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comparison NGSrich_0.5.5/src/datastructures/TargetLine.java @ 0:89ad0a9cca52 default tip

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author pfrommolt
date Mon, 21 Nov 2011 08:12:19 -0500
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-1:000000000000 0:89ad0a9cca52
1 package datastructures;
2
3 import java.util.Scanner;
4
5 import exceptions.ChromosomeFormatException;
6 import exceptions.ChromosomeNotFoundException;
7 import exceptions.NullOrNegativeRangeException;
8 import exceptions.RangeFormatException;
9 import exceptions.RangeLimitNotFoundException;
10
11 /**
12 * Represents a target Line from the target file.
13 *
14 * @author Ali Abdallah
15 * @version 19.07.2011
16 * @since Java 1.6
17 */
18
19 public class TargetLine {
20
21 String line;
22 String chrom;
23 int start, end;
24
25 public TargetLine(String line) throws RangeFormatException,
26 ChromosomeFormatException,
27 ChromosomeNotFoundException,
28 RangeLimitNotFoundException,
29 NullOrNegativeRangeException {
30 this.line = line;
31 Scanner s = new Scanner(line);
32 if(s.hasNext()){
33 chrom = s.next();
34 if(!(chrom.toLowerCase().startsWith("chr") || chrom.equals("*")))
35 throw new ChromosomeFormatException(chrom);
36 }
37 else
38 throw new ChromosomeNotFoundException();
39
40 if(s.hasNextInt()){
41 start = s.nextInt();
42 if(start < 0){
43 throw new RangeFormatException("Start position of the target must be a " +
44 "positive integer.");
45 }
46 }
47 else if(!s.hasNext())
48 throw new RangeLimitNotFoundException("No target range start found!");
49 else
50 throw new RangeFormatException("Target start position" +
51 " is not an integer. It must be a positive" +
52 " integer."+ " Found: "+start);
53
54 if(s.hasNextInt()){
55 end = s.nextInt();
56 if(end < 0){
57 throw new RangeFormatException("Target end position must be a positive " +
58 "integer."+ " Found: "+end);
59 }
60 }
61 else if(!s.hasNext())
62 throw new RangeLimitNotFoundException("No range end found!");
63 else
64 throw new RangeFormatException("Found: "+end+". End position ist not an integer. " +
65 "It must be a positive integer.");
66
67 if(start >= end)
68 throw new NullOrNegativeRangeException("Target line \""+line+"\"");
69 }
70
71 public String chrom(){
72 return chrom;
73 }
74
75 public int start(){
76 return start;
77 }
78
79 public int end(){
80 return end;
81 }
82
83 public String toString(){
84 return line;
85 }
86
87 }