2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
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3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
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5 * This file is part of Jalview.
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7 * Jalview is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License
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9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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11 * Jalview is distributed in the hope that it will be useful, but
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12 * WITHOUT ANY WARRANTY; without even the implied warranty
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13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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14 * PURPOSE. See the GNU General Public License for more details.
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16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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18 package jalview.schemes;
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20 public class ScoreMatrix
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25 * reference to integer score matrix
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30 * 0 for Protein Score matrix. 1 for dna score matrix
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34 ScoreMatrix(String name, int[][] matrix, int type)
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36 this.matrix = matrix;
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40 public boolean isDNA()
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45 public boolean isProtein()
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50 public int[][] getMatrix()
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59 * @return score for substituting first char in A1 with first char in A2
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61 public int getPairwiseScore(String A1, String A2)
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63 return getPairwiseScore(A1.charAt(0), A2.charAt(0));
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66 public int getPairwiseScore(char c, char d)
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72 int a = (type == 0) ? ResidueProperties.aaIndex[c]
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73 : ResidueProperties.nucleotideIndex[c];
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74 int b = (type == 0) ? ResidueProperties.aaIndex[d]
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75 : ResidueProperties.nucleotideIndex[d];
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78 } catch (Exception e)
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80 // System.out.println("Unknown residue in " + A1 + " " + A2);
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87 * pretty print the matrix
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89 public String toString()
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91 return outputMatrix(false);
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94 public String outputMatrix(boolean html)
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96 StringBuffer sb = new StringBuffer();
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97 int[] symbols = (type == 0) ? ResidueProperties.aaIndex
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98 : ResidueProperties.nucleotideIndex;
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99 int symMax = (type == 0) ? ResidueProperties.maxProteinIndex
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100 : ResidueProperties.maxNucleotideIndex;
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101 boolean header = true;
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104 sb.append("<table>");
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106 for (char sym = 'A'; sym <= 'Z'; sym++)
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108 if (symbols[sym] >= 0 && symbols[sym] < symMax)
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112 sb.append(html ? "<tr><td></td>" : "");
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113 for (char sym2 = 'A'; sym2 <= 'Z'; sym2++)
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115 if (symbols[sym2] >= 0 && symbols[sym2] < symMax)
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117 sb.append((html ? "<td> " : "\t") + sym2
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118 + (html ? " </td>" : ""));
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122 sb.append(html ? "</tr>\n" : "\n");
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128 sb.append((html ? "<td>" : "") + sym + (html ? "</td>" : ""));
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129 for (char sym2 = 'A'; sym2 <= 'Z'; sym2++)
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131 if (symbols[sym2] >= 0 && symbols[sym2] < symMax)
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133 sb.append((html ? "<td>" : "\t")
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134 + matrix[symbols[sym]][symbols[sym2]]
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135 + (html ? "</td>" : ""));
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138 sb.append(html ? "</tr>\n" : "\n");
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143 sb.append("</table>");
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145 return sb.toString();
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