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+<title>Jalview Command Line Arguments (pre 2.11.3.0) - DEPRECATED</title>
+<body>
+ <p>
+ <strong>The Jalview Executable's Command Line Arguments (pre 2.11.3.0) - DEPRECATED</strong>
+ </p>
+
+ <table border="1">
+ <tr><td>
+ <em>
+ This page describes the command line arguments used pre 2.11.3.0 (released mid 2023).
+ <br/>
+ Whilst these arguments will be supported for some versions after 2.11.3.0, they are now deprecated
+ and will be removed at some time in the future.
+ </em>
+ </td></tr>
+ </table>
+
+
+ See
+ <a href="commandline.html">running Jalview from the command line</a>
+ for more information.
+ <br />
+ <br />Jalview processes arguments on the command line sequentially. If
+ you would like to pass a <a href="jvlfiles.html">'JVL' file</a> containing
+ <a href="../memory.html">memory settings</a> or any other launch
+ parameters, then include it at the beginning of the command line to
+ ensure they are processed before any remaining arguments.
+ <br>
+ Typical command line execution follows the following pattern:
+ <pre>
+ jalview -open <Alignment File/URL> [additional import arguments] [export arguments]
+ </pre>
+
+ <table width="100%" border="1" cellspacing="0" cellpadding="0">
+ <tr>
+ <td width="27%"><div align="center">-nodisplay</div></td>
+ <td width="73%"><div align="left">Run Jalview without
+ User Interface. (automatically disables questionnaire, version
+ and usage stats checks)</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-nowebservicediscovery</div></td>
+ <td><div align="left">Do not query configured servers to
+ discover web services (<em>Since 2.11.2.0</em>)</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-open FILE/URL</div></td>
+ <td><div align="left">Specify the alignment file to
+ open or process by providing additional arguments.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-props FILE/URL</div></td>
+ <td><div align="left">Use the given Jalview properties
+ file instead of users default.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-setprop PROPERTY=value</div></td>
+ <td><div align="left">(JalviewJS ONLY) sets the given
+ property to the given value</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-features FILE/URL</div></td>
+ <td><div align="left">
+ <p>
+ Use the given file to add sequence features to an alignment.
+ See <a href="featuresFormat.html" target="NEW">Features
+ File</a> (Known as Groups file prior to 2.08) description.
+ </p>
+
+ </div></td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-colour COLOURSCHEME</div>
+ </td>
+ <td>Set the colourscheme for the alignment. This can be any
+ of the built-in colourschemes, a name of a predefined
+ colourscheme (defined in the Jalview properties file), or an
+ 'inline' colourscheme (see the applet's colour parameter for
+ more information).</td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-annotations FILE/URL</div>
+ </td>
+ <td>Add precalculated annotations to the alignment. See <a
+ href="annotationsFormat.html" target="NEW">Annotation
+ File</a> description.
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-no-annotation</div>
+ </td>
+ <td>Do not display annotation below the alignment.
+ </td>
+ </tr>
+
+ <tr>
+ <td>
+ <div align="center">-tree FILE/URL</div>
+ <td>
+ <div align="left">Load the given newick format tree file
+ onto the alignment</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-questionnaire URL</div>
+ <td>
+ <div align="left">Queries the given URL for information
+ about any Jalview user questionnaires</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-noquestionnaire</div>
+ <td>
+ <div align="left">Turn off questionnaire check</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-nonews</div>
+ <td>
+ <div align="left">
+ Disable check for <a href="../webServices/newsreader.html">Jalview
+ news</a> on startup (not recommended other than for classroom /
+ demo usage)
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-nousagestats</div>
+ <td>
+ <div align="left">Turn off google analytics usage tracking</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-[no]sortbytree</div>
+ <td>
+ <div align="left">Enable or disable automatic sorting of
+ associated view when a new tree is displayed</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-groovy FILE/URL</div>
+ <td>
+ <div align="left">Execute groovy script in FILE (where
+ FILE may be 'STDIN' to read from the standard input) after all
+ other arguments have been processed</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-jabaws URL</div>
+ <td>
+ <div align="left">Specify the URL of the preferred JABAWS
+ server</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-fasta FILE</div>
+ </td>
+
+ <td>
+ <div align="left">Create alignment file FILE in Fasta
+ format.</div>
+ </td>
+ </tr>
+ <tr>
+ <td><div align="center">-clustal FILE</div></td>
+ <td><div align="left">Create alignment file FILE in
+ Clustal format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-msf FILE</div></td>
+
+ <td><div align="left">Create alignment file FILE in MSF
+ format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-pileup FILE</div></td>
+ <td><div align="left">Create alignment file FILE in
+ Pileup format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-pir FILE</div></td>
+
+ <td><div align="left">Create alignment file FILE in PIR
+ format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-pfam FILE</div></td>
+ <td><div align="left">Create alignment file FILE in
+ PFAM format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-blc FILE</div></td>
+ <td><div align="left">Create alignment file FILE in BLC
+ format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-json FILE</div></td>
+ <td><div align="left">Create alignment file FILE in
+ JSON format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-jalview FILE</div></td>
+
+ <td><div align="left">Create alignment file FILE in
+ Jalview format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-png FILE</div></td>
+ <td><div align="left">Create PNG image FILE from
+ alignment.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-imgMap FILE</div></td>
+
+ <td><div align="left">Create HTML file FILE with image
+ map of PNG image.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-eps FILE</div></td>
+ <td><div align="left">Create EPS file FILE from
+ alignment.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-svg FILE</div></td>
+ <td><div align="left">Create Scalable Vector Graphics
+ file FILE from alignment.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-biojsMSA FILE</div></td>
+ <td><div align="left">Write an HTML page to display
+ the alignment with the <a href="biojsmsa.html">
+ BioJS MSAviewer MSA</a>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td><div align="center">-jvmmempc=PERCENT</div></td>
+ <td><div align="left"><em>Only available with standalone executable jar or jalview.bin.Launcher.</em>
+ Limit maximum heap size (memory) to PERCENT% of total physical memory detected.
+ This defaults to 90 if total physical memory can be detected.
+ See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td><div align="center">-jvmmemmax=MAXMEMORY</div></td>
+ <td><div align="left"><em>Only available with standalone executable jar or jalview.bin.Launcher.</em>
+ Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m),
+ gigabytes(g) or if you're lucky enough, terabytes(t).
+ This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected.
+ See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.
+ </div>
+ </td>
+ </tr>
+ </table>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff