X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FdesktopMenu.html;h=374aa9c2cbac0a5486b57479251c4fe7a5e405eb;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=7dd7b4084579cf08d46ce7a94691487bb1980bfb;hpb=5a6d8d69732445af2189fc4bab7a09dbd77bb829;p=jalview.git

diff --git a/help/html/menus/desktopMenu.html b/help/html/menus/desktopMenu.html
index 7dd7b40..374aa9c 100755
--- a/help/html/menus/desktopMenu.html
+++ b/help/html/menus/desktopMenu.html
@@ -1,4 +1,24 @@
 <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>
@@ -31,17 +51,52 @@
 		<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>
