From: jprocter Date: Sat, 12 Jun 2010 12:45:49 +0000 (+0000) Subject: documented the -colour command line argument. X-Git-Tag: Release_2_5_1~8 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=2be644b535dd34da958a831f877cf63d87912b5b;p=jalview.git documented the -colour command line argument. --- diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html index 9bca344..9b527d6 100644 --- a/help/html/features/clarguments.html +++ b/help/html/features/clarguments.html @@ -16,33 +16,55 @@ * * You should have received a copy of the GNU General Public License along with Jalview. If not, see . --> -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"