Last change
on this file since 1586 was
1586,
checked in by rkrimmel, 10 years ago
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Adding simple smith waterman and changing alignment algorithm creation to factory pattern
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File size:
1000 bytes
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Line | |
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1 | package de.ugoe.cs.autoquest.tasktrees.alignment.matrix; |
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2 | |
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3 | |
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4 | import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithm; |
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5 | |
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6 | public class BinaryAlignmentStorage { |
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7 | |
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8 | private AlignmentAlgorithm[][] alignments; |
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9 | UPGMAMatrix sequenceDistances; |
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10 | |
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11 | public BinaryAlignmentStorage(int sizex, int sizey) { |
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12 | alignments = new AlignmentAlgorithm[sizex+1][sizey+1]; |
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13 | sequenceDistances = new UPGMAMatrix(Math.max(sizex,sizey)); |
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14 | sequenceDistances.initialize(Double.POSITIVE_INFINITY); |
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15 | } |
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16 | |
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17 | public void set(int i,int j,AlignmentAlgorithm sw) { |
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18 | alignments[i][j] = sw; |
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19 | } |
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20 | |
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21 | public AlignmentAlgorithm get(int i,int j) { |
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22 | return alignments[i][j]; |
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23 | } |
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24 | |
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25 | public void setDistance(int i,int j,double distance) { |
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26 | sequenceDistances.set(i, j, distance); |
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27 | } |
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28 | |
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29 | public double getDistance(int i,int j) { |
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30 | return sequenceDistances.get(i,j); |
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31 | } |
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32 | |
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33 | public UPGMAMatrix getDistanceMatrix() { |
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34 | return sequenceDistances; |
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35 | } |
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36 | } |
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37 | |
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