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
|