X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FdesktopMenu.html;h=5b06f55a6e1a466b0a394b43a50d8351aa3cb42e;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=e1ef461750fb2663349d686a4d970dedc0aec36e;hpb=8891eedbf7430d8a98edc1cccb32fceac8e3a9bb;p=jalview.git
diff --git a/help/html/menus/desktopMenu.html b/help/html/menus/desktopMenu.html
index e1ef461..5b06f55 100755
--- a/help/html/menus/desktopMenu.html
+++ b/help/html/menus/desktopMenu.html
@@ -1,60 +1,124 @@
-
-Desktop Menu
-
-
-Desktop Menu
-
- - 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 visible
- settings as a Jalview File, with the .jar extension. Each alignment will
- also save the currently active tree associated with the window, if one
- exists.
- - Load Project
- Loads Jalview file formatted alignments 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.
+ - 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.
+
+
+
+
+