[1586] | 1 | package de.ugoe.cs.autoquest.tasktrees.alignment.algorithms; |
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| 2 | |
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| 3 | import java.util.ArrayList; |
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| 4 | import java.util.logging.Level; |
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| 5 | |
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| 6 | import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.SubstitutionMatrix; |
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| 7 | import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.Constants; |
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| 8 | import de.ugoe.cs.util.console.Console; |
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| 9 | |
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| 10 | public class SmithWaterman implements AlignmentAlgorithm { |
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| 11 | |
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| 12 | /** |
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| 13 | * The first input |
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| 14 | */ |
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| 15 | private int[] input1; |
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| 16 | |
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| 17 | /** |
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| 18 | * The second input String |
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| 19 | */ |
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| 20 | private int[] input2; |
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| 21 | |
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| 22 | /** |
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| 23 | * The lengths of the input |
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| 24 | */ |
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| 25 | private int length1, length2; |
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| 26 | |
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| 27 | /** |
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| 28 | * The score matrix. The true scores should be divided by the normalization |
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| 29 | * factor. |
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| 30 | */ |
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| 31 | private MatrixEntry[][] matrix; |
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| 32 | |
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| 33 | private ArrayList<NumberSequence> alignment; |
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| 34 | |
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| 35 | /** |
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| 36 | * Substitution matrix to calculate scores |
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| 37 | */ |
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| 38 | private SubstitutionMatrix submat; |
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| 39 | |
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[1733] | 40 | @Override |
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| 41 | public void align(NumberSequence input1, NumberSequence input2, |
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| 42 | SubstitutionMatrix submat, float threshold) { |
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| 43 | this.input1 = input1.getSequence(); |
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| 44 | this.input2 = input2.getSequence(); |
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| 45 | length1 = input1.size(); |
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| 46 | length2 = input2.size(); |
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| 47 | this.submat = submat; |
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[1586] | 48 | |
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[1733] | 49 | // System.out.println("Starting SmithWaterman algorithm with a " |
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| 50 | // + submat.getClass() + " Substitution Matrix: " + |
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| 51 | // submat.getClass().getCanonicalName()); |
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| 52 | |
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| 53 | matrix = new MatrixEntry[length1 + 1][length2 + 1]; |
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| 54 | alignment = new ArrayList<NumberSequence>(); |
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| 55 | |
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| 56 | for (int i = 0; i < (length1 + 1); i++) { |
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| 57 | for (int j = 0; j < (length2 + 1); j++) { |
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| 58 | matrix[i][j] = new MatrixEntry(); |
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| 59 | } |
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| 60 | } |
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| 61 | |
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| 62 | buildMatrix(); |
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| 63 | traceback(); |
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| 64 | |
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[1586] | 65 | } |
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| 66 | |
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| 67 | /** |
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| 68 | * Build the score matrix using dynamic programming. |
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| 69 | */ |
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| 70 | private void buildMatrix() { |
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| 71 | if (submat.getGapPenalty() >= 0) { |
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| 72 | throw new Error("Indel score must be negative"); |
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| 73 | } |
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| 74 | |
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| 75 | // it's a gap |
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| 76 | matrix[0][0].setScore(0); |
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| 77 | matrix[0][0].setPrevious(null); // starting point |
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| 78 | |
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| 79 | // the first column |
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[1587] | 80 | for (int j = 1; j < length2; j++) { |
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[1586] | 81 | matrix[0][j].setScore(0); |
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| 82 | matrix[0][j].setPrevious(matrix[0][j - 1]); |
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| 83 | matrix[0][j].setYvalue(input2[j]); |
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| 84 | matrix[0][j].setXvalue(Constants.GAP_SYMBOL); |
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| 85 | } |
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| 86 | // the first row |
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| 87 | |
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[1587] | 88 | for (int j = 1; j < length1; j++) { |
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[1586] | 89 | matrix[j][0].setScore(0); |
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| 90 | matrix[j][0].setPrevious(matrix[j - 1][0]); |
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| 91 | matrix[j][0].setXvalue(input1[j]); |
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| 92 | matrix[j][0].setYvalue(Constants.GAP_SYMBOL); |
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| 93 | } |
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| 94 | |
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| 95 | for (int i = 1; i < length1; i++) { |
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| 96 | |
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| 97 | for (int j = 1; j < length2; j++) { |
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[1733] | 98 | final double diagScore = matrix[i - 1][j - 1].getScore() |
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[1586] | 99 | + similarity(i, j); |
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[1733] | 100 | final double upScore = matrix[i][j - 1].getScore() |
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[1586] | 101 | + submat.getGapPenalty(); |
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[1733] | 102 | final double leftScore = matrix[i - 1][j].getScore() |
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[1586] | 103 | + submat.getGapPenalty(); |
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| 104 | |
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| 105 | matrix[i][j].setScore(Math.max(diagScore, |
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| 106 | Math.max(upScore, Math.max(leftScore, 0)))); |
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| 107 | |
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| 108 | // find the directions that give the maximum scores. |
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| 109 | // TODO: Multiple directions are ignored, we choose the first |
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| 110 | // maximum score |
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| 111 | // True if we had a match |
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| 112 | if (diagScore == matrix[i][j].getScore()) { |
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| 113 | matrix[i][j].setPrevious(matrix[i - 1][j - 1]); |
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| 114 | matrix[i][j].setXvalue(input1[i - 1]); |
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| 115 | matrix[i][j].setYvalue(input2[j - 1]); |
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| 116 | } |
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| 117 | // true if we took an event from sequence x and not from y |
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| 118 | if (leftScore == matrix[i][j].getScore()) { |
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| 119 | matrix[i][j].setXvalue(input1[i - 1]); |
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| 120 | matrix[i][j].setYvalue(Constants.GAP_SYMBOL); |
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| 121 | matrix[i][j].setPrevious(matrix[i - 1][j]); |
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| 122 | } |
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| 123 | // true if we took an event from sequence y and not from x |
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| 124 | if (upScore == matrix[i][j].getScore()) { |
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| 125 | matrix[i][j].setXvalue(Constants.GAP_SYMBOL); |
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| 126 | matrix[i][j].setYvalue(input2[j - 1]); |
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| 127 | matrix[i][j].setPrevious(matrix[i][j - 1]); |
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| 128 | } |
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| 129 | if (0 == matrix[i][j].getScore()) { |
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| 130 | matrix[i][j].setPrevious(matrix[0][0]); |
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| 131 | matrix[i][j].setXvalue(-2); |
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| 132 | matrix[i][j].setYvalue(-2); |
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| 133 | } |
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| 134 | } |
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| 135 | |
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| 136 | // Set the complete score cell |
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| 137 | |
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| 138 | } |
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| 139 | } |
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| 140 | |
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[1733] | 141 | /* |
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| 142 | * (non-Javadoc) |
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| 143 | * |
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| 144 | * @see |
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| 145 | * de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithm |
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| 146 | * #getAlignment() |
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[1586] | 147 | */ |
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[1733] | 148 | @Override |
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| 149 | public ArrayList<NumberSequence> getAlignment() { |
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| 150 | return alignment; |
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[1586] | 151 | } |
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| 152 | |
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| 153 | /* |
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| 154 | * (non-Javadoc) |
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| 155 | * |
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| 156 | * @see |
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| 157 | * de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithm |
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| 158 | * #getAlignmentScore() |
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| 159 | */ |
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| 160 | @Override |
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| 161 | public double getAlignmentScore() { |
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| 162 | return getMaxScore(); |
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| 163 | } |
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| 164 | |
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[1733] | 165 | @Override |
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| 166 | public ArrayList<Match> getMatches() { |
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| 167 | // TODO Auto-generated method stub |
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| 168 | return null; |
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| 169 | } |
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[1586] | 170 | |
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[1733] | 171 | /** |
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| 172 | * Get the maximum value in the score matrix. |
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| 173 | */ |
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| 174 | @Override |
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| 175 | public double getMaxScore() { |
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| 176 | double maxScore = 0; |
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[1586] | 177 | |
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[1733] | 178 | // skip the first row and column |
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| 179 | for (int i = 1; i <= length1; i++) { |
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| 180 | for (int j = 1; j < length2; j++) { |
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| 181 | if (matrix[i][j].getScore() > maxScore) { |
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| 182 | maxScore = matrix[i][j].getScore(); |
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| 183 | } |
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| 184 | } |
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[1586] | 185 | } |
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| 186 | |
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[1733] | 187 | return maxScore; |
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[1586] | 188 | } |
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| 189 | |
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[1733] | 190 | @Override |
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[1586] | 191 | public void printAlignment() { |
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| 192 | MatrixEntry tmp = matrix[length1 + 1][0]; |
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| 193 | String aligned1 = ""; |
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| 194 | String aligned2 = ""; |
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| 195 | int count = 0; |
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| 196 | do { |
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| 197 | String append1 = ""; |
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| 198 | String append2 = ""; |
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| 199 | |
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| 200 | if (tmp.getXvalue() == Constants.GAP_SYMBOL) { |
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| 201 | append1 = " ___"; |
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| 202 | } else { |
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| 203 | append1 = String.format("%5d", tmp.getXvalue()); |
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| 204 | } |
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| 205 | |
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| 206 | if (tmp.getYvalue() == Constants.GAP_SYMBOL) { |
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| 207 | append2 = " ___"; |
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| 208 | } else { |
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| 209 | append2 = String.format("%5d", tmp.getYvalue()); |
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| 210 | } |
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| 211 | if (count != 0) { |
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| 212 | aligned1 = append1 + aligned1; |
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| 213 | aligned2 = append2 + aligned2; |
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| 214 | } |
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| 215 | |
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| 216 | tmp = tmp.getPrevious(); |
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| 217 | count++; |
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| 218 | |
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| 219 | } while (tmp != null); |
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| 220 | System.out.println(aligned1); |
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| 221 | System.out.println(aligned2); |
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| 222 | } |
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| 223 | |
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| 224 | /** |
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| 225 | * print the dynmaic programming matrix |
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| 226 | */ |
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[1733] | 227 | @Override |
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[1586] | 228 | public void printDPMatrix() { |
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| 229 | System.out.print(" "); |
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[1733] | 230 | for (int i = 1; i <= length1; i++) { |
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[1586] | 231 | System.out.format("%5d", input1[i - 1]); |
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[1733] | 232 | } |
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[1586] | 233 | System.out.println(); |
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[1587] | 234 | for (int j = 0; j <= length2; j++) { |
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[1733] | 235 | if (j > 0) { |
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[1586] | 236 | System.out.format("%5d ", input2[j - 1]); |
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[1733] | 237 | } else { |
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[1586] | 238 | System.out.print(" "); |
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| 239 | } |
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[1587] | 240 | for (int i = 0; i <= length1; i++) { |
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[1733] | 241 | System.out.format("%4.1f ", matrix[i][j].getScore()); |
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[1586] | 242 | } |
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| 243 | System.out.println(); |
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| 244 | } |
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| 245 | } |
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| 246 | |
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| 247 | public void setAlignment(ArrayList<NumberSequence> alignment) { |
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| 248 | this.alignment = alignment; |
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| 249 | } |
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| 250 | |
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[1733] | 251 | /** |
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| 252 | * Compute the similarity score of substitution The position of the first |
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| 253 | * character is 1. A position of 0 represents a gap. |
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| 254 | * |
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| 255 | * @param i |
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| 256 | * Position of the character in str1 |
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| 257 | * @param j |
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| 258 | * Position of the character in str2 |
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| 259 | * @return Cost of substitution of the character in str1 by the one in str2 |
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| 260 | */ |
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| 261 | private double similarity(int i, int j) { |
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| 262 | return submat.getScore(input1[i - 1], input2[j - 1]); |
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[1592] | 263 | } |
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| 264 | |
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[1733] | 265 | public void traceback() { |
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| 266 | MatrixEntry tmp = matrix[length1][length2]; |
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| 267 | final int aligned1[] = new int[length1 + length2 + 2]; |
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| 268 | final int aligned2[] = new int[length1 + length2 + 2]; |
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| 269 | int count = 0; |
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| 270 | do { |
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| 271 | if ((length1 + length2 + 2) == count) { |
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| 272 | Console.traceln(Level.WARNING, |
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| 273 | "Traceback longer than both sequences summed up!"); |
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| 274 | break; |
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| 275 | } |
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| 276 | aligned1[count] = tmp.getXvalue(); |
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| 277 | aligned2[count] = tmp.getYvalue(); |
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[1612] | 278 | |
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[1733] | 279 | tmp = tmp.getPrevious(); |
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| 280 | count++; |
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[1612] | 281 | |
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[1733] | 282 | } while (tmp != null); |
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| 283 | count--; |
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| 284 | // reverse order of the alignment |
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| 285 | final int reversed1[] = new int[count]; |
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| 286 | final int reversed2[] = new int[count]; |
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[1612] | 287 | |
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[1733] | 288 | for (int i = count - 1; i > 0; i--) { |
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| 289 | reversed1[reversed1.length - i] = aligned1[i]; |
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| 290 | reversed2[reversed2.length - i] = aligned2[i]; |
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[1612] | 291 | } |
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| 292 | |
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[1733] | 293 | final NumberSequence ns1 = new NumberSequence(reversed1.length); |
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| 294 | final NumberSequence ns2 = new NumberSequence(reversed2.length); |
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| 295 | ns1.setSequence(reversed1); |
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| 296 | ns2.setSequence(reversed2); |
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| 297 | |
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| 298 | alignment.add(ns1); |
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| 299 | alignment.add(ns2); |
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[1612] | 300 | } |
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| 301 | |
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[1586] | 302 | } |
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