X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FdesktopMenu.html;h=9c41b7e6a4cfe44b33ffac84ea146fe4ae0edc1c;hb=26ce1755b5ec689580d683184f7e2d921143a0ba;hp=1fa861a18c6c6fe507ccda09ce89f9df84f3988b;hpb=72f4770815185305bd18aeeb74f829b1f9ed55c8;p=jalview.git
diff --git a/help/html/menus/desktopMenu.html b/help/html/menus/desktopMenu.html
index 1fa861a..9c41b7e 100755
--- a/help/html/menus/desktopMenu.html
+++ b/help/html/menus/desktopMenu.html
@@ -1,58 +1,146 @@
-
-Desktop Menus
-
-
-Desktop Menus
-
- - File
-
- - Input Alignment from (See more on file
- formats)
-
- - File
- open file(s) on your local file system
- - URL
- open a file from a website. The URL MUST start with http://
- - Textbox
- copy and paste an alignment into a text window
-
-
- - Save Project
- Saves all currently open alignment windows with their current view
- settings and any associated trees, as a Jalview Archive (which has a .jar extension).
- - Load Project
- Loads Jalview archives only.
- - Quit
- Close Jalview. Warning - any annotations you have made on alignments
- will be lost unless you Save your work before quitting.
-
-
-
- - Tools
-
- - Preferences
- Change the default visual settings for opening new alignment
- windows.
-
-
-
- - Help
-
- - About
- Displays the version and creation date of the application,
- as well as acknowledgements and a citation reference.
- - Documentation
- Displays help files as a browseable, searchable set of pages
- with a table of contents.
-
-
-
- - Window
- Each time a new window is added to the Jalview Desktop a new
- menu item will be added to the "Window" menu. If you are working
- with several alignments, trees or other types of windows use the "Window"
- menu to bring your window of choice to the top of the pile if it has been
- hidden by other windows.
-
-
-
+
+
+
+Desktop Menus
+
+
+
+
+ Desktop Menus
+
+
+ - File
+
+ - Input Alignment from (See
+ more on file formats)
+
+
+ - File (Control O)
open
+ file(s) on your local file system
+ - URL
open a file
+ from a website. The URL MUST start with http://
+ - Textbox
copy and
+ paste an alignment into a text window
+
+ - Fetch Sequence
+ Shows a dialog window in which you can select known ids
+ from Uniprot, EMBL, EMBLCDS or PDB database using Web
+ Services provided by the European Bioinformatics Institute.
+ - Save Project
Saves
+ all currently open alignment windows with their current view
+ settings and any associated trees, as a Jalview Archive (which has a .jar extension).
+
+ - Load Project
Loads
+ Jalview archives only.
+
+ - Quit
Close Jalview.
+
Note - any annotation you have
+ made on alignments will be lost unless you Save your work
+ before quitting.
+
+
+ - Tools
+
+ - Preferences
+ Change the default visual settings for opening new
+ alignment windows.
+ - Show Memory Usage
When
+ ticked, the currently available memory will be displayed in
+ the bottom right of the desktop background area.
+ See the help on Jalview memory
+ settings for more information.
+
+ - 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
+
+ - About
+ Displays the version and creation date of the
+ application, as well as acknowledgements and a citation
+ reference.
+ - Documentation
+ Displays help files as a browseable, searchable set of
+ pages with a table of contents.
+
+ - Window
Each time a new
+ window is added to the Jalview Desktop a corresponding menu item
+ will be added to the "Window" menu that will bring the
+ window to the top of the pile when it is selected.
+
+ - Close All
Close all
+ alignment and analysis windows.
+ Note: This will erase all alignments from
+ memory, and cannot be undone!
+ - Raise Associated Windows
+ Bring all windows associated with the current alignment to
+ the top of the pile.
+ - Minimise Associated Windows
+ Hide all windows related to the current alignment behind
+ icons on the Jalview Desktop.
+
+
+
+
+