X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2FdesktopMenu.html;h=4098c6763c2656dfc69821cc894aa48248f4ff30;hb=205a4ac63d5d8ffcf5cf8d3556b5aca94f6cce06;hp=40cfff8804e0315995a09fdd6e73a68ab528e79b;hpb=1328521a8b2c123a4b4bc4d85d41738561bf4c2d;p=jalview.git
diff --git a/help/html/menus/desktopMenu.html b/help/html/menus/desktopMenu.html
index 40cfff8..4098c67 100755
--- a/help/html/menus/desktopMenu.html
+++ b/help/html/menus/desktopMenu.html
@@ -1,4 +1,21 @@
+
Desktop Menus
@@ -37,7 +54,7 @@
- Tools
+ Tools
- Preferences
Change the default visual settings for opening new alignment
@@ -49,11 +66,36 @@
- Collect Garbage
Selecting this will initiate the Java Virtual Machine garbage collector, which might help free up some memory... perhaps.
+ - Java Console
+ Toggles the display of a the Jalview Java Console window. This setting will be remembered in your user preferences.
+ - Jalview News
+ Opens the Jalview News dialog box.
- Groovy Console... (only available if groovy is on the classpath)
Open's the Groovy Console for interactive scripting.
+ Vamsas
+ For more details, read the Jalview VAMSAS documentation.
+ When no session is active, the menu provides options for initiating a new VAMSAS session:
+
+ - Connect to
+ Connect to one of the existing sessions available.
+ - New VAMSAS session
+ Initiates a new local VAMSAS session.
+ - Load VAMSAS session...
+ Opens a file browser allowing you to choose a VAMSAS document to import into a new local session.
+
+ When Jalview is joined to a VAMSAS session, the menu contains the following:
+
+ - Session Update
+ Sends alignment data in the Jalview desktop to the VAMSAS session.
+ - Save VAMSAS Session...
+ Saves the current session to a VAMSAS document archive.
+ - Stop VAMSAS Session
+ 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.
+
+
Help