<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
<head>
<title>Desktop Menus</title>
</head>
<li><strong>Load Project</strong><br>
<em>Loads Jalview archives <strong>only</strong>.</em></li>
<li><strong>Quit</strong><br>
- <em>Close Jalview. <br><strong>Note - any annotation you have made on
- alignments will be lost unless you Save your work before quitting.<br></em><br>
- </li>
+ <em>Close Jalview. <br>
+ <strong>Note - any annotation you have made on alignments will be lost
+ unless you Save your work before quitting.</strong></em><br>
+ </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
- windows.</em><strong><br>
- </strong></li>
+ windows.</em></li>
+ <li><strong>Show Memory Usage<br></strong>
+ <em>When ticked, the currently available memory will be displayed in the
+ bottom right of the desktop background area.<br>
+ See the <a href="../memory.html">help on jalview memory settings</a> for more information.</em></li>
+ <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>Jalview News<br/></strong>
+ <em>Opens the <a href="../webServices/newsreader.html">Jalview News</a> dialog box. </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>
git://source.jalview.org / jalview.git / blobdiff