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=1eecfb9738dd15ef2e4767378598e575b480a65d;hb=f3d57563c0364d1d44889156e264414fa32b5443;hp=60db0695f1d317bb1a164c1a8dff86b9f7ce9083;hpb=d7f65ab5aed90618588864660d3e45bd18367a2b;p=jalview.git

diff --git a/help/help/html/features/clarguments.html b/help/help/html/features/clarguments.html
index 60db069..1eecfb9 100644
--- a/help/help/html/features/clarguments.html
+++ b/help/help/html/features/clarguments.html
@@ -34,6 +34,11 @@
   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>
@@ -41,7 +46,11 @@
           User Interface. (automatically disables questionnaire, version
           and usage stats checks)</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
@@ -225,6 +234,25 @@
           </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>