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 | //TODO: This is old code used for generating pairwise distances between alignments (to build |
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34 | // a guide tree |
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35 | /* |
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36 | AlignmentAlgorithm sameSequence1 = AlignmentAlgorithmFactory |
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37 | .create(); |
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38 | sameSequence1.align(ns1, ns1, |
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39 | submat, smithWatermanThreshold); |
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40 | AlignmentAlgorithm sameSequence2 = AlignmentAlgorithmFactory |
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41 | .create(); |
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42 | sameSequence2.align(ns2, ns2, |
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43 | submat, smithWatermanThreshold); |
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44 | AlignmentAlgorithm randomSequence = AlignmentAlgorithmFactory |
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45 | .create(); |
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46 | randomSequence.align(ns1.shuffle(), ns2 |
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47 | .shuffle(), submat, |
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48 | smithWatermanThreshold); |
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49 | |
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50 | // Score of the aligmnment |
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51 | double score = alignments.get(i, j).getAlignmentScore(); |
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52 | |
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53 | |
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54 | // Scores of the sequence being aligned to itself (maximum |
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55 | // score) |
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56 | double sSelf1 = sameSequence1.getAlignmentScore(); |
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57 | double sSelf2 = sameSequence2.getAlignmentScore(); |
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58 | // Score of sequences shuffled before aligned |
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59 | double sRand = randomSequence.getAlignmentScore(); |
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60 | |
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61 | double sMax = (sSelf1 + sSelf2) / 2; |
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62 | double sEff = (score - sRand) / (sMax - sRand); |
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63 | if (sEff < 0) { |
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64 | sEff = 0; |
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65 | } |
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66 | double distance = -Math.log(sEff); |
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67 | |
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68 | if (!Double.isInfinite(distance) && !Double.isNaN(distance)) { |
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69 | if (distance < alignments.getDistance(i, j)) { |
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70 | alignments.setDistance(i, j, distance); |
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71 | } |
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72 | } |
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73 | */ |
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74 | } |
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75 | } |
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76 | } |
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77 | return alignments; |
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78 | } |
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79 | } |
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