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
|
package sort;
import java.util.Comparator;
import assemble.Contig;
import shared.Tools;
/**
* Sorts longest contig first
* @author Brian Bushnell
* @date Jul 12, 2018
*
*/
public final class ContigLengthComparator implements Comparator<Contig> {
private ContigLengthComparator(){}
@Override
public int compare(Contig a, Contig b) {
int x=compareInner(a, b);
if(x==0){x=a.coverage>b.coverage ? 1 : a.coverage<b.coverage ? -1 : 0;}
if(x==0){x=compareVectors(a.bases, b.bases);}
if(x==0){x=a.id>b.id ? 1 : a.id<b.id ? -1 : 0;}
return ascending*x;
}
private static int compareInner(Contig a, Contig b) {
if(a==b){return 0;}
if(a==null){return 1;}
if(b==null){return -1;}
int x=a.length()-b.length();
return x;
}
private static int compareVectors(final byte[] a, final byte[] b){
if(a==null || b==null){
if(a==null && b!=null){return 1;}
if(a!=null && b==null){return -1;}
return 0;
}
final int lim=Tools.min(a.length, b.length);
for(int i=0; i<lim; i++){
if(a[i]<b[i]){return -1;}
if(a[i]>b[i]){return 1;}
}
return 0;
}
public static final ContigLengthComparator comparator=new ContigLengthComparator();
private int ascending=-1;
public void setAscending(boolean asc){
ascending=(asc ? 1 : -1);
}
}
|
