annotations files are imported into Jalview in the following ways:<br />
<ul>
<li>from the command line<strong><pre>
- -annotations <<em>Annotations filename</em>></pre></strong></li>
+ --annotations <<em>Annotations filename</em>></pre></strong></li>
<li>Dragging an annotations file onto an alignment window</li>
<li>Via the "Load Features / Annotations" entry in
the <strong>File</strong> menu of an alignment window.
templates for HTML export from our public GitHub Repository.
Normally, this should happen without you needing to do anything, but
if you do encounter problems, then please get in contact via the
- jalview-discuss mailing list, or file a bug report.</p>
+ Jalview Discussion Forum, or file a bug report.</p>
<p>Templates are downloaded to a directory called
'.biojs_templates' in your user's home storage space (e.g.
~/.biojs_templates).</p>
<ul>
<li>from the command line <pre>
-<strong> -features <<em>Features filename</em>></strong>
+<strong> --features <<em>Features filename</em>></strong>
</pre>
</li>
</p>
<p>
<strong>Executing groovy scripts on Jalview startup</strong><br>
- The -groovy <script> option on the <a href="commandline.html">
+ The --groovy <script> option on the <a href="commandline.html">
Jalview command line</a> will execute the contents of <script>.
<script> may be a file, a URL, or alternatively if it is
"STDIN" then the standard input will be used.<br> <em>Note:
window which is currently being looked at by the user</li>
</ul></li>
<li><strong>currentAlFrame</strong> - this is only defined when
- running a Groovy script via the -groovy command line argument. It
+ running a Groovy script via the --groovy command line argument. It
returns the first alignment window created after acting on the
other arguments passed on the command line.</li>
</ul>
</ol>
<strong>Work in Progress!</strong>
<p>VCF support in Jalview is under active development. Please get
- in touch via our mailing list if you have any questions, problems or
+ in touch via our discussion forum if you have any questions, problems or
otherwise find it useful !</p>
</body>
</html>
<p>
For other queries or comments about Jalview, remember you can
contact the Jalview team using email via the
- <a href="https://www.jalview.org/mailman/listinfo/jalview-discuss">Jalview
- discussion list</a>, on Twitter <a
+ <a href="https://discourse.jalview.org/">Jalview
+ Discussion Forum</a>, on Twitter <a
href="https://twitter.com/Jalview/">@Jalview</a>, or for technical
discussions, via the Jalview developer's chatroom at
<a href="https://gitter.im/jalview/developers">https://gitter.im/jalview/developers</a>.
/PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl /path/to/alignments/myalignment.fa</pre>
Alternatively, you can use the standard Jalview command line
arguments with or without the jvl file (first), e.g. <pre>
- /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl -open https://www.jalview.org/examples/jpred_msa.fasta -annotations https://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre>
+ /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl --open https://www.jalview.org/examples/jpred_msa.fasta --annotations https://www.jalview.org/examples/jpred_msa.seq.concise --colour Clustal</pre>
You can use command line arguments to control memory settings in
Windows and macOS too: <br /> In Windows you must use, e.g. <pre>
- \PATH_TO_JALVIEW\Jalview.exe %HOMEPATH%\mymemorysetting.jvl -open %HOMEPATH%\myalignment.fa</pre>
+ \PATH_TO_JALVIEW\Jalview.exe %HOMEPATH%\mymemorysetting.jvl --open %HOMEPATH%\myalignment.fa</pre>
In macOS you can use the macOS <em>open</em> command like this: <pre>
- open /Applications/Jalview.app --args ~/mymemorysetting.jvl -open ~/myalignment.fa</pre><em>(put
+ open /Applications/Jalview.app --args ~/mymemorysetting.jvl --open ~/myalignment.fa</pre><em>(put
all the Jalview arguments <em>after</em> the --args parameter)
</em><br />
<br /></li>
</li>
<li><em><font size="3"><a name="jar">Command line arguments when using the executable jar (jalview-all.jar) or jalview.bin.Launcher</a></em><br/>
If you are using the Jalview standalone executable jar (usually named <em>jalview-all-....jar</em> with a Jalview and Java version designation) or using <em>jalview.bin.Launcher</em> to start Jalview,
- then you can set the <em>jvmmempc</em> and <em>jvmmemmax</em> values using application command line arguments <em>-jvmmempc=PERCENT</em>
- and <em>-jvmmemmax=MAXMEMORY</em> respectively. <em>PERCENT</em> should be an integer between 1 and 100, and MAXMEMORY should be an amount of memory in bytes, or you can append a "k", "m", "g", or "t" to use units of kilobytes, megabytes, gigabytes or terabytes, e.g.
- <pre>java -jar jalview-all-2.11.1.0-j1.8.jar -jvmmempc=50 -jvmmemmax=20g</pre>
+ then you can set the <em>jvmmempc</em> and <em>jvmmemmax</em> values using application command line arguments <em>--jvmmempc=PERCENT</em>
+ and <em>--jvmmemmax=MAXMEMORY</em> respectively. <em>PERCENT</em> should be an integer between 1 and 100, and MAXMEMORY should be an amount of memory in bytes, or you can append a "k", "m", "g", or "t" to use units of kilobytes, megabytes, gigabytes or terabytes, e.g.
+ <pre>java -jar jalview-all-2.11.1.0-j1.8.jar --jvmmempc=50 --jvmmemmax=20g</pre>
(this example will launch Jalview with a maximum heap size of the smaller of 20GB or 50% of physical memory detected).
<br/>The default value for jvmmempc is 90, whilst the default value for jvmmemmax is 32g if Jalview can determine a total physical memory size of the host system, and a more cautious 8g if Jalview is unable to determine a total physical memory size.
<br/><br/>
git://source.jalview.org / jalview.git / commitdiff