</li>
</ul>
</li>
- <li><strong>Tools </strong>
+ <li><strong>Tools</strong>
<ul>
<li><strong><a href="../features/preferences.html">Preferences<br>
</a></strong><em>Change the default visual settings for opening new alignment
<li><strong>Collect Garbage<br></strong>
<em>Selecting this will initiate the Java Virtual Machine garbage collector, which might help free up some memory... perhaps.
</em></li>
+ <li><strong>Java Console<br/></strong>
+ <em>Toggles the display of a the Jalview Java Console window. This setting will be remembered in your user preferences.</em></li>
<li><strong>Groovy Console...<em> (only available if groovy is on the classpath)</em><br></strong>
<em>Open's the <a href="../groovy.html">Groovy Console</a> for interactive scripting.</em><strong><br></strong></li>
</ul>
</li>
+ <li><strong>Vamsas</strong>
+ <em>For more details, read the <a href="../vamsas/index.html">Jalview VAMSAS documentation</a>.<br/>
+ When no session is active, the menu provides options for initiating a new VAMSAS session:</em>
+ <ul>
+ <li><strong>Connect to<br/></strong>
+ <em>Connect to one of the existing sessions available.</em></li>
+ <li><strong>New VAMSAS session<br/></strong>
+ <em>Initiates a new local VAMSAS session.</em></li>
+ <li><strong>Load VAMSAS session...<br/></strong>
+ <em>Opens a file browser allowing you to choose a VAMSAS document to import into a new local session.</em></li>
+ </ul>
+ <em>When Jalview is joined to a VAMSAS session, the menu contains the following:</em>
+ <ul>
+ <li><strong>Session Update<br/></strong>
+ <em>Sends alignment data in the Jalview desktop to the VAMSAS session.</em></li>
+ <li><strong>Save VAMSAS Session...<br/></strong>
+ <em>Saves the current session to a VAMSAS document archive.</em></li>
+ <li><strong>Stop VAMSAS Session<br/></strong>
+ <em>Disconnects from the current session. You may be asked if you want to save the current session's data if no other VAMSAS clients are connected.</em></li>
+ </ul>
+ </li>
<li><strong>Help </strong>
<ul>
<li><strong>About<br>