From ee684c859bd7cddaa517a81cf11e168d4596ddbe Mon Sep 17 00:00:00 2001 From: jprocter Date: Sat, 12 Jun 2010 12:45:52 +0000 Subject: [PATCH] documented the -colour command line argument. --- help/html/features/clarguments.html | 12 +++++++++++- src/jalview/bin/Jalview.java | 1 + 2 files changed, 12 insertions(+), 1 deletion(-) diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html index 9bca344..67fca9b 100644 --- a/help/html/features/clarguments.html +++ b/help/html/features/clarguments.html @@ -41,7 +41,17 @@ 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). diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 64ffd38..fc6d23e 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" -- 1.7.10.2