3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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6 * This file is part of Jalview.
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15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
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20 * The Jalview Authors are detailed in the 'AUTHORS' file.
22 <title>Jalview Command Line Arguments: introduction</title>
25 <h1>Jalview Command Line Arguments: introduction</h1>
28 <a href="clarguments.html">Jalview Command Line Arguments: summary</a>
30 Jalview Command Line Arguments: introduction
32 <a href="clarguments-basic.html">Jalview Command Line Arguments: basic usage</a>
34 <a href="clarguments-advanced.html">Jalview Command Line Arguments: advanced usage</a>
36 <a href="clarguments-argfiles.html">Jalview Command Line Arguments: argfiles</a>
42 From version 2.11.3.0 Jalview processes a new set of command line arguments
43 which allow more powerful and flexible combinations of arguments, though can
44 also be used for very simple use cases too.
48 These new arguments are all accessed with a <code>--doubledash</code> form of
49 command line argument (with the one exception where simply opening one or more
50 files can be performed without any arguments other than the filenames).
54 The old command line arguments can still be used (see
55 <a href="clarguments-old.html">the old page on command line arguments</a>) so
56 existing scripts utilising them should not break.
58 <strong>These are now deprecated and will be removed</strong> in a future version of Jalview.
62 However, you cannot mix old and new style arguments, so if you use any
63 <code>-singledash</code> arguments (with the exception of <code>-help</code> or <code>-h</code>), they will all be interpreted as
64 old style arguments with the new <code>--doubledash</code>
65 arguments being ignored. If you have a script
66 that uses the old arguments without any dashes, and uses the bare-word
67 <code>open</code> then these will also be interpreted as old style arguments.
70 <strong>Warning!</strong> If you use command line arguments without any dashes and
71 <em>don't</em> use the bare-word argument <code>open</code> then all
72 your arguments will be interpreted as alignment files to be opened by the
73 new command line argument process!
77 To launch Jalview from the command line, see
78 <a href="commandline.html">running Jalview from the command line</a>.
82 Continue to <a href="clarguments-basic.html">Jalview Command Line Arguments: basic usage</a>.
84 Return to <a href="clarguments.html">Jalview Command Line Arguments: summary</a>.