JAL-3608 added to LaF documentation

[jalview.git] / help / help / html / features / commandline.html

diff --git a/help/help/html/features/commandline.html b/help/help/html/features/commandline.html
index 27a1a68..ac462e0 100644 (file)
--- a/help/help/html/features/commandline.html
+++ b/help/help/html/features/commandline.html
@@ -38,7 +38,7 @@
 
   <ul>
     <li>Standard installation on Linux/Unix:<pre>
-       /PATH_TO_JALVIEW/Jalview -open http://www.jalview.org/examples/jpred_msa.fasta -annotations http://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre>
+       /PATH_TO_JALVIEW/Jalview -open https://www.jalview.org/examples/jpred_msa.fasta -annotations https://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre>
     </li>
     <li>Standard installation on Windows:<pre>
       \PATH_TO_JALVIEW\Jalview.exe -open %HOMEPATH%\myalignment.fa</pre>
@@ -49,7 +49,7 @@ open /Applications/Jalview.app --args -open ~/myalignment.fa</pre><em>(put
     </em><br />
     <br /></li>
     <li>Jalview standalone executable Jar<pre>
-        &lt;Path to Java home&gt;/bin/java -jar %lt;Path to Jalview Jar&gt;/jalview-all-1.8.jar -open myalignment.fa</pre></li>
+        &lt;Path to Java home&gt;/bin/java -jar &lt;Path to Jalview Jar&gt;/jalview-all-1.8.jar -open myalignment.fa</pre></li>
   </ul>
   <p>
     If you have installed Jalview via <em>conda</em> or another package
@@ -65,10 +65,34 @@ open /Applications/Jalview.app --args -open ~/myalignment.fa</pre><em>(put
   </p>
   <p>
     <strong>Passing JVM Arguments to Jalview</strong><br /> If you need
-    to modify parameters for Jalview's Java Virtual Machine, then take a
-    look at the instructions for how to <a href="../memory.html#jvm">setting
-      the JVM's maximum memory</a>.
+    to modify parameters for Jalview's Java Virtual Machine, or
+    configure system properties, then take a look at the instructions
+    for how to <a href="../memory.html#jvm">setting the JVM's
+      maximum memory</a>.<br /> 
+  <p>
+    <strong>Changing Jalview's 'Look and Feel'</strong> <br />If you
+    are experiencing issues with the font size or layout of Jalview's
+    GUI, you can try changing Jalview's 'Look and feel' by
+    specifying a custom system property 'laf' on startup (see <a
+      href="../memory.html#jvm">setting the JVM's memory</a> for
+    instructions on how to do this for your platform). <br />For the
+    Jalview standalone executable jar, simply provide one of the
+    property settings before the -jar argument
   </p>
+  <ul>
+    <li>-Dlaf=system (default look and feel for the OS)</li>
+    <li>-Dlaf=crossplatform (Java's Metal Look and Feel)</li>
+    <li>-Dlaf=nimbus (Java's alternative Nimbus Look and Feel)</li>
+    <li>-Dlaf=mac (only has an effect on OSX)</li>
+    <li>-Dlaf=gtk (only has an effect on Linux)</li>
+    <li>-Dlaf=metal (force Java's Metal Look and Feel, default on linux)</li>
+    <li>-Dlaf=quaqua (macOS only. Force attempt at old macOS theme)</li>
+    <li>-Dlaf=vaqua (macOS only. Force attempt at modern macOS theme)</li>
+  </ul>
+  The currently configured look and feel is logged to Jalview's console.
+  Once the look and feel has been changed, it will be stored in
+  Jalview's .jalview_properties file for future Jalview sessions.  This property is <strong>PREFERRED_LAF</strong> and can also be used to set the Look and feel by editing your .jalview_properties file.
+
   <p>&nbsp;</p>
   <p>&nbsp;</p>
 </body>