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>
User Interface. (automatically disables questionnaire, version
and usage stats checks)</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</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>
</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>