From: Ben Soares <b.soares@dundee.ac.uk>
Date: Sun, 13 Nov 2022 10:50:57 +0000 (+0000)
Subject: JAL-4019 small but important corrections to array order, and X colour
X-Git-Tag: Release_2_11_3_0~23^2~8^2~4^2~7
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=aeaf52866c6d5e82a38cc438a66fa0a4b8b36309

JAL-4019 small but important corrections to array order, and X colour
---

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 2ce3e6d..42d03ec 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -140,7 +140,7 @@ public class ResidueProperties
         { "b", "Not A (G or C or T)" },
         { "h", "Not G (A or C or T)" },
         { "d", "Not C (A or G or T)" },
-        { "v", "Not T (A or G or C" },
+        { "v", "Not T (A or G or C)" },
         { "n", "Unknown" } };
     // "gap" index
     maxNucleotideIndex = namesArray.length;
@@ -350,17 +350,17 @@ public class ResidueProperties
       Color.white, // Gap
   };
 
+  // this colour scheme devised by sduce
   public static final Color[] nucleotideAmbiguity = {
       Color.decode("#f0fff0"), // a
-      Color.decode("#f0fff0"), // g
       Color.decode("#f0fff0"), // c
+      Color.decode("#f0fff0"), // g
       Color.decode("#f0fff0"), // t
       Color.decode("#f0fff0"), // u
       Color.decode("#ffffff"), // i
-      Color.decode("#ffffff"), // x
+      Color.decode("#4f6f6f"), // x
       Color.decode("#CD5C5C"), // r
       Color.decode("#008000"), // y
-      Color.decode("#2f4f4f"), // n
       Color.decode("#4682B4"), // w
       Color.decode("#FF8C00"), // s
       Color.decode("#9ACD32"), // m
@@ -369,6 +369,7 @@ public class ResidueProperties
       Color.decode("#808080"), // h
       Color.decode("#483D8B"), // d
       Color.decode("#b8860b"), // v
+      Color.decode("#2f4f4f"), // n
       Color.white, // Gap
   };