Merge branch 'develop' into improvement/JAL-3830_remove_dock_icon_in_headless_mode

[jalview.git] / help / help / html / features / clarguments-reference.html

diff --git a/help/help/html/features/clarguments-reference.html b/help/help/html/features/clarguments-reference.html
index 6b98b7c..dd0bd52 100644 (file)
--- a/help/help/html/features/clarguments-reference.html
+++ b/help/help/html/features/clarguments-reference.html
@@ -98,8 +98,13 @@
     </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">
@@ -124,6 +129,13 @@
 
 <!--
     <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>
@@ -232,7 +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>
@@ -240,7 +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/>
@@ -281,6 +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>