1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
|
package prok;
import java.util.ArrayList;
import java.util.Arrays;
import dna.AminoAcid;
import gff.GffLine;
import stream.Read;
import structures.IntList;
/**
* Tracks information about a scaffold for AnalyzeGenes.
* @author Brian Bushnell
* @date Sep 24, 2018
*
*/
class ScafData {
/*--------------------------------------------------------------*/
/*---------------- Initialization ----------------*/
/*--------------------------------------------------------------*/
ScafData(Read r){
this(r.id, r.bases, new byte[r.length()]);
}
ScafData(String name_, byte[] bases_, byte[] frames_){
name=name_;
bases=bases_;
frames=frames_;
cdsLines[0]=new ArrayList<GffLine>();
cdsLines[1]=new ArrayList<GffLine>();
rnaLines[0]=new ArrayList<GffLine>();
rnaLines[1]=new ArrayList<GffLine>();
}
/*--------------------------------------------------------------*/
/*---------------- Methods ----------------*/
/*--------------------------------------------------------------*/
void clear(){
Arrays.fill(frames, (byte)0);
starts.clear();
stops.clear();
}
void reverseComplement(){
AminoAcid.reverseComplementBasesInPlace(bases);
strand=1^strand;
}
void addCDS(GffLine gline){
assert(gline.strand>=0) : gline+"\n"+gline.strand;
cdsLines[gline.strand].add(gline);
}
void addRNA(GffLine gline){
assert(gline.strand>=0) : gline+"\n"+gline.strand;
rnaLines[gline.strand].add(gline);
}
byte[] fetch(int start, int stop){
assert(start>=0 && stop<bases.length);
assert(start<stop);
return Arrays.copyOfRange(bases, start, stop+1);
}
int strand(){return strand;}
public int length() {return bases==null ? 0 : bases.length;}
/*--------------------------------------------------------------*/
/*---------------- Fields ----------------*/
/*--------------------------------------------------------------*/
final String name;
final byte[] bases;
final byte[] frames;
final IntList starts=new IntList(8);
final IntList stops=new IntList(8);
private int strand=0;
/** gLines[strand] holds the GffLines for that strand */
@SuppressWarnings("unchecked")
ArrayList<GffLine>[] cdsLines=new ArrayList[2];
@SuppressWarnings("unchecked")
ArrayList<GffLine>[] rnaLines=new ArrayList[2];
}
|
