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+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+
+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.
+
+
+
+
+