X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fclarguments.html;fp=help%2Fhelp%2Fhtml%2Ffeatures%2Fclarguments.html;h=60db0695f1d317bb1a164c1a8dff86b9f7ce9083;hb=6a05eb3f55d97e685f0c723822384633d5636778;hp=fa273a5d1cf58f2dc6632ca1707de0890bfbe52c;hpb=d113749a183a3ea8f3f7e22c725511f59f1d833f;p=jalview.git

diff --git a/help/help/html/features/clarguments.html b/help/help/html/features/clarguments.html
index fa273a5..60db069 100644
--- 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>