Merge branch 'bug/JAL-4214_system_freeze_when_opening_file_using_gui_in_linux' into...

[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 0221a67..60951d8 100644 (file)
--- a/help/help/html/features/clarguments-reference.html
+++ b/help/help/html/features/clarguments-reference.html
@@ -65,10 +65,10 @@
     <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 / &#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.
+    <td><code>&#8209;&#8209;headless</code></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>--noheadless</code> or <code>--gui</code>.
+    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>
 
@@ -244,7 +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>
@@ -252,7 +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/>
@@ -293,6 +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>
@@ -516,6 +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>