X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FdesktopMenu.html;h=1ccbbcfafed99988bcb711ec840a0041ad4d7167;hb=f9e3f75dec30e85fa177f0a5f952616fc677a1fc;hp=374aa9c2cbac0a5486b57479251c4fe7a5e405eb;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git diff --git a/help/html/menus/desktopMenu.html b/help/html/menus/desktopMenu.html index 374aa9c..1ccbbcf 100755 --- a/help/html/menus/desktopMenu.html +++ b/help/html/menus/desktopMenu.html @@ -24,106 +24,122 @@ -

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. -
-

+ 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...
  Opens + 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. +
+