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-<title>Command Line: introduction</title>
-<body>
-
- <h1>Command Line: introduction</h1>
-
- <p>
- <a href="clarguments.html">Command Line: summary</a>
- <br/>
- Command Line: introduction
- <br/>
- <a href="clarguments-basic.html">Command Line: basic usage</a>
- <br/>
- <a href="clarguments-advanced.html">Command Line: advanced usage</a>
- <br/>
- <a href="clarguments-argfiles.html">Command Line: argument files</a>
- </p>
-
- <hr/>
-
- <p>
- From version 2.11.3.0 Jalview processes a new set of command line arguments
- which allow more powerful and flexible combinations of arguments, though can
- also be used for very simple use cases too.
- </p>
-
- <p>
- These new arguments are all accessed with a <code>--doubledash</code> form of
- command line argument (with the one exception where simply opening one or more
- files can be performed without any arguments other than the filenames).
- </p>
-
- <p>
- The old command line arguments can still be used (see
- <a href="clarguments-old.html">the old page on command line arguments</a>) so
- existing scripts utilising them should not break.
- <br/>
- <strong>These are now deprecated and will be removed</strong> in a future version of Jalview.
- </p>
-
- <p>
- However, you cannot mix old and new style arguments, so if you use any
- <code>-singledash</code> arguments (with the exception of <code>-help</code> or <code>-h</code>), they will all be interpreted as
- old style arguments with the new <code>--doubledash</code>
- arguments being ignored. If you have a script
- that uses the old arguments without any dashes, and uses the bare-word
- <code>open</code> then these will also be interpreted as old style arguments.
- </p>
- <p>
- <strong>Warning!</strong> If you use command line arguments without any dashes and
- <em>don't</em> use the bare-word argument <code>open</code> then all
- your arguments will be interpreted as alignment files to be opened by the
- new command line argument process!
- </p>
-
- <p>
- To launch Jalview from the command line, see
- <a href="commandline.html">running Jalview from the command line</a>.
- </p>
-
- <hr/>
- Continue to <a href="clarguments-basic.html">Command Line: basic usage</a>.
- <br/>
- Return to <a href="clarguments.html">Command Line: summary</a>.
-
-
-</body>
-</html>