<table width="100%" border="1" cellspacing="0" cellpadding="0">
<tr >
<td width="27%"><div align="center">-nodisplay</div></td>
- <td width="73%"><div align="left">Run Jalview without User Interface.</div></td>
+ <td width="73%"><div align="left">Run Jalview without User Interface. (automatically disables questionnaire, version and usage stats checks)</div></td>
</tr>
<tr>
</tr>
<tr>
<td>
- <div align="center"></div>
+ <div align="center">-tree FILE</div>
<td>
- <div align="left"></div>
+ <div align="left">Load the given newick format tree file onto
+ the alignment</div>
</td>
</tr>
<tr>
<td>
- <div align="center">-nodisplay</div>
+ <div align="center">-questionnaire URL</div>
<td>
- <div align="left">Run Jalview without User Interface</div>
+ <div align="left">Queries the given URL for information about
+ any Jalview user questionnaires</div>
</td>
</tr>
<tr>
<td>
- <div align="center">-props FILE</div>
+ <div align="center">-noquestionnaire</div>
<td>
- <div align="left">Use the given Jalview properties file instead
- of users default</div>
+ <div align="left">Turn off questionnaire check</div>
</td>
</tr>
- <tr>
+ <tr><td>
+ <div align="center">-nousagestats</div>
<td>
- <div align="center">-tree FILE</div>
+ <div align="left">Turn off google analytics usage tracking</div>
+ </td>
+ </tr>
+ <tr><td>
+ <div align="center">-[no]sortbytree</div>
<td>
- <div align="left">Load the given newick format tree file onto
- the alignment</div>
+ <div align="left">Enable or disable automatic sorting of associated view when a new tree is displayed</div>
</td>
</tr>
<tr>
<td>
- <div align="center">-features FILE</div>
+ <div align="center">-dasserver nickname=URL</div>
<td>
- <div align="left">Use the given file to mark features on the
- alignment</div>
+ <div align="left">Add and enable a <a href="dassettings.html">DAS server</a> with given
+ nickname (alphanumeric or underscores only) for retrieval of features
+ for all alignments<br>
+ Sources that also support the sequence command may be specified by prepending the URL with 'sequence:'<br>
+ <em>e.g.</em> sequence:http://localdas.somewhere.org/das/source</div>
</td>
</tr>
<tr>
<td>
- <div align="center">-questionnaire URL</div>
+ <div align="center">-fetchfrom nickname</div>
<td>
- <div align="left">Queries the given URL for information about
- any Jalview user questionnaires</div>
+ <div align="left">Query a <a href="dassettings.html">DAS source</a> called nickname for features for the alignments
+ and display them</div>
</td>
</tr>
<tr>
<td>
- <div align="center">-noquestionnaire</div>
+ <div align="center">-groovy FILE</div>
<td>
- <div align="left">Turn off questionnaire check</div>
+ <div align="left">Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other
+ arguments have been processed</div>
</td>
</tr>
<tr>
+ <td>
+ <div align="center">-vdoc VAMSAS DOCUMENT FILE or URL</div>
<td>
- <div align="center">-dasserver nickname=URL</div>
- <td>
- <div align="left">Add and enable a das server with given
- nickname (alphanumeric or underscores only) for retrieval of features
- for all alignments</div>
+ <div align="left">Import the given vamsas document into a new session.<br><em>New in 2.5</em></div>
</td>
</tr>
<tr>
<td>
- <div align="center">-fetchfrom nickname</div>
+ <div align="center">-vsess VAMSAS SESSION URL</div>
<td>
- <div align="left">Query nickname for features for the alignments
- and display them</div>
+ <div align="left">Join the given vamsas session<br>If a document was also specified, this will be imported first and then committed as new data from Jalview to the specified session (Experimental - not yet enabled!).<em>New in 2.5</em></div></div>
</td>
</tr>
<tr>