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.