X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fclarguments.html;h=c0f4c42d428855c0276075006c08561ef50dfe20;hb=f439cd77032a5b7fc79d925db1c85bf6d3e6bb92;hp=ebdfcf3a21ee2473a79bc126c3619bc0ce9549b5;hpb=88153d5bb04acd2b8e7fbc3e6789622b77b6cf58;p=jalview.git

diff --git a/help/help/html/features/clarguments.html b/help/help/html/features/clarguments.html
index ebdfcf3..c0f4c42 100644
--- a/help/help/html/features/clarguments.html
+++ b/help/help/html/features/clarguments.html
@@ -27,7 +27,18 @@
   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 &lt;Alignment File/URL&gt; [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>
@@ -35,13 +46,27 @@
           User Interface. (automatically disables questionnaire, version
           and usage stats checks)</div></td>
     </tr>
-
+    <tr>
+      <td><div align="center">-nowebservicediscovery</div></td>
+      <td><div align="left">Do not query configured servers to
+          discover web services (<em>Since 2.11.2.0</em>)</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 instead of users default.</div></td>
     </tr>
     <tr>
+      <td><div align="center">-setprop PROPERTY=value</div></td>
+      <td><div align="left">(JalviewJS ONLY) sets the given
+          property to the given value</div></td>
+    </tr>
+    <tr>
       <td><div align="center">-features FILE/URL</div></td>
       <td><div align="left">
           <p>
@@ -71,6 +96,14 @@
           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>
@@ -219,6 +252,25 @@
           </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>