X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FScoreMatrix.java;h=e2aa232fba0f2e2733b69d651f5e5ce328f6a054;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=03b6778cf32828bef78cdbc71423111c633c6f2a;hpb=a442f71fc61f1b8b41cedd2c2fd78a5c5323bafb;p=jalview.git
diff --git a/src/jalview/schemes/ScoreMatrix.java b/src/jalview/schemes/ScoreMatrix.java
index 03b6778..e2aa232 100644
--- a/src/jalview/schemes/ScoreMatrix.java
+++ b/src/jalview/schemes/ScoreMatrix.java
@@ -1,54 +1,173 @@
-package jalview.schemes;
-
-public class ScoreMatrix {
- String name;
- /**
- * reference to integer score matrix
- */
- int[][] matrix;
- /**
- * 0 for Protein Score matrix. 1 for dna score matrix
- */
- int type;
- ScoreMatrix(String name, int[][] matrix, int type) {
- this.matrix=matrix;
- this.type=type;
- }
- public boolean isDNA() {
- return type==1;
- }
- public boolean isProtein() {
- return type==0;
- }
- public int[][] getMatrix() {
- return matrix;
- }
- /**
- *
- * @param A1
- * @param A2
- * @return score for substituting first char in A1 with first char in A2
- */
- public int getPairwiseScore(String A1, String A2)
- {
- return getPairwiseScore(A1.charAt(0),A2.charAt(0));
- }
- public int getPairwiseScore(char c, char d) {
- int pog = 0;
-
- try
- {
- int a = (type==0) ? ResidueProperties.aaIndex[c] : ResidueProperties.nucleotideIndex[c];
- int b = (type==0) ? ResidueProperties.aaIndex[d] : ResidueProperties.nucleotideIndex[d];
-
- pog = matrix[a][b];
- }
- catch (Exception e)
- {
- //System.out.println("Unknown residue in " + A1 + " " + A2);
- }
-
- return pog;
- }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * 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
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see
" : ""); + for (char sym2 = 'A'; sym2 <= 'Z'; sym2++) + { + if (symbols[sym2] >= 0 && symbols[sym2] < symMax) + { + sb.append((html ? " | " : "\t") + sym2 + + (html ? " | " : "")); + } + } + header = false; + sb.append(html ? "
" : "") + sym + (html ? " | " : "")); + for (char sym2 = 'A'; sym2 <= 'Z'; sym2++) + { + if (symbols[sym2] >= 0 && symbols[sym2] < symMax) + { + sb.append((html ? "" : "\t") + + matrix[symbols[sym]][symbols[sym2]] + + (html ? " | " : "")); + } + } + sb.append(html ? "