[1589] | 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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[1618] | 4 | import java.util.logging.Level; |
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[1589] | 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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[1618] | 9 | import de.ugoe.cs.util.console.Console; |
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[1589] | 10 | |
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| 11 | public class PairwiseAlignmentGenerator { |
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| 12 | |
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[1617] | 13 | public static PairwiseAlignmentStorage generate( |
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| 14 | ArrayList<NumberSequence> numberseqs, |
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[1620] | 15 | ObjectDistanceSubstitionMatrix submat, |
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| 16 | int threshold) { |
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[1617] | 17 | PairwiseAlignmentStorage alignments = new PairwiseAlignmentStorage( |
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| 18 | numberseqs.size(), numberseqs.size()); |
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[1620] | 19 | int smithWatermanThreshold = threshold; |
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[1589] | 20 | |
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[1617] | 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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[1589] | 25 | |
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[1617] | 26 | if (i != j) { |
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[1618] | 27 | Console.traceln(Level.FINEST,"Aligning sequence " + i + " with sequence " + j); |
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[1620] | 28 | |
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[1617] | 29 | AlignmentAlgorithm aa = AlignmentAlgorithmFactory.create(); |
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[1620] | 30 | aa.align(ns1, ns2, submat, |
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[1617] | 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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[1589] | 38 | } |
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