JAL-3477 Added -help text for jvmmempc and jvmmemmax. Fixed typo and slight rewording...

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

diff --git a/help/help/html/features/clarguments.html b/help/help/html/features/clarguments.html
index fa273a5..0d800cf 100644 (file)
--- a/help/help/html/features/clarguments.html
+++ b/help/help/html/features/clarguments.html
@@ -27,6 +27,12 @@
   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>
   <table width="100%" border="1" cellspacing="0" cellpadding="0">
     <tr>
@@ -139,29 +145,6 @@
     </tr>
     <tr>
       <td>
-        <div align="center">-vdoc VAMSAS DOCUMENT FILE/URL</div>
-      <td>
-        <div align="left">
-          Import the given vamsas document into a new session.<br>
-          <em>New in 2.5</em>
-        </div>
-      </td>
-    </tr>
-    <tr>
-      <td>
-        <div align="center">-vsess VAMSAS SESSION URL</div>
-      <td>
-        <div align="left">
-          Join the given vamsas session<br>If a document was also
-          specified, this will be imported first and then committed as
-          new data from Jalview to the specified session (Experimental -
-          not yet enabled!).<em>New in 2.5</em>
-        </div>
-        </div>
-      </td>
-    </tr>
-    <tr>
-      <td>
         <div align="center">-fasta FILE</div>
       </td>
 
@@ -242,6 +225,25 @@
           </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>