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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93 public String outputMatrix(boolean html)
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95 StringBuffer sb=new StringBuffer();
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96 int[] symbols=(type==0) ? ResidueProperties.aaIndex : ResidueProperties.nucleotideIndex;
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97 int symMax = (type==0) ? ResidueProperties.maxProteinIndex :ResidueProperties.maxNucleotideIndex;
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98 boolean header=true;
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101 sb.append("<table>");
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103 for (char sym='A';sym<='Z';sym++)
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105 if (symbols[sym]>=0 && symbols[sym]<symMax)
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108 sb.append(html ? "<tr><td></td>" : "");
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109 for (char sym2='A';sym2<='Z';sym2++)
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111 if (symbols[sym2]>=0 && symbols[sym2]<symMax)
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113 sb.append((html ? "<td> " : "\t")+sym2 +(html ? " </td>": ""));
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117 sb.append(html ? "</tr>\n" : "\n");
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123 sb.append((html ? "<td>" : "")+sym+(html ? "</td>" : ""));
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124 for (char sym2='A';sym2<='Z';sym2++)
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126 if (symbols[sym2]>=0 && symbols[sym2]<symMax)
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128 sb.append((html ? "<td>" : "\t")+matrix[symbols[sym]][symbols[sym2]]+(html ? "</td>" : ""));
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131 sb.append(html ? "</tr>\n" : "\n");
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136 sb.append("</table>");
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138 return sb.toString();
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