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.Iterator; |
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8 | import java.util.LinkedList; |
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9 | |
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10 | import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.SubstitutionMatrix; |
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11 | import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.Constants; |
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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 SmithWatermanRepeated. |
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16 | */ |
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17 | public class SmithWatermanRepeated 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 | /** The score threshold. */ |
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38 | private float scoreThreshold; |
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39 | |
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40 | /** Substitution matrix to calculate scores. */ |
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41 | private SubstitutionMatrix submat; |
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42 | |
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43 | /** |
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44 | * Instantiates a new smith waterman repeated. |
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45 | */ |
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46 | public SmithWatermanRepeated() { |
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47 | |
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48 | } |
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49 | |
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50 | /* (non-Javadoc) |
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51 | * @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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52 | */ |
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53 | @Override |
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54 | public void align(NumberSequence input1, NumberSequence input2, |
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55 | SubstitutionMatrix submat, float threshold) { |
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56 | |
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57 | alignment = new ArrayList<NumberSequence>(); |
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58 | alignment.add(input1); |
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59 | alignment.add(input2); |
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60 | |
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61 | this.input1 = input1.getSequence(); |
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62 | this.input2 = input2.getSequence(); |
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63 | |
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64 | length1 = input1.size(); |
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65 | length2 = input2.size(); |
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66 | this.submat = submat; |
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67 | |
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68 | // System.out.println("Starting SmithWaterman algorithm with a " |
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69 | // + submat.getClass() + " Substitution Matrix: " + |
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70 | // submat.getClass().getCanonicalName()); |
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71 | this.scoreThreshold = threshold; |
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72 | |
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73 | matrix = new MatrixEntry[length1 + 2][length2 + 1]; |
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74 | |
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75 | for (int i = 0; i <= (length1 + 1); i++) { |
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76 | for (int j = 0; j <= length2; j++) { |
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77 | matrix[i][j] = new MatrixEntry(); |
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78 | } |
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79 | } |
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80 | |
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81 | // Console.traceln(Level.INFO,"Generating DP Matrix"); |
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82 | buildMatrix(); |
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83 | // Console.traceln(Level.INFO,"Doing traceback"); |
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84 | traceback(); |
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85 | } |
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86 | |
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87 | /** |
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88 | * Build the score matrix using dynamic programming. |
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89 | */ |
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90 | private void buildMatrix() { |
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91 | if (submat.getGapPenalty() >= 0) { |
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92 | throw new Error("Indel score must be negative"); |
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93 | } |
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94 | |
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95 | // it's a gap |
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96 | matrix[0][0].setScore(0); |
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97 | matrix[0][0].setPrevious(null); // starting point |
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98 | matrix[0][0].setXvalue(Constants.UNMATCHED_SYMBOL); |
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99 | matrix[0][0].setYvalue(Constants.UNMATCHED_SYMBOL); |
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100 | |
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101 | // the first column |
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102 | for (int j = 1; j < length2; j++) { |
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103 | matrix[0][j].setScore(0); |
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104 | // We don't need to go back to [0][0] if we reached matrix[0][x], so |
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105 | // just end here |
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106 | // matrix[0][j].setPrevious(matrix[0][j-1]); |
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107 | matrix[0][j].setPrevious(null); |
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108 | } |
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109 | |
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110 | for (int i = 1; i < (length1 + 2); i++) { |
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111 | |
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112 | // Formula for first row: |
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113 | // F(i,0) = max { F(i-1,0), F(i-1,j)-T j=1,...,m |
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114 | |
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115 | final double firstRowLeftScore = matrix[i - 1][0].getScore(); |
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116 | // for sequences of length 1 |
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117 | double tempMax; |
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118 | int maxRowIndex; |
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119 | if (length2 == 1) { |
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120 | tempMax = matrix[i - 1][0].getScore(); |
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121 | maxRowIndex = 0; |
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122 | } else { |
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123 | tempMax = matrix[i - 1][1].getScore(); |
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124 | maxRowIndex = 1; |
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125 | // position of the maximal score of the previous row |
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126 | |
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127 | for (int j = 2; j <= length2; j++) { |
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128 | if (matrix[i - 1][j].getScore() > tempMax) { |
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129 | tempMax = matrix[i - 1][j].getScore(); |
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130 | maxRowIndex = j; |
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131 | } |
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132 | } |
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133 | |
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134 | } |
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135 | |
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136 | tempMax -= scoreThreshold; |
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137 | matrix[i][0].setScore(Math.max(firstRowLeftScore, tempMax)); |
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138 | if (tempMax == matrix[i][0].getScore()) { |
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139 | matrix[i][0].setPrevious(matrix[i - 1][maxRowIndex]); |
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140 | } |
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141 | |
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142 | if (firstRowLeftScore == matrix[i][0].getScore()) { |
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143 | matrix[i][0].setPrevious(matrix[i - 1][0]); |
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144 | } |
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145 | |
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146 | // The last additional score is not related to a character in the |
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147 | // input sequence, it's the total score. Therefore we don't need to |
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148 | // save something for it |
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149 | // and can end here |
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150 | if (i < (length1 + 1)) { |
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151 | matrix[i][0].setXvalue(input1[i - 1]); |
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152 | matrix[i][0].setYvalue(Constants.UNMATCHED_SYMBOL); |
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153 | } else { |
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154 | return; |
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155 | } |
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156 | |
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157 | for (int j = 1; j <= length2; j++) { |
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158 | final double diagScore = matrix[i - 1][j - 1].getScore() |
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159 | + similarity(i, j); |
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160 | final double upScore = matrix[i][j - 1].getScore() |
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161 | + submat.getGapPenalty(); |
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162 | final double leftScore = matrix[i - 1][j].getScore() |
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163 | + submat.getGapPenalty(); |
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164 | |
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165 | matrix[i][j].setScore(Math.max( |
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166 | diagScore, |
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167 | Math.max(upScore, |
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168 | Math.max(leftScore, matrix[i][0].getScore())))); |
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169 | |
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170 | // find the directions that give the maximum scores. |
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171 | // TODO: Multiple directions are ignored, we choose the first |
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172 | // maximum score |
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173 | // True if we had a match |
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174 | if (diagScore == matrix[i][j].getScore()) { |
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175 | matrix[i][j].setPrevious(matrix[i - 1][j - 1]); |
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176 | matrix[i][j].setXvalue(input1[i - 1]); |
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177 | matrix[i][j].setYvalue(input2[j - 1]); |
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178 | } |
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179 | // true if we took an event from sequence x and not from y |
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180 | if (leftScore == matrix[i][j].getScore()) { |
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181 | matrix[i][j].setXvalue(input1[i - 1]); |
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182 | matrix[i][j].setYvalue(Constants.GAP_SYMBOL); |
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183 | matrix[i][j].setPrevious(matrix[i - 1][j]); |
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184 | } |
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185 | // true if we took an event from sequence y and not from x |
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186 | if (upScore == matrix[i][j].getScore()) { |
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187 | matrix[i][j].setXvalue(Constants.GAP_SYMBOL); |
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188 | matrix[i][j].setYvalue(input2[j - 1]); |
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189 | matrix[i][j].setPrevious(matrix[i][j - 1]); |
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190 | } |
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191 | // true if we ended a matching region |
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192 | if (matrix[i][0].getScore() == matrix[i][j].getScore()) { |
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193 | matrix[i][j].setPrevious(matrix[i][0]); |
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194 | matrix[i][j].setXvalue(input1[i - 1]); |
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195 | matrix[i][j].setYvalue(Constants.UNMATCHED_SYMBOL); |
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196 | } |
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197 | } |
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198 | |
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199 | // Set the complete score cell |
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200 | |
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201 | } |
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202 | } |
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203 | |
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204 | /* |
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205 | * (non-Javadoc) |
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206 | * |
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207 | * @see |
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208 | * de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithm |
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209 | * #getAlignment() |
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210 | */ |
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211 | @Override |
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212 | public ArrayList<NumberSequence> getAlignment() { |
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213 | return alignment; |
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214 | } |
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215 | |
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216 | /* |
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217 | * (non-Javadoc) |
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218 | * |
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219 | * @see |
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220 | * de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithm |
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221 | * #getAlignmentScore() |
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222 | */ |
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223 | @Override |
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224 | public double getAlignmentScore() { |
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225 | return matrix[length1 + 1][0].getScore(); |
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226 | } |
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227 | |
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228 | /* (non-Javadoc) |
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229 | * @see de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithm#getMatches() |
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230 | */ |
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231 | @Override |
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232 | public ArrayList<Match> getMatches() { |
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233 | final ArrayList<Match> result = new ArrayList<Match>(); |
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234 | |
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235 | // both alignment sequences should be equally long |
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236 | int i = 0; |
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237 | final int[] seq1 = alignment.get(0).getSequence(); |
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238 | final int[] seq2 = alignment.get(1).getSequence(); |
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239 | int start = 0; |
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240 | while (i < seq1.length) { |
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241 | if (seq2[i] != Constants.UNMATCHED_SYMBOL) { |
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242 | start = i; |
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243 | int count = 0; |
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244 | while ((i < seq2.length) |
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245 | && (seq2[i] != Constants.UNMATCHED_SYMBOL)) { |
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246 | i++; |
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247 | count++; |
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248 | } |
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249 | // I am really missing memcpy here? How does one do this better |
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250 | // in java? |
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251 | final int[] tmp1 = new int[count]; |
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252 | final int[] tmp2 = new int[count]; |
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253 | for (int j = 0; j < count; j++) { |
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254 | tmp1[j] = seq1[start + j]; |
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255 | tmp2[j] = seq2[start + j]; |
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256 | } |
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257 | final NumberSequence tmpns1 = new NumberSequence(count); |
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258 | final NumberSequence tmpns2 = new NumberSequence(count); |
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259 | tmpns1.setSequence(tmp1); |
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260 | tmpns2.setSequence(tmp2); |
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261 | final Match tmpal = new Match(); |
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262 | tmpal.setFirstSequence(tmpns1); |
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263 | tmpal.setSecondSequence(tmpns2); |
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264 | // tmpal.addOccurence(new |
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265 | // MatchOccurence(start,alignment.get(0).getId())); |
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266 | // tmpal.addOccurence(new |
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267 | // MatchOccurence(start,alignment.get(1).getId())); |
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268 | result.add(tmpal); |
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269 | } |
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270 | i++; |
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271 | } |
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272 | return result; |
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273 | } |
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274 | |
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275 | /** |
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276 | * Get the maximum value in the score matrix. |
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277 | * |
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278 | * @return the max score |
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279 | */ |
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280 | @Override |
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281 | public double getMaxScore() { |
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282 | double maxScore = 0; |
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283 | |
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284 | // skip the first row and column |
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285 | for (int i = 1; i <= length1; i++) { |
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286 | for (int j = 1; j <= length2; j++) { |
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287 | if (matrix[i][j].getScore() > maxScore) { |
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288 | maxScore = matrix[i][j].getScore(); |
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289 | } |
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290 | } |
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291 | } |
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292 | |
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293 | return maxScore; |
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294 | } |
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295 | |
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296 | /* (non-Javadoc) |
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297 | * @see de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithm#printAlignment() |
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298 | */ |
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299 | @Override |
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300 | public void printAlignment() { |
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301 | final int[] tmp1 = alignment.get(0).getSequence(); |
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302 | final int[] tmp2 = alignment.get(1).getSequence(); |
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303 | for (int i = 0; i < tmp1.length; i++) { |
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304 | if (tmp1[i] == Constants.GAP_SYMBOL) { |
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305 | System.out.print(" ___"); |
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306 | } else if (tmp1[i] == Constants.UNMATCHED_SYMBOL) { |
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307 | System.out.print(" ..."); |
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308 | } else { |
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309 | System.out.format("%5d", tmp1[i]); |
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310 | } |
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311 | |
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312 | } |
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313 | System.out.println(); |
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314 | for (int i = 0; i < tmp2.length; i++) { |
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315 | if (tmp2[i] == Constants.GAP_SYMBOL) { |
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316 | System.out.print(" ___"); |
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317 | } else if (tmp2[i] == Constants.UNMATCHED_SYMBOL) { |
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318 | System.out.print(" ..."); |
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319 | } else { |
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320 | System.out.format("%5d", tmp2[i]); |
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321 | } |
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322 | |
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323 | } |
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324 | System.out.println(); |
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325 | |
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326 | } |
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327 | |
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328 | /** |
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329 | * print the dynmaic programming matrix. |
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330 | */ |
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331 | @Override |
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332 | public void printDPMatrix() { |
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333 | System.out.print(" "); |
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334 | for (int i = 1; i <= length1; i++) { |
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335 | System.out.format("%5d", input1[i - 1]); |
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336 | } |
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337 | System.out.println(); |
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338 | for (int j = 0; j <= length2; j++) { |
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339 | if (j > 0) { |
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340 | System.out.format("%5d ", input2[j - 1]); |
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341 | } else { |
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342 | System.out.print(" "); |
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343 | } |
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344 | for (int i = 0; i <= (length1 + 1); i++) { |
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345 | if ((i < (length1 + 1)) || ((i == (length1 + 1)) && (j == 0))) { |
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346 | System.out.format("%4.1f ", matrix[i][j].getScore()); |
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347 | } |
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348 | |
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349 | } |
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350 | System.out.println(); |
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351 | } |
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352 | } |
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353 | |
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354 | /** |
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355 | * Sets the alignment. |
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356 | * |
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357 | * @param alignment the new alignment |
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358 | */ |
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359 | public void setAlignment(ArrayList<NumberSequence> alignment) { |
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360 | this.alignment = alignment; |
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361 | } |
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362 | |
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363 | /** |
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364 | * Compute the similarity score of substitution The position of the first |
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365 | * character is 1. A position of 0 represents a gap. |
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366 | * |
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367 | * @param i |
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368 | * Position of the character in str1 |
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369 | * @param j |
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370 | * Position of the character in str2 |
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371 | * @return Cost of substitution of the character in str1 by the one in str2 |
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372 | */ |
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373 | private double similarity(int i, int j) { |
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374 | return submat.getScore(input1[i - 1], input2[j - 1]); |
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375 | } |
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376 | |
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377 | /** |
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378 | * Traceback. |
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379 | */ |
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380 | public void traceback() { |
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381 | MatrixEntry tmp = matrix[length1 + 1][0].getPrevious(); |
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382 | final LinkedList<Integer> aligned1 = new LinkedList<Integer>(); |
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383 | final LinkedList<Integer> aligned2 = new LinkedList<Integer>(); |
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384 | while (tmp.getPrevious() != null) { |
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385 | |
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386 | aligned1.add(new Integer(tmp.getXvalue())); |
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387 | aligned2.add(new Integer(tmp.getYvalue())); |
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388 | |
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389 | tmp = tmp.getPrevious(); |
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390 | } |
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391 | |
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392 | // reverse order of the alignment |
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393 | final int reversed1[] = new int[aligned1.size()]; |
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394 | final int reversed2[] = new int[aligned2.size()]; |
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395 | |
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396 | int count = 0; |
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397 | for (final Iterator<Integer> it = aligned1.iterator(); it.hasNext();) { |
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398 | count++; |
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399 | reversed1[reversed1.length - count] = it.next(); |
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400 | |
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401 | } |
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402 | count = 0; |
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403 | for (final Iterator<Integer> it = aligned2.iterator(); it.hasNext();) { |
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404 | count++; |
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405 | reversed2[reversed2.length - count] = it.next(); |
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406 | } |
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407 | |
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408 | final NumberSequence ns1 = new NumberSequence(reversed1.length); |
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409 | final NumberSequence ns2 = new NumberSequence(reversed2.length); |
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410 | ns1.setSequence(reversed1); |
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411 | ns2.setSequence(reversed2); |
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412 | ns1.setId(alignment.get(0).getId()); |
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413 | ns2.setId(alignment.get(1).getId()); |
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414 | |
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415 | alignment.set(0, ns1); |
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416 | alignment.set(1, ns2); |
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417 | } |
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418 | |
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419 | } |
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