="center">-pir FILE</div></td>
166 <td><div align="left">Create alignment file FILE in PIR format.</div></td>
169 <td><div align="center">-pfam FILE</div></td>
170 <td><div align="left">Create alignment file FILE in PFAM format.</div></td>
173 <td><div align="center">-blc FILE</div></td>
174 <td><div align="left">Create alignment file FILE in BLC format.</div></td>
177 <td><div align="center">-jalview FILE</div></td>
179 <td><div align="left">Create alignment file FILE in Jalview format.</div></td>
182 <td><div align="center">-png FILE</div></td>
183 <td><div align="left">Create PNG image FILE from alignment.</div></td>
186 <td><div align="center">-imgMap FILE</div></td>
188 <td><div align="left">Create HTML file FILE with image map of PNG
192 <td><div align="center">-eps FILE</div></td>
193 <td><div align="left">Create EPS file FILE from alignment.</div></td>