From aeaf52866c6d5e82a38cc438a66fa0a4b8b36309 Mon Sep 17 00:00:00 2001 From: Ben Soares Date: Sun, 13 Nov 2022 10:50:57 +0000 Subject: [PATCH] JAL-4019 small but important corrections to array order, and X colour --- src/jalview/schemes/ResidueProperties.java | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) 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 }; -- 1.7.10.2