Merge branch 'develop' into menard

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

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 300ed34..0ca155a 100755 (executable)
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -98,14 +98,15 @@ public class ResidueProperties
   }
 
   /**
-   * maximum (gap) index for matrices involving protein alphabet 
+   * maximum (gap) index for matrices involving protein alphabet
    */
-  public final static int maxProteinIndex=23;
+  public final static int maxProteinIndex = 23;
+
   /**
-   * maximum (gap) index for matrices involving nucleotide alphabet 
+   * maximum (gap) index for matrices involving nucleotide alphabet
    */
-  public final static int maxNucleotideIndex=10;
-  
+  public final static int maxNucleotideIndex = 10;
+
   static
   {
     nucleotideIndex = new int[255];
@@ -586,22 +587,22 @@ public class ResidueProperties
   // 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, -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 }, // -
+  { 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
+      { 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 }, // -
   };
-/**
+  /**
    * register matrices in list
    */
   static
@@ -609,7 +610,7 @@ 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 =