From 1c11be95c0d9372566efe6f7489d33f3c98a0cf4 Mon Sep 17 00:00:00 2001 From: jprocter Date: Thu, 8 Dec 2011 17:14:46 +0000 Subject: [PATCH] JAL-1027 fixed up nucleotide subt matrix so it is symmetric and scores for ambiguity codes properly reflect residue class --- src/jalview/schemes/ResidueProperties.java | 31 +++++++++++++++++----------- 1 file changed, 19 insertions(+), 12 deletions(-) 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 = -- 1.7.10.2