-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. - |
- |
|
- -annotations FILE
+
|
- Add precalculated annotations to the alignment. See Annotation File - description. | ||
| - - |
-
+ -colour COLOURSCHEME
|
- ||
|
- -nodisplay
- |
- Run Jalview without User Interface
- |
- 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). | +|
|
- -props FILE
- |
- Use the given Jalview properties file instead
- of users default
+ -annotations FILE/URL
|
+ Add precalculated annotations to the alignment. See Annotation File + description. | |
|
- -tree FILE
+ -tree FILE/URL
|
Load the given newick format tree file onto
the alignment
@@ -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
@@ -87,11 +84,23 @@
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
|
- Add and enable a das server with given
+ 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:' @@ -102,19 +111,33 @@
| -fetchfrom nickname
- |
Query nickname for features for the alignments
+ Query a DAS source called nickname for features for the alignments
and display them
|
|
- -groovy FILE
+ -groovy FILE/URL
|
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/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 |
+ ||
|
-fasta FILE
|