X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fclarguments-reference.html;h=0221a6777e79c028fa6e6634e194460c938f5c15;hb=65ed1da9a1710a9ce132c7edfce54955dc1ddf99;hp=6d65033cbec1a7671283af037413d0b2d89a403a;hpb=847c502d6186eb62a30f37f608852e77c67c217f;p=jalview.git

diff --git a/help/help/html/features/clarguments-reference.html b/help/help/html/features/clarguments-reference.html
index 6d65033..0221a67 100644
--- a/help/help/html/features/clarguments-reference.html
+++ b/help/help/html/features/clarguments-reference.html
@@ -65,8 +65,16 @@
     <tr valign="top"><td><code>&#8209;&#8209;help&#8209;all</code></td><td>Help for all arguments</td></tr>
 
     <tr valign="top">
-    <td><code>&#8209;&#8209;headless</code></td>
-    <td>Run Jalview in headless mode.  No GUI interface will be created and Jalview will quit after all arguments have been processed.</td>
+    <td><code>&#8209;&#8209;headless / &#8209;&#8209;noheadless</code></td>
+    <td>Run Jalview in headless (/ or not in headless) mode.  In headless mode, no GUI interface will be created and Jalview will quit after all arguments have been processed.
+    <br/>
+    If you use a command line argument to specify an output file of some kind (<code>--output</code>, <code>--image</code> or <code>--structureimage</code>) then <strong>headless mode will be assumed</strong>.  If you don't want this behaviour use <code>--noheadless</code> or <code>--gui</code>.
+    </td>
+    </tr>
+
+    <tr valign="top">
+    <td><code>&#8209;&#8209;gui</code></td>
+    <td>Force Jalview to run in graphical mode.  This can be used to counter the assumption of headless mode when an argument that creates an output file is used.  <code>--gui</code> takes precedence over <code>--headless</code>.</td>
     </tr>
 
     <tr valign="top">
@@ -76,27 +84,32 @@
 
     <tr valign="top">
     <td><code>&#8209;&#8209;news / &#8209;&#8209;nonews</code></td>
-    <td>Show (or don't show) the news feed.</td>
+    <td>Show (/ or don't show) the news feed.</td>
     </tr>
 
     <tr valign="top">
     <td><code>&#8209;&#8209;splash / &#8209;&#8209;nosplash</code></td>
-    <td>Show (or don't show) the About Jalview splash screen.</td>
+    <td>Show (/ or don't show) the About Jalview splash screen.</td>
     </tr>
 
     <tr valign="top">
     <td><code>&#8209;&#8209;questionnaire / &#8209;&#8209;noquestionnaire</code></td>
-    <td>Show (or don't show) the questionnaire if one is available.</td>
+    <td>Show (/ or don't show) the questionnaire if one is available.</td>
+    </tr>
+
+    <tr valign="top">
+    <td><code>&#8209;&#8209;nousagestats</code></td>
+    <td>Don't send usage stats via Google analytics for this session. <em>Note: usage stats are useful for future funding for Jalview!</em></td>
     </tr>
 
     <tr valign="top">
-    <td><code>&#8209;&#8209;usagestats / &#8209;&#8209;nousagestats</code></td>
-    <td>Send (or don't send) initial launch usage stats. <em>Note: usage stats are useful for future funding for Jalview!</em></td>
+    <td><code>&#8209;&#8209;nostartupfile</code></td>
+    <td>Don't show the default startup file.</td>
     </tr>
 
     <tr valign="top">
     <td><code>&#8209;&#8209;webservicediscovery / &#8209;&#8209;nowebservicediscovery</code></td>
-    <td>Attempt (or don't attempt) to connect to JABAWS web services.</td>
+    <td>Attempt (/ or don't attempt) to connect to JABAWS web services.</td>
     </tr>
 
     <tr valign="top">
@@ -114,10 +127,19 @@
     <td>Stop all output to STDOUT (after the Java Virtual Machine has started).  Use <code>&#8209;&#8209;quiet</code> a second time to stop all output to STDERR.</td>
     </tr>
 
+<!--
+    <tr valign="top">
+    <td><code>&#8209;&#8209;P<em>PREFERENCE=VALUE</em></code></td>
+    <td>Set a Jalview preference for this session only.  Experimental.</td>
+    </tr>
+-->
+
+<!--
     <tr valign="top">
     <td><code>&#8209;&#8209;initsubstitutions / &#8209;&#8209;noinitsubstitutions</code></td>
     <td>Set <code>&#8209;&#8209;substitutions</code> to be initially enabled (or initially disabled).</td>
     </tr>
+-->
 
 <!--
     <tr valign="top">