2 * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
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3 * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.schemes;
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21 public class ScoreMatrix
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26 * reference to integer score matrix
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31 * 0 for Protein Score matrix. 1 for dna score matrix
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35 ScoreMatrix(String name, int[][] matrix, int type)
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37 this.matrix = matrix;
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41 public boolean isDNA()
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46 public boolean isProtein()
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51 public int[][] getMatrix()
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60 * @return score for substituting first char in A1 with first char in A2
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62 public int getPairwiseScore(String A1, String A2)
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64 return getPairwiseScore(A1.charAt(0), A2.charAt(0));
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67 public int getPairwiseScore(char c, char d)
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73 int a = (type == 0) ? ResidueProperties.aaIndex[c]
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74 : ResidueProperties.nucleotideIndex[c];
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75 int b = (type == 0) ? ResidueProperties.aaIndex[d]
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76 : ResidueProperties.nucleotideIndex[d];
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79 } catch (Exception e)
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81 // System.out.println("Unknown residue in " + A1 + " " + A2);
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