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JAL-4019 small but important corrections to array order, and X colour
author
Ben Soares
<b.soares@dundee.ac.uk>
Sun, 13 Nov 2022 10:50:57 +0000
(10:50 +0000)
committer
Ben Soares
<b.soares@dundee.ac.uk>
Sun, 13 Nov 2022 10:50:57 +0000
(10:50 +0000)
src/jalview/schemes/ResidueProperties.java
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diff --git
a/src/jalview/schemes/ResidueProperties.java
b/src/jalview/schemes/ResidueProperties.java
index
2ce3e6d
..
42d03ec
100755
(executable)
--- 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)" },
{ "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;
{ "n", "Unknown" } };
// "gap" index
maxNucleotideIndex = namesArray.length;
@@
-350,17
+350,17
@@
public class ResidueProperties
Color.white, // Gap
};
Color.white, // Gap
};
+ // this colour scheme devised by sduce
public static final Color[] nucleotideAmbiguity = {
Color.decode("#f0fff0"), // a
public static final Color[] nucleotideAmbiguity = {
Color.decode("#f0fff0"), // a
- Color.decode("#f0fff0"), // g
Color.decode("#f0fff0"), // c
Color.decode("#f0fff0"), // c
+ Color.decode("#f0fff0"), // g
Color.decode("#f0fff0"), // t
Color.decode("#f0fff0"), // u
Color.decode("#ffffff"), // i
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("#CD5C5C"), // r
Color.decode("#008000"), // y
- Color.decode("#2f4f4f"), // n
Color.decode("#4682B4"), // w
Color.decode("#FF8C00"), // s
Color.decode("#9ACD32"), // m
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("#808080"), // h
Color.decode("#483D8B"), // d
Color.decode("#b8860b"), // v
+ Color.decode("#2f4f4f"), // n
Color.white, // Gap
};
Color.white, // Gap
};