1 | package de.ugoe.cs.autoquest.tasktrees.alignment.matrix; |
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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.algorithms.AlignmentAlgorithm; |
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7 | import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithmFactory; |
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8 | import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.NumberSequence; |
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9 | import de.ugoe.cs.util.console.Console; |
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10 | |
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11 | public class PairwiseAlignmentGenerator { |
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12 | |
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13 | public static PairwiseAlignmentStorage generate( |
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14 | ArrayList<NumberSequence> numberseqs, |
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15 | ObjectDistanceSubstitionMatrix submat, |
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16 | int threshold) { |
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17 | PairwiseAlignmentStorage alignments = new PairwiseAlignmentStorage( |
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18 | numberseqs.size(), numberseqs.size()); |
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19 | int smithWatermanThreshold = threshold; |
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20 | |
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21 | for (int i = 0; i < numberseqs.size(); i++) { |
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22 | NumberSequence ns1 = numberseqs.get(i); |
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23 | for (int j = 0; j < numberseqs.size(); j++) { |
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24 | NumberSequence ns2 = numberseqs.get(j); |
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25 | |
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26 | if (i != j) { |
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27 | Console.traceln(Level.FINEST,"Aligning sequence " + i + " with sequence " + j); |
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28 | |
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29 | AlignmentAlgorithm aa = AlignmentAlgorithmFactory.create(); |
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30 | aa.align(ns1, ns2, submat, |
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31 | smithWatermanThreshold); |
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32 | alignments.set(i, j, aa); |
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33 | } |
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34 | } |
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35 | } |
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36 | return alignments; |
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37 | } |
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38 | } |
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