JAL-1027 JAL-1167 documentation and patched DNA/RNA matrix

[jalview.git] / src / jalview / schemes / ResidueProperties.java

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 98b7101..99fc074 100755 (executable)
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -589,15 +589,15 @@ public class ResidueProperties
   // 
   static final int[][] DNA =
   {
-      { 10, -8, -8, -8, -8, 1,  1, -8,  1,  1, 1 }, // C
-      { -8, 10, -8, -8, 10, 1,  1, -8,  1,  1, 1 }, // T
-      { -8, -8, 10, -8, -8, 1,  1,  1, -8,  1, 1 }, // A
-      { -8, -8, -8, 10, -8, 1,  1,  1, -8,  1, 1 }, // G
-      { -8, 10, -8, -8, 10, 1,  1, -8,  1,  1, 1 }, // U
+      { 10, -8, -8, -8, -8, 1,  1,  1, -8,  1, 1 }, // A
+      { -8, 10, -8, -8, -8, 1,  1, -8,  1,  1, 1 }, // C
+      { -8, -8, 10, -8, -8, 1,  1,  1, -8,  1, 1 }, // G
+      { -8, -8, -8, 10, 10, 1,  1, -8,  1,  1, 1 }, // T
+      { -8, -8, -8, 10, 10, 1,  1, -8,  1,  1, 1 }, // U
       {  1,  1,  1,  1,  1, 10, 0,  0,  0,  1, 1 }, // I
       {  1,  1,  1,  1,  1, 0, 10,  0,  0,  1, 1 }, // X
-      { -8, -8,  1,  1, -8, 0,  0, 10,  0,  1, 1 }, // R
-      {  1,  1, -8, -8,  1, 0,  0,  0, 10,  1, 1 }, // Y
+      {  1, -8,  1, -8, -8, 0,  0, 10, -8,  1, 1 }, // R
+      { -8,  1, -8,  1,  1, 0,  0, -8, 10,  1, 1 }, // Y
       {  1,  1,  1,  1,  1, 1,  1,  1,  1, 10, 1 }, // N
       {  1,  1,  1,  1,  1, 1,  1,  1,  1,  1, 1 }, // -
   };