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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 public class AnnotationLine implements Comparable<Object>{
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6
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7 String seqName, chrom, gene;
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8 int start, end;
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9
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10 public AnnotationLine(String seqName, String chrom, String gene,
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11 int start, int end){
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12 this.seqName = seqName;
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13 this.chrom = chrom;
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14 this.gene = gene;
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15 this.start = start;
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16 this.end = end;
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17 }
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18
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19 public AnnotationLine(String line){
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20 Scanner s = new Scanner(line);
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21 seqName = s.next();
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22 this.chrom = s.next();
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23 this.start = s.nextInt();
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24 this.end = s.nextInt();
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25 this.gene = s.next();
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26 }
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27
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28 public String seqName() {
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29 return seqName;
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30 }
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31
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32 public String chrom() {
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33 return chrom;
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34 }
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35
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36 public String gene() {
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37 return gene;
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38 }
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39
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40 public int start() {
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41 return start;
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42 }
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43
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44 public int end() {
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45 return end;
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46 }
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47
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48 public static AnnotationLine targetLine(String chrom, int tstart, int tend){
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49 return new AnnotationLine("000\t"+chrom+"\t"+tstart+"\t"+tend+"\tdummy");
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50 }
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51
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52 public int compareTo(Object otherLine) {
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53 AnnotationLine other = (AnnotationLine)otherLine;
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54
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55 if(chrom.compareTo(other.chrom()) < 0
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56 && !other.gene.equals("dummy"))
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57 return -1;
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58 else if(chrom.compareTo(other.chrom()) > 0
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59 && !other.chrom().equals("dummy"))
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60 return 1;
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61 else{
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62 /*
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63 * 1. Eine Region überlappt mit einem Gen, wenn einer der folgenden
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64 * 3 Fälle eintritt:
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65 * a) Targetanfang kleiner als Genanfang und Targetende größer als
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66 * Genende. (Gen ganz im Target enthalten)
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67 * b) Targetanfang liegt zwischen Genanfang und Genende.
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68 * c) Targetende liegt zwischen Genanfang und Genende.
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69 */
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70
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71 // Für Targetsuche
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72 if(this.gene().equals("dummy") &&
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73 this.chrom().equals(other.chrom()) && (
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74 (this.start() <= other.start() && this.end() >= other.end()) ||
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75 (this.start() >= other.start() && this.start() <= other.end()) ||
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76 (this.end() >= other.start() && this.end() <= other.end())
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77 )
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78 )
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79 return 0;
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80 // Für Gensuche zu Insertzwecken.
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81 else if(start < other.start())
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82 return -1;
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83 else if(start > other.start())
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84 return 1;
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85 else{
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86 if(end < other.end())
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87 return -1;
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88 else if(end > other.end())
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89 return 1;
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90 else return 0;
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91 }
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92 }
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93 }
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94
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95 public String toString(){
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96 return seqName +"\t" + chrom + "\t" + start + "\t" + end + "\t" + gene;
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97 }
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98
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99 }
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