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
|
package kmer;
import java.util.ArrayList;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.concurrent.atomic.AtomicLong;
import fileIO.ByteStreamWriter;
import shared.Shared;
import shared.Tools;
import structures.ByteBuilder;
/**
* @author Brian Bushnell
* @date Nov 16, 2015
*
*/
public class DumpThread extends Thread{
public static boolean dump(final int k, final int mincount, final int maxcount, final AbstractKmerTable[] tables, final ByteStreamWriter bsw, AtomicLong remaining){
final int threads=NUM_THREADS>0 ? NUM_THREADS : Tools.min(tables.length, (Tools.mid(1, Shared.threads()-1, 6)));
final AtomicInteger lock=new AtomicInteger(0);
final ArrayList<DumpThread> list=new ArrayList<DumpThread>(threads);
for(int i=0; i<threads; i++){
list.add(new DumpThread(k, mincount, maxcount, lock, tables, bsw, remaining));
}
for(DumpThread t : list){t.start();}
boolean success=true;
for(DumpThread t : list){
while(t.getState()!=Thread.State.TERMINATED){
try {
t.join();
} catch (InterruptedException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
success&=t.success;
}
return success;
}
public DumpThread(final int k_, final int mincount_, final int maxcount_, final AtomicInteger nextTable_, final AbstractKmerTable[] tables_, final ByteStreamWriter bsw_, final AtomicLong toDump_){
k=k_;
mincount=mincount_;
maxcount=maxcount_;
nextTable=nextTable_;
tables=tables_;
bsw=bsw_;
remaining=toDump_;
}
@Override
public void run(){
final ByteBuilder bb=new ByteBuilder(16300);
for(int i=nextTable.getAndIncrement(); i<tables.length; i=nextTable.getAndIncrement()){
AbstractKmerTable t=tables[i];
t.dumpKmersAsBytes_MT(bsw, bb, k, mincount, maxcount, remaining);
}
if(bb.length()>0){
synchronized(bsw){bsw.addJob(bb);}
}
success=true;
}
final int k;
final int mincount;
final int maxcount;
final AtomicLong remaining;
final AtomicInteger nextTable;
final AbstractKmerTable[] tables;
final ByteStreamWriter bsw;
boolean success=false;
public static int NUM_THREADS=-1;
}
|
