JAL-4160 --colour can now take user defined scheme names and colour scheme-spec defin...

[jalview.git] / src / jalview / bin / argparser / Arg.java

diff --git a/src/jalview/bin/argparser/Arg.java b/src/jalview/bin/argparser/Arg.java
index 0d6e3b1..5616953 100644 (file)
--- a/src/jalview/bin/argparser/Arg.java
+++ b/src/jalview/bin/argparser/Arg.java
@@ -80,7 +80,7 @@ public enum Arg
           "Specifies the title for the open alignment window as string.",
           Opt.STRING, Opt.LINKED),
   COLOUR(Type.OPENING, "color", // being a bit soft on the Americans!
-          "Applies the colour scheme to the open alignment window. Valid values are:\n"
+          "Applies the colour scheme to the open alignment window. Valid values include:\n"
                   + "clustal,\n" + "blosum62,\n" + "pc-identity,\n"
                   + "zappo,\n" + "taylor,\n" + "gecos-flower,\n"
                   + "gecos-blossom,\n" + "gecos-sunset,\n"
@@ -89,7 +89,11 @@ public enum Arg
                   + "turn-propensity,\n" + "buried-index,\n"
                   + "nucleotide,\n" + "nucleotide-ambiguity,\n"
                   + "purine-pyrimidine,\n" + "rna-helices,\n"
-                  + "t-coffee-scores,\n" + "sequence-id.",
+                  + "t-coffee-scores,\n" + "sequence-id.\n"
+                  +"\n"
+                  + "Names of user defined colourschemes will also work,\n"
+                 +"and jalview colourscheme specifications like\n"
+                  +"--colour=\"D,E=red; K,R,H=0022FF; C,c=yellow\"",
           Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
   FEATURES(Type.OPENING, "Add a feature file or URL to the open alignment.",
           Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS),