Last change
on this file since 1570 was
1568,
checked in by rkrimmel, 10 years ago
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Building distance matrix between sequences
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File size:
1.0 KB
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1 | /** |
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2 | * |
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3 | */ |
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4 | package de.ugoe.cs.autoquest.tasktrees.alignment.substitution; |
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5 | |
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6 | import java.util.Collection; |
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7 | import java.util.List; |
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8 | |
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9 | import de.ugoe.cs.autoquest.eventcore.Event; |
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10 | import de.ugoe.cs.autoquest.tasktrees.treeifc.IUserSession; |
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11 | |
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12 | /** |
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13 | * @author Ralph Krimmel |
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14 | * |
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15 | */ |
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16 | public class NearbySubstitutionMatrix implements SubstitutionMatrix { |
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17 | |
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18 | private int[] input1; |
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19 | private int[] input2; |
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20 | private int range; |
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21 | |
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22 | public NearbySubstitutionMatrix(int[] input1,int[] input2, int range) { |
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23 | this.input1 = input1; |
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24 | this.input2 = input2; |
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25 | this.range = range; |
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26 | } |
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27 | |
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28 | /* (non-Javadoc) |
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29 | * @see de.ugoe.cs.autoquest.plugin.alignment.SubstitutionMatrix#getDistance(int, int) |
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30 | */ |
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31 | public double getDistance(int pos1, int pos2) { |
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32 | int difference = Math.abs(input1[pos1]-input2[pos2]); |
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33 | if(difference < range) { |
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34 | return range-difference; |
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35 | } |
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36 | else { |
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37 | return -range; |
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38 | } |
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39 | } |
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40 | |
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41 | |
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42 | @Override |
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43 | public double getGapPenalty() { |
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44 | return -range-1; |
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45 | } |
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46 | |
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47 | |
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48 | @Override |
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49 | public void generate() { |
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50 | // TODO Auto-generated method stub |
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51 | |
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52 | } |
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53 | |
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54 | |
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55 | |
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56 | } |
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