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.