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
89
90
|
package structures;
import shared.Tools;
public class SeqPosM implements Cloneable, Comparable<SeqPosM>{
public SeqPosM(byte[] seq_, int pos_) {this(seq_, pos_, 1);}
public SeqPosM(SeqPosM sp) {this(sp.seq, sp.pos, sp.count, sp.hashcode, sp.gc);}
public SeqPosM(byte[] seq_, int pos_, int count_) {
// synchronized(this) {
Object o=(seq_==null ? this : seq_);
// synchronized(o) {
seq=seq_;
pos=pos_;
count=count_;
hashcode=Tools.hash(seq, 22);
gc=Tools.calcGC(seq);
assert(count>=0);
// }
// }
}
private SeqPosM(byte[] seq_, int pos_, int count_, int code_, float gc_) {
// synchronized(this) {
// synchronized(seq_) {
seq=seq_;
pos=pos_;
count=count_;
hashcode=code_;
assert(count>=0);
gc=gc_;
// }
// }
}
public void setFrom(SeqPos sp) {
// synchronized(sp) {
// synchronized(sp.seq()) {synchronized(this) {
seq=sp.seq();
pos=sp.pos();
count=sp.count;
hashcode=sp.hashcode;
assert(count>=0);
// }}
// }
}
@Override
public boolean equals(Object o) {
return equals((SeqPosM)o);
}
public boolean equals(SeqPosM o) {
if(pos!=o.pos || hashcode!=o.hashcode) {return false;}
return Tools.equals(seq, o.seq);
}
@Override
public int hashCode() {
return hashcode;
}
@Override
public SeqPosM clone() {
try {
return (SeqPosM) super.clone();
} catch (CloneNotSupportedException e) {
throw new RuntimeException(e);
}
}
@Override
public int compareTo(SeqPosM o) {
if(count!=o.count) {return o.count-count;}
if(seq.length!=o.seq.length) {return o.seq.length-seq.length;}
// if(pos!=o.pos) {return o.pos-pos;}
// return Tools.compare(seq, o.seq);//Slow; not needed for deterministic behavior if using a stable sort
return 0;
}
public final byte[] seq() {return seq;}
public final int pos() {return pos;}
public void setPos(int x) {pos=x;}
public byte[] seq;
public int pos;
public int hashcode;
public int count;
public float gc;
}
|
