-nodisplay |
- Run Jalview without User Interface. |
+ Run Jalview without User Interface. (automatically disables questionnaire, version and usage stats checks) |
-props FILE |
+ -props FILE/URL |
Use the given Jalview properties file instead
of users default. |
-features FILE |
+ -features FILE/URL |
Use the given file to add sequence features to an alignment. See Features File (Known as Groups file prior to 2.08) 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). | |
|
- -annotations FILE
+ -annotations FILE/URL
|
Add precalculated annotations to the alignment. See Annotation File @@ -36,80 +66,85 @@ | |
|
-
+ -tree FILE/URL
|
-
+ 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
- |
- Load the given newick format tree file onto
- the alignment
+ Turn off google analytics usage tracking
|
|
+ -[no]sortbytree
|
- -features FILE
- |
- Use the given file to mark features on the
- alignment
+ Enable or disable automatic sorting of associated view when a new tree is displayed
|
|
- -questionnaire URL
+ -dasserver nickname=URL
|
- Queries the given URL for information about
- any Jalview user questionnaires
+ 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 |
|
|
- -noquestionnaire
+ -fetchfrom nickname
|
- Turn off questionnaire check
+ Query a DAS source called nickname for features for the alignments
+ and display them
|
|
|
- -dasserver nickname=URL
+ -groovy FILE/URL
|
- Add and enable a das server with given
- nickname (alphanumeric or underscores only) for retrieval of features
- for all alignments
+ Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other
+ arguments have been processed
|
|
|
+ -jabaws URL
+ |
+ Specify the URL of the preferred JABAWS server
+ |
+ |
|
+ -vdoc VAMSAS DOCUMENT FILE/URL
|
- -fetchfrom nickname
- |
- Query nickname for features for the alignments
- and display them
+ Import the given vamsas document into a new session.
New in 2.5 |
|
- -groovy FILE
+ -vsess VAMSAS SESSION URL
|
- Execute groovy script in FILE, after all other
- arguments have been processed
+ 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 |
|
-eps FILE |
Create EPS file FILE from alignment. |
|
-svg FILE |
+ Create Scalable Vector Graphics file FILE from alignment. |
+