JAL-629 add in jvmArgs for memory for tests and keep increased clover memory

[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 369c565..c0f4c42 100644 (file)
--- 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>
   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>
   <table width="100%" border="1" cellspacing="0" cellpadding="0">
     <tr>
       <td width="27%"><div align="center">-nodisplay</div></td>

@@ -41,13 +46,27 @@
           User Interface. (automatically disables questionnaire, version
           and usage stats checks)</div></td>
     </tr>
           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>
     <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>
       <td><div align="center">-features FILE/URL</div></td>
       <td><div align="left">
           <p>

@@ -77,6 +96,14 @@
           File</a> description.
       </td>
     </tr>
           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>
     <tr>
       <td>
         <div align="center">-tree FILE/URL</div>

@@ -227,7 +254,7 @@
     </tr>
     <tr>
       <td><div align="center">-jvmmempc=PERCENT</div></td>
     </tr>
     <tr>
       <td><div align="center">-jvmmempc=PERCENT</div></td>

-      <td><div align="left"><em>Standalone executable jar only.</em>
+      <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.
           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.

@@ -236,10 +263,10 @@
     </tr>
     <tr>
       <td><div align="center">-jvmmemmax=MAXMEMORY</div></td>
     </tr>
     <tr>
       <td><div align="center">-jvmmemmax=MAXMEMORY</div></td>

-      <td><div align="left"><em>Standalone executable jar only.</em>
+      <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).
           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 physcial memory can be detected, or to 8g if total physical memory cannot be detected.
+         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>
          See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.
           </div>
       </td>