Jalview Command Line Arguments -

. --> -Jalview Command Line Arguments - +Jalview Command Line Arguments -

The Jalview Executable's Command Line - Arguments

- See running Jalview from the command - line for more information.
- - - - - +

The Jalview Executable's Command Line Arguments

+See +running Jalview from the command line +for more information. +
+

-nodisplay

Run Jalview without User Interface. (automatically disables questionnaire, version and usage stats checks)

+ + + + - - - - - - - + + + + + + - + + + + + + + - + - + @@ -101,38 +127,47 @@ - @@ -144,51 +179,91 @@

Create alignment file FILE in Fasta format.

- - - - - - + + + + + + - - - - - - - - + + + + + + + + - - - - - - - - - - - - + + + + + + + + + + + + - - - - - - - - + + + + + + + + - - - - - - -

+ -nodisplay +	+ Run Jalview without User Interface. + (automatically disables questionnaire, version and usage stats checks) +
-props FILE	Use the given Jalview properties file instead - of users default.
-features FILE	- Use the given file to add sequence features to an alignment. - See Features - File (Known as Groups file prior to 2.08) description. +
+ -props FILE +	+ Use the given Jalview properties file instead + of users default. +
+ -features FILE +	+ + 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 @@ -74,26 +96,30 @@ Turn off questionnaire check
+
-nousagestats	Turn off google analytics usage tracking
- -[no]sortbytree +
+ -[no]sortbytree	- Enable or disable automatic sorting of associated view when a new tree is displayed + 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 - 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:' + 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
-fetchfrom nickname	- Query a DAS source called nickname for features for the alignments - and display them + Query a DAS + source called nickname for features for the alignments and display + them
-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 + 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	- Import the given vamsas document into a new session. New in 2.5 + 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 + 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 + Execute groovy script in FILE (where FILE may + be 'STDIN' to read from the standard input) after all other arguments + have been processed
-clustal FILE	Create alignment file FILE in Clustal format.
-msf FILE
+ -clustal FILE +	+ Create alignment file FILE in Clustal format. +
+ -msf FILE +	Create alignment file FILE in MSF format.
-pileup FILE	Create alignment file FILE in Pileup format.
-pir FILE	+ Create alignment file FILE in MSF format. +
+ -pileup FILE +	+ Create alignment file FILE in Pileup format. +
+ -pir FILE +	Create alignment file FILE in PIR format.
-pfam FILE	Create alignment file FILE in PFAM format.
-blc FILE	Create alignment file FILE in BLC format.
-jalview FILE	+ Create alignment file FILE in PIR format. +
+ -pfam FILE +	+ Create alignment file FILE in PFAM format. +
+ -blc FILE +	+ Create alignment file FILE in BLC format. +
+ -jalview FILE +	Create alignment file FILE in Jalview format.
-png FILE	Create PNG image FILE from alignment.
-imgMap FILE	+ Create alignment file FILE in Jalview format. +
+ -png FILE +	+ Create PNG image FILE from alignment. +
+ -imgMap FILE +	Create HTML file FILE with image map of PNG - image.
-eps FILE	Create EPS file FILE from alignment.

+ +

Create HTML file FILE with image map of PNG + image.

+ + + + +

-eps FILE

+ + +

Create EPS file FILE from alignment.

+ + + diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 04f68f3..b62c83f 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -94,6 +94,7 @@ public class Jalview .println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n" + "-nodisplay\tRun Jalview without User Interface.\n" + "-props FILE\tUse the given Jalview properties file instead of users default.\n" + + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n" + "-annotations FILE\tAdd precalculated annotations to the alignment.\n" + "-tree FILE\tLoad the given newick format tree file onto the alignment\n" + "-features FILE\tUse the given file to mark features on the alignment.\n"