X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fclarguments-reference.html;h=60951d8303793a643a74e28a628115a5450b59ef;hb=fd814da2180509657dbc6a644cf3e812e8e00c92;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..60951d8 100644
--- a/help/help/html/features/clarguments-reference.html
+++ b/help/help/html/features/clarguments-reference.html
@@ -66,7 +66,15 @@
 
     <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>Run Jalview 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>--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;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;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;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">
@@ -222,7 +244,7 @@
     </tr>
 
     <tr valign="top">
-    <td><code>&#8209;&#8209;title&nbsp;<em>"string""</em></code></td>
+    <td><code>&#8209;&#8209;title&nbsp;<em>"string"</em></code></td>
     <td>Specifies the title for the open alignment window as <em>string</em>.</td>
     <td></td>
     <td align="center">&#x2713;</td>
@@ -230,7 +252,7 @@
 
     <tr valign="top">
     <td><code>&#8209;&#8209;colour&nbsp;<em>name</em></code></td>
-    <td>Applies the colour scheme <em>name</em> to the open alignment window.  Valid values for <em>name</em> are:
+    <td>Applies the colour scheme <em>name</em> to the open alignment window.  Valid values for <em>name</em> include:
     <br/>
     <code>clustal</code>,
     <br/>
@@ -271,6 +293,11 @@
     <code>t-coffee-scores</code>,
     <br/>
     <code>sequence-id</code>.
+    <br/>
+    <br/>
+    Names of user defined schemes will also work, and jalview colour scheme specifications like:
+    <br/>
+	<code>&#8209;&#8209;colour "D,E=red; K,R,H=0022FF; C,c=yellow"</code>
     <td></td>
     <td align="center">&#x2713;</td>
     </tr>
@@ -494,6 +521,8 @@
     <code>phylip</code> (<code>phy</code>),
     <br/>
     <code>jalview</code> (<code>jvp, jar</code>).
+    <br/>
+    To output directly to STDOUT (console output) use the filename <code>-</code> (a single hyphen).  In this case all STDOUT messages will instead go to STDERR.  If no <code>format</code> is supplied then Fasta will be assumed.
     </td>
     <td><code>format=<em>name</em></code></td>
     <td align="center">&#x2713;</td>