From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 8 Dec 2011 17:14:46 +0000 (+0000)
Subject: JAL-1027 fixed up nucleotide subt matrix so it is symmetric and scores for ambiguity... 
X-Git-Tag: Jalview_2_9~463^2~8
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=1c11be95c0d9372566efe6f7489d33f3c98a0cf4;p=jalview.git

JAL-1027 fixed up nucleotide subt matrix so it is symmetric and scores for ambiguity codes properly reflect residue class
---

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index c46c07d..a78a079 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -514,21 +514,27 @@ public class ResidueProperties
    * new Color(60, 136, 238), // U Color.white, // I Color.white, // X
    * Color.white, // R Color.white, // Y Color.white, // N Color.white, // Gap
    */
+
+  // JBPNote: patch matrix for T/U equivalence when working with DNA or RNA.
+  // Will equate sequences if working with mixed nucleotide sets.
+  // treats T and U identically. R and Y weak equivalence with AG and CTU.
+  // N matches any other base weakly
+  // 
   static final int[][] DNA =
   {
-  { 10, -8, -8, -8, 1, 0, 0, 0, 0, 0, 1 }, // C
-      { -8, 10, -8, -8, 1, 0, 0, 0, 0, 0, 1 }, // T
-      { -8, -8, 10, -8, 1, 0, 0, 0, 0, 0, 1 }, // A
-      { -8, -8, -8, 10, 1, 0, 0, 0, 0, 0, 1 }, // G
-      { 1, 1, 1, 1, 10, 0, 0, 0, 0, 0, 1 }, // -
-      { 1, 1, 1, 1, 1, 10, 0, 0, 0, 0, 1 }, // -
-      { 1, 1, 1, 1, 1, 0, 10, 0, 0, 0, 1 }, // -
-      { 1, 1, 1, 1, 1, 0, 0, 10, 0, 0, 1 }, // -
-      { 1, 1, 1, 1, 1, 0, 0, 0, 10, 0, 1 }, // -
-      { 1, 1, 1, 1, 1, 0, 0, 0, 0, 10, 1 }, // -
-      { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 }, // -
+      { 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
+      {  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,  1,  1,  1,  1, 1,  1,  1,  1, 10, 1 }, // N
+      {  1,  1,  1,  1,  1, 1,  1,  1,  1,  1, 1 }, // -
   };
-  /**
+/**
    * register matrices in list
    */
   static
@@ -536,6 +542,7 @@ public class ResidueProperties
     scoreMatrices.put("BLOSUM62", new ScoreMatrix("BLOSUM62", BLOSUM62, 0));
     scoreMatrices.put("PAM250", new ScoreMatrix("PAM250", PAM250, 0));
     scoreMatrices.put("DNA", new ScoreMatrix("DNA", DNA, 1));
+    
   }
 
   public static final Color[] pidColours =