Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/kmer/OwnershipThread.java @ 68:5028fdace37b

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 16:23:26 -0400
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67:0e9998148a16 68:5028fdace37b
1 package kmer;
2
3 import java.util.ArrayList;
4 import java.util.concurrent.atomic.AtomicInteger;
5
6 import shared.KillSwitch;
7 import shared.Shared;
8 import shared.Tools;
9
10 public class OwnershipThread extends Thread {
11
12 public static void clear(AbstractKmerTable[] tables){
13 process(tables, CLEAR);
14 }
15
16 public static void initialize(AbstractKmerTable[] tables){
17 process(tables, INITIALIZE);
18 }
19
20 private static void process(AbstractKmerTable[] tables, int mode){
21 if(tables.length<2){
22 if(mode==INITIALIZE){
23 for(AbstractKmerTable akt : tables){akt.initializeOwnership();}
24 }else if(mode==CLEAR){
25 for(AbstractKmerTable akt : tables){akt.clearOwnership();}
26 }else{
27 KillSwitch.kill("Bad mode: "+mode);
28 }
29 return;
30 }
31 final int threads=Tools.min(Shared.threads(), tables.length);
32 final AtomicInteger next=new AtomicInteger(0);
33 ArrayList<OwnershipThread> alpt=new ArrayList<OwnershipThread>(threads);
34 for(int i=0; i<threads; i++){alpt.add(new OwnershipThread(tables, mode, next));}
35 for(OwnershipThread pt : alpt){pt.start();}
36
37 for(OwnershipThread pt : alpt){
38 while(pt.getState()!=Thread.State.TERMINATED){
39 try {
40 pt.join();
41 } catch (InterruptedException e) {
42 // TODO Auto-generated catch block
43 e.printStackTrace();
44 }
45 }
46 }
47 }
48
49 public OwnershipThread(AbstractKmerTable[] tables_, int mode_, AtomicInteger next_){
50 tables=tables_;
51 mode=mode_;
52 next=next_;
53 }
54
55 @Override
56 public void run(){
57 for(int i=next.getAndIncrement(); i<tables.length; i=next.getAndIncrement()){
58 if(mode==INITIALIZE){
59 tables[i].initializeOwnership();
60 }else if(mode==CLEAR){
61 tables[i].clearOwnership();
62 }else{
63 KillSwitch.kill("Bad mode: "+mode);
64 }
65 }
66 }
67
68 private final AbstractKmerTable[] tables;
69 private final AtomicInteger next;
70 private final int mode;
71
72 public static final int INITIALIZE=0;
73 public static final int CLEAR=1;
74
75 }