<tr valign="top">
<td><code>‑‑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>‑‑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">
<tr valign="top">
<td><code>‑‑news / ‑‑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>‑‑splash / ‑‑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>‑‑questionnaire / ‑‑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>‑‑usagestats / ‑‑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>‑‑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>‑‑nostartupfile</code></td>
+ <td>Don't show the default startup file.</td>
</tr>
<tr valign="top">
<td><code>‑‑webservicediscovery / ‑‑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">
<td>Stop all output to STDOUT (after the Java Virtual Machine has started). Use <code>‑‑quiet</code> a second time to stop all output to STDERR.</td>
</tr>
+<!--
+ <tr valign="top">
+ <td><code>‑‑P<em>PREFERENCE=VALUE</em></code></td>
+ <td>Set a Jalview preference for this session only. Experimental.</td>
+ </tr>
+-->
+
+<!--
<tr valign="top">
<td><code>‑‑initsubstitutions / ‑‑noinitsubstitutions</code></td>
<td>Set <code>‑‑substitutions</code> to be initially enabled (or initially disabled).</td>
</tr>
+-->
<!--
<tr valign="top">
</tr>
<tr valign="top">
- <td><code>‑‑title <em>"string""</em></code></td>
+ <td><code>‑‑title <em>"string"</em></code></td>
<td>Specifies the title for the open alignment window as <em>string</em>.</td>
<td></td>
<td align="center">✓</td>
<tr valign="top">
<td><code>‑‑colour <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/>
<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>‑‑colour "D,E=red; K,R,H=0022FF; C,c=yellow"</code>
<td></td>
<td align="center">✓</td>
</tr>
<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">✓</td>