3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
4 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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/>.
19 <title>Jalview Command Line Arguments</title>
21 <p><strong>The Jalview Executable's Command Line Arguments</strong></p>
23 <a href="commandline.html">running Jalview from the command line</a>
26 <table width="100%" border="1" cellspacing="0" cellpadding="0">
29 <div align="center">-nodisplay</div>
32 <div align="left">Run Jalview without User Interface.
33 (automatically disables questionnaire, version and usage stats checks)</div>
39 <div align="center">-props FILE</div>
42 <div align="left">Use the given Jalview properties file instead
43 of users default.</div>
48 <div align="center">-features FILE</div>
52 <p>Use the given file to add sequence features to an alignment.
53 See <a href="featuresFormat.html" target="NEW">Features File</a>
54 (Known as Groups file prior to 2.08) description.</p>
61 <div align="center">-colour COLOURSCHEME</div>
63 <td>Set the colourscheme for the alignment. This can be any of
64 the built-in colourschemes, a name of a predefined colourscheme
65 (defined in the jalview properties file), or an 'inline' colourscheme
66 (see the applet's colour parameter for more information).</td>
70 <div align="center">-annotations FILE</div>
72 <td>Add precalculated annotations to the alignment. See <a
73 href="annotationsFormat.html" target="NEW">Annotation File</a>
78 <div align="center">-tree FILE</div>
80 <div align="left">Load the given newick format tree file onto
86 <div align="center">-questionnaire URL</div>
88 <div align="left">Queries the given URL for information about
89 any Jalview user questionnaires</div>
94 <div align="center">-noquestionnaire</div>
96 <div align="left">Turn off questionnaire check</div>
101 <div align="center">-nousagestats</div>
103 <div align="left">Turn off google analytics usage tracking</div>
108 <div align="center">-[no]sortbytree</div>
110 <div align="left">Enable or disable automatic sorting of
111 associated view when a new tree is displayed</div>
116 <div align="center">-dasserver nickname=URL</div>
118 <div align="left">Add and enable a <a href="dassettings.html">DAS
119 server</a> with given nickname (alphanumeric or underscores only) for
120 retrieval of features for all alignments<br>
121 Sources that also support the sequence command may be specified by
122 prepending the URL with 'sequence:'<br>
123 <em>e.g.</em> sequence:http://localdas.somewhere.org/das/source</div>
128 <div align="center">-fetchfrom nickname</div>
130 <div align="left">Query a <a href="dassettings.html">DAS
131 source</a> called nickname for features for the alignments and display
137 <div align="center">-groovy FILE</div>
139 <div align="left">Execute groovy script in FILE (where FILE may
140 be 'STDIN' to read from the standard input) after all other arguments
141 have been processed</div>
146 <div align="center">-vdoc VAMSAS DOCUMENT FILE or URL</div>
148 <div align="left">Import the given vamsas document into a new
150 <em>New in 2.5</em></div>
155 <div align="center">-vsess VAMSAS SESSION URL</div>
157 <div align="left">Join the given vamsas session<br>
158 If a document was also specified, this will be imported first and then
159 committed as new data from Jalview to the specified session
160 (Experimental - not yet enabled!).<em>New in 2.5</em></div>
166 <div align="center">-groovy FILE</div>
168 <div align="left">Execute groovy script in FILE (where FILE may
169 be 'STDIN' to read from the standard input) after all other arguments
170 have been processed</div>
175 <div align="center">-fasta FILE</div>
179 <div align="left">Create alignment file FILE in Fasta format.</div>
184 <div align="center">-clustal FILE</div>
187 <div align="left">Create alignment file FILE in Clustal format.</div>
192 <div align="center">-msf FILE</div>
196 <div align="left">Create alignment file FILE in MSF format.</div>
201 <div align="center">-pileup FILE</div>
204 <div align="left">Create alignment file FILE in Pileup format.</div>
209 <div align="center">-pir FILE</div>
213 <div align="left">Create alignment file FILE in PIR format.</div>
218 <div align="center">-pfam FILE</div>
221 <div align="left">Create alignment file FILE in PFAM format.</div>
226 <div align="center">-blc FILE</div>
229 <div align="left">Create alignment file FILE in BLC format.</div>
234 <div align="center">-jalview FILE</div>
238 <div align="left">Create alignment file FILE in Jalview format.</div>
243 <div align="center">-png FILE</div>
246 <div align="left">Create PNG image FILE from alignment.</div>
251 <div align="center">-imgMap FILE</div>
255 <div align="left">Create HTML file FILE with image map of PNG
261 <div align="center">-eps FILE</div>
264 <div align="left">Create EPS file FILE from alignment.</div>