[1311] | 1 | package de.ugoe.cs.autoquest.plugin.alignment; |
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| 2 | |
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| 3 | import java.util.ArrayList; |
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| 4 | import java.util.List; |
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| 5 | |
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| 6 | public class SmithWaterman implements Alignment { |
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| 7 | |
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| 8 | /** |
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| 9 | * The first input |
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| 10 | */ |
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| 11 | private int[] input1; |
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| 12 | |
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| 13 | /** |
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| 14 | * The second input String |
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| 15 | */ |
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| 16 | private int[] input2; |
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| 17 | |
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| 18 | /** |
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| 19 | * The lengths of the input |
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| 20 | */ |
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| 21 | private int length1, length2; |
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| 22 | |
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| 23 | /** |
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| 24 | * The score matrix. The true scores should be divided by the normalization |
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| 25 | * factor. |
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| 26 | */ |
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| 27 | private double[][] score; |
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| 28 | |
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| 29 | /** |
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| 30 | * Score threshold |
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| 31 | */ |
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| 32 | private int scoreThreshold;; |
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| 33 | |
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| 34 | /** |
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| 35 | * The similarity function constants. |
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| 36 | */ |
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| 37 | // static final int MATCH_SCORE = 10; |
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| 38 | // static final int MISMATCH_SCORE = -8; |
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| 39 | // static final int INDEL_SCORE = -9; |
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| 40 | |
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| 41 | /** |
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| 42 | * Constants of directions. Multiple directions are stored by bits. The zero |
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| 43 | * direction is the starting point. |
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| 44 | */ |
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| 45 | static final int DR_LEFT = 1; // 0001 |
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| 46 | static final int DR_UP = 2; // 0010 |
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| 47 | static final int DR_DIAG = 4; // 0100 |
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| 48 | static final int DR_ZERO = 8; // 1000 |
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| 49 | |
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| 50 | /** |
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| 51 | * The directions pointing to the cells that give the maximum score at the |
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| 52 | * current cell. The first index is the column index. The second index is |
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| 53 | * the row index. |
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| 54 | */ |
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| 55 | private int[][] prevCells; |
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| 56 | |
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| 57 | /** |
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| 58 | * Substitution matrix to calculate scores |
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| 59 | */ |
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| 60 | private SubstitutionMatrix submat; |
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| 61 | |
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| 62 | public SmithWaterman(int[] input1, int[] input2, SubstitutionMatrix submat) { |
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| 63 | this.input1 = input1; |
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| 64 | this.input2 = input2; |
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| 65 | length1 = input1.length; |
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| 66 | length2 = input2.length; |
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| 67 | this.submat = submat; |
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| 68 | |
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| 69 | System.out.println("Starting SmithWaterman algorithm with a " |
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| 70 | + submat.getClass() + " Substitution Matrix: " + submat.info()); |
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| 71 | scoreThreshold = 20; |
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| 72 | score = new double[length1 + 1][length2 + 1]; |
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| 73 | prevCells = new int[length1 + 1][length2 + 1]; |
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| 74 | |
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| 75 | buildMatrix(); |
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| 76 | } |
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| 77 | |
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| 78 | /** |
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| 79 | * Compute the similarity score of substitution The position of the first |
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| 80 | * character is 1. A position of 0 represents a gap. |
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| 81 | * |
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| 82 | * @param i |
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| 83 | * Position of the character in str1 |
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| 84 | * @param j |
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| 85 | * Position of the character in str2 |
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| 86 | * @return Cost of substitution of the character in str1 by the one in str2 |
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| 87 | */ |
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| 88 | private double similarity(int i, int j) { |
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| 89 | if (i == 0 || j == 0) { |
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| 90 | // it's a gap (indel) |
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| 91 | return submat.getGapPenalty(); |
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| 92 | } |
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| 93 | // System.out.println("Diag letters: " + input1[i-1] + " " + |
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| 94 | // input2[j-1]); |
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| 95 | // return (input1[i - 1] == input2[j - 1]) ? MATCH_SCORE : |
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| 96 | // MISMATCH_SCORE; |
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| 97 | return submat.getDistance(i - 1, j - 1); |
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| 98 | } |
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| 99 | |
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| 100 | /** |
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| 101 | * Build the score matrix using dynamic programming. Note: The indel scores |
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| 102 | * must be negative. Otherwise, the part handling the first row and column |
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| 103 | * has to be modified. |
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| 104 | */ |
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| 105 | private void buildMatrix() { |
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| 106 | if (submat.getGapPenalty() >= 0) { |
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| 107 | throw new Error("Indel score must be negative"); |
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| 108 | } |
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| 109 | |
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| 110 | int i; // length of prefix substring of str1 |
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| 111 | int j; // length of prefix substring of str2 |
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| 112 | |
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| 113 | // base case |
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| 114 | score[0][0] = 0; |
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| 115 | prevCells[0][0] = DR_ZERO; // starting point |
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| 116 | |
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| 117 | // the first row |
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| 118 | for (i = 1; i <= length1; i++) { |
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| 119 | score[i][0] = 0; |
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| 120 | prevCells[i][0] = DR_ZERO; |
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| 121 | } |
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| 122 | |
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| 123 | // the first column |
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| 124 | for (j = 1; j <= length2; j++) { |
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| 125 | score[0][j] = 0; |
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| 126 | prevCells[0][j] = DR_ZERO; |
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| 127 | } |
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| 128 | |
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| 129 | // the rest of the matrix |
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| 130 | for (i = 1; i <= length1; i++) { |
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| 131 | for (j = 1; j <= length2; j++) { |
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| 132 | double diagScore = score[i - 1][j - 1] + similarity(i, j); |
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| 133 | double upScore = score[i][j - 1] + similarity(0, j); |
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| 134 | double leftScore = score[i - 1][j] + similarity(i, 0); |
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| 135 | |
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| 136 | score[i][j] = Math.max(diagScore, |
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| 137 | Math.max(upScore, Math.max(leftScore, 0))); |
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| 138 | prevCells[i][j] = 0; |
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| 139 | |
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| 140 | // find the directions that give the maximum scores. |
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| 141 | // the bitwise OR operator is used to record multiple |
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| 142 | // directions. |
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| 143 | if (diagScore == score[i][j]) { |
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| 144 | prevCells[i][j] |= DR_DIAG; |
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| 145 | } |
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| 146 | if (leftScore == score[i][j]) { |
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| 147 | prevCells[i][j] |= DR_LEFT; |
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| 148 | } |
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| 149 | if (upScore == score[i][j]) { |
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| 150 | prevCells[i][j] |= DR_UP; |
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| 151 | } |
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| 152 | if (0 == score[i][j]) { |
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| 153 | prevCells[i][j] |= DR_ZERO; |
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| 154 | } |
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| 155 | } |
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| 156 | } |
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| 157 | } |
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| 158 | |
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| 159 | /** |
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| 160 | * Get the maximum value in the score matrix. |
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| 161 | */ |
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| 162 | private double getMaxScore() { |
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| 163 | double maxScore = 0; |
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| 164 | |
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| 165 | // skip the first row and column |
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| 166 | for (int i = 1; i <= length1; i++) { |
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| 167 | for (int j = 1; j <= length2; j++) { |
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| 168 | if (score[i][j] > maxScore) { |
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| 169 | maxScore = score[i][j]; |
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| 170 | } |
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| 171 | } |
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| 172 | } |
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| 173 | |
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| 174 | return maxScore; |
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| 175 | } |
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| 176 | |
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| 177 | /** |
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| 178 | * Get the alignment score between the two input strings. |
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| 179 | */ |
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| 180 | public double getAlignmentScore() { |
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| 181 | return getMaxScore(); |
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| 182 | } |
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| 183 | |
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| 184 | /** |
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| 185 | * TODO: Iterative Version!!! Output the local alignments ending in the (i, |
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| 186 | * j) cell. aligned1 and aligned2 are suffixes of final aligned strings |
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| 187 | * found in backtracking before calling this function. Note: the strings are |
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| 188 | * replicated at each recursive call. Use buffers or stacks to improve |
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| 189 | * efficiency. |
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| 190 | */ |
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| 191 | private void printAlignments(int i, int j, String aligned1, String aligned2) { |
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| 192 | // we've reached the starting point, so print the alignments |
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| 193 | |
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| 194 | if ((prevCells[i][j] & DR_ZERO) > 0) { |
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| 195 | System.out.println(aligned1); |
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| 196 | System.out.println(aligned2); |
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| 197 | System.out.println(); |
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| 198 | |
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| 199 | // Note: we could check other directions for longer alignments |
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| 200 | // with the same score. we don't do it here. |
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| 201 | return; |
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| 202 | } |
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| 203 | |
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| 204 | // find out which directions to backtrack |
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| 205 | if ((prevCells[i][j] & DR_LEFT) > 0) { |
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| 206 | printAlignments(i - 1, j, input1[i - 1] + aligned1, "_ " + aligned2); |
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| 207 | } |
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| 208 | if ((prevCells[i][j] & DR_UP) > 0) { |
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| 209 | printAlignments(i, j - 1, "_ " + aligned1, input2[j - 1] + aligned2); |
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| 210 | } |
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| 211 | if ((prevCells[i][j] & DR_DIAG) > 0) { |
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| 212 | printAlignments(i - 1, j - 1, input1[i - 1] + " " + aligned1, |
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| 213 | input2[j - 1] + " " + aligned2); |
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| 214 | } |
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| 215 | } |
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| 216 | |
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| 217 | /** |
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| 218 | * given the bottom right corner point trace back the top left conrner. at |
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| 219 | * entry: i, j hold bottom right (end of Aligment coords) at return: hold |
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| 220 | * top left (start of Alignment coords) |
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| 221 | */ |
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| 222 | private int[] traceback(int i, int j) { |
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| 223 | |
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| 224 | // find out which directions to backtrack |
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| 225 | while (true) { |
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| 226 | if ((prevCells[i][j] & DR_LEFT) > 0) { |
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| 227 | if (score[i - 1][j] > 0) |
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| 228 | i--; |
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| 229 | else |
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| 230 | break; |
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| 231 | } |
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| 232 | if ((prevCells[i][j] & DR_UP) > 0) { |
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| 233 | // return traceback(i, j-1); |
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| 234 | if (score[i][j - 1] > 0) |
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| 235 | j--; |
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| 236 | else |
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| 237 | break; |
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| 238 | } |
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| 239 | if ((prevCells[i][j] & DR_DIAG) > 0) { |
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| 240 | // return traceback(i-1, j-1); |
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| 241 | if (score[i - 1][j - 1] > 0) { |
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| 242 | i--; |
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| 243 | j--; |
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| 244 | } else |
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| 245 | break; |
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| 246 | } |
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| 247 | } |
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| 248 | int[] m = { i, j }; |
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| 249 | return m; |
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| 250 | } |
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| 251 | |
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| 252 | /** |
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| 253 | * Output the local alignments with the maximum score. |
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| 254 | */ |
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| 255 | public void printAlignments() { |
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| 256 | // find the cell with the maximum score |
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| 257 | double maxScore = getMaxScore(); |
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| 258 | |
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| 259 | /* |
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| 260 | * for (int i = 0; i < matches.length; i++) { |
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| 261 | * System.out.println("Match #" + i + ":" + matches.get(i)); } |
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| 262 | */ |
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| 263 | |
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| 264 | // skip the first row and column |
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| 265 | for (int i = 1; i <= length1; i++) { |
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| 266 | for (int j = 1; j <= length2; j++) { |
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| 267 | if (score[i][j] == maxScore) { |
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| 268 | printAlignments(i, j, "", ""); |
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| 269 | } |
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| 270 | } |
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| 271 | } |
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| 272 | // Note: empty alignments are not printed. |
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| 273 | } |
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| 274 | |
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| 275 | /** |
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| 276 | * print the dynmaic programming matrix |
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| 277 | */ |
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| 278 | public void printDPMatrix() { |
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| 279 | System.out.print(" "); |
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| 280 | for (int j = 1; j <= length2; j++) |
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| 281 | System.out.print(" " + input2[j - 1]); |
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| 282 | System.out.println(); |
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| 283 | for (int i = 0; i <= length1; i++) { |
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| 284 | if (i > 0) |
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| 285 | System.out.print(input1[i - 1] + " "); |
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| 286 | else |
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| 287 | System.out.print(" "); |
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| 288 | for (int j = 0; j <= length2; j++) { |
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| 289 | System.out.print(score[i][j] + " "); |
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| 290 | } |
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| 291 | System.out.println(); |
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| 292 | } |
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| 293 | } |
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| 294 | |
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| 295 | /** |
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| 296 | * Return a set of Matches identified in Dynamic programming matrix. A match |
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| 297 | * is a pair of subsequences whose score is higher than the preset |
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| 298 | * scoreThreshold |
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| 299 | **/ |
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| 300 | public List<Match> getMatches() { |
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| 301 | ArrayList<Match> matchList = new ArrayList(); |
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| 302 | int fA = 0, fB = 0; |
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| 303 | // skip the first row and column, find the next maxScore after |
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| 304 | // prevmaxScore |
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| 305 | for (int i = 1; i <= length1; i++) { |
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| 306 | for (int j = 1; j <= length2; j++) { |
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| 307 | if (score[i][j] > scoreThreshold |
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| 308 | && score[i][j] > score[i - 1][j - 1] |
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| 309 | && score[i][j] > score[i - 1][j] |
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| 310 | && score[i][j] > score[i][j - 1]) { |
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| 311 | if (i == length1 || j == length2 |
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| 312 | || score[i][j] > score[i + 1][j + 1]) { |
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| 313 | // should be lesser than prev maxScore |
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| 314 | fA = i; |
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| 315 | fB = j; |
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| 316 | int[] f = traceback(fA, fB); // sets the x, y to |
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| 317 | // startAlignment |
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| 318 | // coordinates |
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| 319 | System.out.println(f[0] + " " + i + " " + f[1] + " " |
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| 320 | + j + " " + score[i][j]); |
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| 321 | // TODO Add matches to matchList |
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| 322 | } |
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| 323 | } |
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| 324 | } |
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| 325 | } |
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| 326 | return matchList; |
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| 327 | } |
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| 328 | |
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| 329 | } |
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