/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, 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
// extend subt. matrices
}
+ /**
+ * maximum (gap) index for matrices involving protein alphabet
+ */
+ public final static int maxProteinIndex = 23;
+
+ /**
+ * maximum (gap) index for matrices involving nucleotide alphabet
+ */
+ public final static int maxNucleotideIndex = 10;
+
static
{
nucleotideIndex = new int[255];
* 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 }, // -
+ { 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 }, // -
};
/**
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 =