-nodisplay |
- Run Jalview without User Interface. |
+ Run Jalview without User Interface. (automatically disables questionnaire, version and usage stats checks) |
|
+ -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). | |
| @@ -36,79 +63,85 @@ | ||
|
-
+ -tree FILE
|
-
+ Load the given newick format tree file onto
+ the alignment
|
|
|
- -nodisplay
+ -questionnaire URL
|
- Run Jalview without User Interface
+ Queries the given URL for information about
+ any Jalview user questionnaires
|
|
|
- -props FILE
+ -noquestionnaire
|
- Use the given Jalview properties file instead
- of users default
+ Turn off questionnaire check
|
|
|
+ -nousagestats
|
- -tree FILE
+ Turn off google analytics usage tracking
+ |
+ |
|
+ -[no]sortbytree
|
- Load the given newick format tree file onto
- the alignment
+ Enable or disable automatic sorting of associated view when a new tree is displayed
|
|
|
- -features FILE
+ -dasserver nickname=URL
|
- Use the given file to mark features on the
- alignment
+ Add and enable a DAS server with given
+ nickname (alphanumeric or underscores only) for retrieval of features
+ for all alignments
+ Sources that also support the sequence command may be specified by prepending the URL with 'sequence:' + e.g. sequence:http://localdas.somewhere.org/das/source |
|
|
- -questionnaire URL
+ -fetchfrom nickname
|
- Queries the given URL for information about
- any Jalview user questionnaires
+ Query a DAS source called nickname for features for the alignments
+ and display them
|
|
|
- -noquestionnaire
+ -groovy FILE
|
- Turn off questionnaire check
+ Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other
+ arguments have been processed
|
|
|
+ -vdoc VAMSAS DOCUMENT FILE or URL
|
- -dasserver nickname=URL
- |
- Add and enable a das server with given
- nickname (alphanumeric or underscores only) for retrieval of features
- for all alignments
+ Import the given vamsas document into a new session.
New in 2.5 |
|
- -fetchfrom nickname
+ -vsess VAMSAS SESSION URL
|
- Query nickname for features for the alignments
- and display them
+ 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, after all other
+ Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other
arguments have been processed
|