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1 package datastructures;
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2
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3 import java.util.Scanner;
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4
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5 import exceptions.ChromosomeFormatException;
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6 import exceptions.ChromosomeNotFoundException;
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7 import exceptions.NullOrNegativeRangeException;
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8 import exceptions.RangeFormatException;
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9 import exceptions.RangeLimitNotFoundException;
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10
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11 /**
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12 * Represents a target Line from the target file.
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13 *
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14 * @author Ali Abdallah
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15 * @version 19.07.2011
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16 * @since Java 1.6
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17 */
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18
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19 public class TargetLine {
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20
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21 String line;
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22 String chrom;
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23 int start, end;
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24
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25 public TargetLine(String line) throws RangeFormatException,
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26 ChromosomeFormatException,
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27 ChromosomeNotFoundException,
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28 RangeLimitNotFoundException,
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29 NullOrNegativeRangeException {
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30 this.line = line;
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31 Scanner s = new Scanner(line);
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32 if(s.hasNext()){
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33 chrom = s.next();
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34 if(!(chrom.toLowerCase().startsWith("chr") || chrom.equals("*")))
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35 throw new ChromosomeFormatException(chrom);
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36 }
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37 else
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38 throw new ChromosomeNotFoundException();
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39
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40 if(s.hasNextInt()){
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41 start = s.nextInt();
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42 if(start < 0){
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43 throw new RangeFormatException("Start position of the target must be a " +
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44 "positive integer.");
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45 }
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46 }
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47 else if(!s.hasNext())
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48 throw new RangeLimitNotFoundException("No target range start found!");
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49 else
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50 throw new RangeFormatException("Target start position" +
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51 " is not an integer. It must be a positive" +
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52 " integer."+ " Found: "+start);
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53
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54 if(s.hasNextInt()){
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55 end = s.nextInt();
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56 if(end < 0){
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57 throw new RangeFormatException("Target end position must be a positive " +
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58 "integer."+ " Found: "+end);
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59 }
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60 }
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61 else if(!s.hasNext())
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62 throw new RangeLimitNotFoundException("No range end found!");
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63 else
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64 throw new RangeFormatException("Found: "+end+". End position ist not an integer. " +
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65 "It must be a positive integer.");
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66
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67 if(start >= end)
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68 throw new NullOrNegativeRangeException("Target line \""+line+"\"");
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69 }
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70
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71 public String chrom(){
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72 return chrom;
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73 }
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74
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75 public int start(){
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76 return start;
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77 }
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78
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79 public int end(){
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80 return end;
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81 }
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82
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83 public String toString(){
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84 return line;
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85 }
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86
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87 }
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