1 | /* |
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2 | * |
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3 | */ |
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4 | package de.ugoe.cs.autoquest.tasktrees.alignment.algorithms; |
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5 | |
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6 | import java.util.ArrayList; |
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7 | import java.util.logging.Level; |
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8 | |
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9 | import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.SubstitutionMatrix; |
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10 | import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.Constants; |
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11 | import de.ugoe.cs.util.console.Console; |
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12 | |
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13 | // TODO: Auto-generated Javadoc |
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14 | /** |
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15 | * The Class SmithWaterman. |
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16 | */ |
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17 | public class SmithWaterman implements AlignmentAlgorithm { |
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18 | |
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19 | /** The first input. */ |
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20 | private int[] input1; |
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21 | |
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22 | /** The second input String. */ |
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23 | private int[] input2; |
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24 | |
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25 | /** The lengths of the input. */ |
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26 | private int length1, length2; |
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27 | |
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28 | /** |
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29 | * The score matrix. The true scores should be divided by the normalization |
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30 | * factor. |
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31 | */ |
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32 | private MatrixEntry[][] matrix; |
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33 | |
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34 | /** The alignment. */ |
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35 | private ArrayList<NumberSequence> alignment; |
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36 | |
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37 | /** Substitution matrix to calculate scores. */ |
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38 | private SubstitutionMatrix submat; |
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39 | |
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40 | /* (non-Javadoc) |
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41 | * @see de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithm#align(de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.NumberSequence, de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.NumberSequence, de.ugoe.cs.autoquest.tasktrees.alignment.matrix.SubstitutionMatrix, float) |
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42 | */ |
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43 | @Override |
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44 | public void align(NumberSequence input1, NumberSequence input2, |
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45 | SubstitutionMatrix submat, float threshold) { |
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46 | this.input1 = input1.getSequence(); |
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47 | this.input2 = input2.getSequence(); |
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48 | length1 = input1.size(); |
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49 | length2 = input2.size(); |
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50 | this.submat = submat; |
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51 | |
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52 | // System.out.println("Starting SmithWaterman algorithm with a " |
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53 | // + submat.getClass() + " Substitution Matrix: " + |
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54 | // submat.getClass().getCanonicalName()); |
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55 | |
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56 | matrix = new MatrixEntry[length1 + 1][length2 + 1]; |
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57 | alignment = new ArrayList<NumberSequence>(); |
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58 | |
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59 | for (int i = 0; i < (length1 + 1); i++) { |
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60 | for (int j = 0; j < (length2 + 1); j++) { |
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61 | matrix[i][j] = new MatrixEntry(); |
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62 | } |
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63 | } |
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64 | |
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65 | buildMatrix(); |
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66 | traceback(); |
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67 | |
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68 | } |
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69 | |
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70 | /** |
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71 | * Build the score matrix using dynamic programming. |
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72 | */ |
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73 | private void buildMatrix() { |
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74 | if (submat.getGapPenalty() >= 0) { |
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75 | throw new Error("Indel score must be negative"); |
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76 | } |
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77 | |
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78 | // it's a gap |
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79 | matrix[0][0].setScore(0); |
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80 | matrix[0][0].setPrevious(null); // starting point |
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81 | |
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82 | // the first column |
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83 | for (int j = 1; j < length2; j++) { |
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84 | matrix[0][j].setScore(0); |
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85 | matrix[0][j].setPrevious(matrix[0][j - 1]); |
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86 | matrix[0][j].setYvalue(input2[j]); |
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87 | matrix[0][j].setXvalue(Constants.GAP_SYMBOL); |
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88 | } |
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89 | // the first row |
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90 | |
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91 | for (int j = 1; j < length1; j++) { |
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92 | matrix[j][0].setScore(0); |
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93 | matrix[j][0].setPrevious(matrix[j - 1][0]); |
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94 | matrix[j][0].setXvalue(input1[j]); |
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95 | matrix[j][0].setYvalue(Constants.GAP_SYMBOL); |
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96 | } |
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97 | |
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98 | for (int i = 1; i < length1; i++) { |
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99 | |
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100 | for (int j = 1; j < length2; j++) { |
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101 | final double diagScore = matrix[i - 1][j - 1].getScore() |
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102 | + similarity(i, j); |
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103 | final double upScore = matrix[i][j - 1].getScore() |
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104 | + submat.getGapPenalty(); |
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105 | final double leftScore = matrix[i - 1][j].getScore() |
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106 | + submat.getGapPenalty(); |
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107 | |
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108 | matrix[i][j].setScore(Math.max(diagScore, |
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109 | Math.max(upScore, Math.max(leftScore, 0)))); |
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110 | |
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111 | // find the directions that give the maximum scores. |
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112 | // TODO: Multiple directions are ignored, we choose the first |
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113 | // maximum score |
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114 | // True if we had a match |
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115 | if (diagScore == matrix[i][j].getScore()) { |
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116 | matrix[i][j].setPrevious(matrix[i - 1][j - 1]); |
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117 | matrix[i][j].setXvalue(input1[i - 1]); |
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118 | matrix[i][j].setYvalue(input2[j - 1]); |
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119 | } |
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120 | // true if we took an event from sequence x and not from y |
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121 | if (leftScore == matrix[i][j].getScore()) { |
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122 | matrix[i][j].setXvalue(input1[i - 1]); |
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123 | matrix[i][j].setYvalue(Constants.GAP_SYMBOL); |
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124 | matrix[i][j].setPrevious(matrix[i - 1][j]); |
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125 | } |
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126 | // true if we took an event from sequence y and not from x |
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127 | if (upScore == matrix[i][j].getScore()) { |
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128 | matrix[i][j].setXvalue(Constants.GAP_SYMBOL); |
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129 | matrix[i][j].setYvalue(input2[j - 1]); |
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130 | matrix[i][j].setPrevious(matrix[i][j - 1]); |
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131 | } |
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132 | if (0 == matrix[i][j].getScore()) { |
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133 | matrix[i][j].setPrevious(matrix[0][0]); |
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134 | matrix[i][j].setXvalue(-2); |
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135 | matrix[i][j].setYvalue(-2); |
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136 | } |
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137 | } |
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138 | |
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139 | // Set the complete score cell |
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140 | |
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141 | } |
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142 | } |
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143 | |
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144 | /* |
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145 | * (non-Javadoc) |
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146 | * |
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147 | * @see |
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148 | * de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithm |
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149 | * #getAlignment() |
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150 | */ |
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151 | @Override |
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152 | public ArrayList<NumberSequence> getAlignment() { |
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153 | return alignment; |
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154 | } |
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155 | |
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156 | /* |
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157 | * (non-Javadoc) |
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158 | * |
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159 | * @see |
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160 | * de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithm |
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161 | * #getAlignmentScore() |
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162 | */ |
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163 | @Override |
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164 | public double getAlignmentScore() { |
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165 | return getMaxScore(); |
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166 | } |
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167 | |
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168 | /* (non-Javadoc) |
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169 | * @see de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithm#getMatches() |
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170 | */ |
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171 | @Override |
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172 | public ArrayList<Match> getMatches() { |
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173 | // TODO Auto-generated method stub |
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174 | return null; |
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175 | } |
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176 | |
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177 | /** |
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178 | * Get the maximum value in the score matrix. |
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179 | * |
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180 | * @return the max score |
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181 | */ |
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182 | @Override |
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183 | public double getMaxScore() { |
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184 | double maxScore = 0; |
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185 | |
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186 | // skip the first row and column |
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187 | for (int i = 1; i <= length1; i++) { |
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188 | for (int j = 1; j < length2; j++) { |
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189 | if (matrix[i][j].getScore() > maxScore) { |
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190 | maxScore = matrix[i][j].getScore(); |
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191 | } |
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192 | } |
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193 | } |
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194 | |
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195 | return maxScore; |
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196 | } |
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197 | |
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198 | /* (non-Javadoc) |
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199 | * @see de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithm#printAlignment() |
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200 | */ |
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201 | @Override |
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202 | public void printAlignment() { |
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203 | MatrixEntry tmp = matrix[length1 + 1][0]; |
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204 | String aligned1 = ""; |
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205 | String aligned2 = ""; |
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206 | int count = 0; |
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207 | do { |
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208 | String append1 = ""; |
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209 | String append2 = ""; |
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210 | |
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211 | if (tmp.getXvalue() == Constants.GAP_SYMBOL) { |
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212 | append1 = " ___"; |
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213 | } else { |
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214 | append1 = String.format("%5d", tmp.getXvalue()); |
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215 | } |
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216 | |
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217 | if (tmp.getYvalue() == Constants.GAP_SYMBOL) { |
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218 | append2 = " ___"; |
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219 | } else { |
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220 | append2 = String.format("%5d", tmp.getYvalue()); |
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221 | } |
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222 | if (count != 0) { |
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223 | aligned1 = append1 + aligned1; |
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224 | aligned2 = append2 + aligned2; |
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225 | } |
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226 | |
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227 | tmp = tmp.getPrevious(); |
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228 | count++; |
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229 | |
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230 | } while (tmp != null); |
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231 | System.out.println(aligned1); |
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232 | System.out.println(aligned2); |
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233 | } |
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234 | |
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235 | /** |
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236 | * print the dynmaic programming matrix. |
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237 | */ |
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238 | @Override |
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239 | public void printDPMatrix() { |
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240 | System.out.print(" "); |
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241 | for (int i = 1; i <= length1; i++) { |
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242 | System.out.format("%5d", input1[i - 1]); |
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243 | } |
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244 | System.out.println(); |
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245 | for (int j = 0; j <= length2; j++) { |
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246 | if (j > 0) { |
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247 | System.out.format("%5d ", input2[j - 1]); |
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248 | } else { |
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249 | System.out.print(" "); |
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250 | } |
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251 | for (int i = 0; i <= length1; i++) { |
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252 | System.out.format("%4.1f ", matrix[i][j].getScore()); |
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253 | } |
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254 | System.out.println(); |
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255 | } |
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256 | } |
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257 | |
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258 | /** |
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259 | * Sets the alignment. |
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260 | * |
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261 | * @param alignment the new alignment |
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262 | */ |
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263 | public void setAlignment(ArrayList<NumberSequence> alignment) { |
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264 | this.alignment = alignment; |
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265 | } |
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266 | |
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267 | /** |
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268 | * Compute the similarity score of substitution The position of the first |
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269 | * character is 1. A position of 0 represents a gap. |
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270 | * |
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271 | * @param i |
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272 | * Position of the character in str1 |
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273 | * @param j |
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274 | * Position of the character in str2 |
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275 | * @return Cost of substitution of the character in str1 by the one in str2 |
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276 | */ |
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277 | private double similarity(int i, int j) { |
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278 | return submat.getScore(input1[i - 1], input2[j - 1]); |
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279 | } |
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280 | |
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281 | /** |
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282 | * Traceback. |
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283 | */ |
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284 | public void traceback() { |
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285 | MatrixEntry tmp = matrix[length1][length2]; |
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286 | final int aligned1[] = new int[length1 + length2 + 2]; |
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287 | final int aligned2[] = new int[length1 + length2 + 2]; |
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288 | int count = 0; |
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289 | do { |
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290 | if ((length1 + length2 + 2) == count) { |
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291 | Console.traceln(Level.WARNING, |
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292 | "Traceback longer than both sequences summed up!"); |
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293 | break; |
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294 | } |
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295 | aligned1[count] = tmp.getXvalue(); |
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296 | aligned2[count] = tmp.getYvalue(); |
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297 | |
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298 | tmp = tmp.getPrevious(); |
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299 | count++; |
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300 | |
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301 | } while (tmp != null); |
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302 | count--; |
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303 | // reverse order of the alignment |
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304 | final int reversed1[] = new int[count]; |
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305 | final int reversed2[] = new int[count]; |
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306 | |
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307 | for (int i = count - 1; i > 0; i--) { |
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308 | reversed1[reversed1.length - i] = aligned1[i]; |
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309 | reversed2[reversed2.length - i] = aligned2[i]; |
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310 | } |
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311 | |
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312 | final NumberSequence ns1 = new NumberSequence(reversed1.length); |
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313 | final NumberSequence ns2 = new NumberSequence(reversed2.length); |
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314 | ns1.setSequence(reversed1); |
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315 | ns2.setSequence(reversed2); |
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316 | |
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317 | alignment.add(ns1); |
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318 | alignment.add(ns2); |
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319 | } |
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320 | |
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321 | } |
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