2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.schemes;
20 public class ScoreMatrix
25 * reference to integer score matrix
30 * 0 for Protein Score matrix. 1 for dna score matrix
34 ScoreMatrix(String name, int[][] matrix, int type)
40 public boolean isDNA()
45 public boolean isProtein()
50 public int[][] getMatrix()
59 * @return score for substituting first char in A1 with first char in A2
61 public int getPairwiseScore(String A1, String A2)
63 return getPairwiseScore(A1.charAt(0), A2.charAt(0));
66 public int getPairwiseScore(char c, char d)
72 int a = (type == 0) ? ResidueProperties.aaIndex[c]
73 : ResidueProperties.nucleotideIndex[c];
74 int b = (type == 0) ? ResidueProperties.aaIndex[d]
75 : ResidueProperties.nucleotideIndex[d];
80 // System.out.println("Unknown residue in " + A1 + " " + A2);
87 * pretty print the matrix
89 public String toString()
91 return outputMatrix(false);
94 public String outputMatrix(boolean html)
96 StringBuffer sb = new StringBuffer();
97 int[] symbols = (type == 0) ? ResidueProperties.aaIndex
98 : ResidueProperties.nucleotideIndex;
99 int symMax = (type == 0) ? ResidueProperties.maxProteinIndex
100 : ResidueProperties.maxNucleotideIndex;
101 boolean header = true;
104 sb.append("<table>");
106 for (char sym = 'A'; sym <= 'Z'; sym++)
108 if (symbols[sym] >= 0 && symbols[sym] < symMax)
112 sb.append(html ? "<tr><td></td>" : "");
113 for (char sym2 = 'A'; sym2 <= 'Z'; sym2++)
115 if (symbols[sym2] >= 0 && symbols[sym2] < symMax)
117 sb.append((html ? "<td> " : "\t") + sym2
118 + (html ? " </td>" : ""));
122 sb.append(html ? "</tr>\n" : "\n");
128 sb.append((html ? "<td>" : "") + sym + (html ? "</td>" : ""));
129 for (char sym2 = 'A'; sym2 <= 'Z'; sym2++)
131 if (symbols[sym2] >= 0 && symbols[sym2] < symMax)
133 sb.append((html ? "<td>" : "\t")
134 + matrix[symbols[sym]][symbols[sym2]]
135 + (html ? "</td>" : ""));
138 sb.append(html ? "</tr>\n" : "\n");
143 sb.append("</table>");
145 return sb.toString();