-nodisplay |
- Run Jalview without User Interface. |
+ Run Jalview without User Interface. (automatically disables questionnaire, version and usage stats checks) |
|
- -annotations FILE
+
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- Add precalculated annotations to the alignment. See Annotation File - description. | |
| - - |
-
+ -colour COLOURSCHEME
|
- Set the colourscheme for the alignment. This can be any of + the built-in colourschemes, a name of a predefined colourscheme + (defined in the jalview properties file), or an 'inline' colourscheme + (see the applet's colour parameter for more information). | +
|
- -nodisplay
- |
- Run Jalview without User Interface
+ -annotations FILE
|
+ Add precalculated annotations to the alignment. See Annotation File + description. |
|
-tree FILE
@@ -66,14 +71,6 @@
| ||
|
- -features FILE
- |
- Use the given file to mark features on the
- alignment
- |
- |
|
-questionnaire URL
|
Queries the given URL for information about
@@ -87,6 +84,18 @@
Turn off questionnaire check
|
|
|
+ -nousagestats
+ |
+ Turn off google analytics usage tracking
+ |
+ |
|
+ -[no]sortbytree
+ |
+ Enable or disable automatic sorting of associated view when a new tree is displayed
+ |
+ |
|
-dasserver nickname=URL
@@ -115,6 +124,28 @@
|
||
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+ -vdoc VAMSAS DOCUMENT FILE or URL
+ |
+ Import the given vamsas document into a new session.
+ New in 2.5 |
+ |
|
+ -vsess VAMSAS SESSION URL
+ |
+ Join the given vamsas session
+ If a document was also specified, this will be imported first and then committed as new data from Jalview to the specified session (Experimental - not yet enabled!).New in 2.5 |
+ |
|
+ -groovy FILE
+ |
+ Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other
+ arguments have been processed
+ |
+ |
|
-fasta FILE
|