X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fclarguments.html;fp=help%2Fhtml%2Ffeatures%2Fclarguments.html;h=0000000000000000000000000000000000000000;hb=4f77328104498504339216829abf5ea87e2791ec;hp=fa273a5d1cf58f2dc6632ca1707de0890bfbe52c;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html deleted file mode 100644 index fa273a5..0000000 --- a/help/html/features/clarguments.html +++ /dev/null @@ -1,247 +0,0 @@ - - -Jalview Command Line Arguments - -

- 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)
-props FILE/URL
Use the given Jalview properties - file instead of users default.
-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/URL
- 		Add precalculated annotations to the alignment. See Annotation - File description. -
-
-tree FILE/URL
- 		-
Load the given newick format tree file - onto the alignment
-
-
-questionnaire URL
- 		-
Queries the given URL for information - about any Jalview user questionnaires
-
-
-noquestionnaire
- 		-
Turn off questionnaire check
-
-
-nonews
- 		-
- Disable check for Jalview - news on startup (not recommended other than for classroom / - demo usage) -
-
-
-nousagestats
- 		-
Turn off google analytics usage tracking
-
-
-[no]sortbytree
- 		-
Enable or disable automatic sorting of - associated view when a new tree is displayed
-
-
-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
-
-
-jabaws URL
- 		-
Specify the URL of the preferred JABAWS - server
-
-
-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
- 		-
Create alignment file FILE in Fasta - format.
-
-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 PIR - format.
-pfam FILE
Create alignment file FILE in - PFAM format.
-blc FILE
Create alignment file FILE in BLC - format.
-json FILE
Create alignment file FILE in - JSON format.
-jalview 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.
-svg FILE
Create Scalable Vector Graphics - file FILE from alignment.
-biojsMSA FILE
Write an HTML page to display - the alignment with the - BioJS MSAviewer MSA -
-
- -