Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/fileIO/LoadThread.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 fileIO;
2
3 import java.util.Arrays;
4
5 import shared.Shared;
6 import shared.Tools;
7
8 /**
9 * @author Brian Bushnell
10 * @date Jan 2, 2013
11 *
12 */
13 public class LoadThread<X> extends Thread{
14
15 public static <Y> LoadThread<Y> load(String fname, Class<Y> c){
16 LoadThread<Y> lt=new LoadThread<Y>(fname, c);
17 lt.start();
18 return lt;
19 }
20
21 private LoadThread(String fname_, Class<X> c_){
22 fname=fname_;
23 c=c_;
24 addThread(1);
25 }
26
27 @Override
28 public void run(){
29 addRunningThread(1);
30 output=ReadWrite.read(c, fname, false);
31 addRunningThread(-1);
32 synchronized(this){this.notify();}
33 }
34
35
36 private static final int addThread(int x){
37 final int lim=(Shared.LOW_MEMORY ? 1 : LIMIT);
38 synchronized(activeThreads){
39 assert(x!=0);
40 if(x>0){
41 activeThreads[0]+=x;
42 activeThreads[1]+=x;
43 }else{
44 addRunningThread(x);
45 }
46 assert(activeThreads[0]==(activeThreads[1]+activeThreads[2]) && activeThreads[0]>=0 && activeThreads[1]>=0 &&
47 activeThreads[2]>=0 && activeThreads[2]<=lim) : Arrays.toString(activeThreads);
48
49 return activeThreads[0];
50 }
51 }
52
53 private static final int addRunningThread(int x){
54 final int lim=(Shared.LOW_MEMORY ? 1 : LIMIT);
55 synchronized(activeThreads){
56 assert(x!=0);
57 if(x>0){
58 assert(activeThreads[1]>=x);
59 while(activeThreads[2]>=lim){
60 try {
61 activeThreads.wait();
62 } catch (InterruptedException e) {
63 // TODO Auto-generated catch block
64 e.printStackTrace();
65 }
66 }
67 activeThreads[1]-=x; //Remove from waiting
68 }else{
69 activeThreads[0]+=x; //Remove from active
70 }
71 activeThreads[2]+=x; //Change number running
72
73 assert(activeThreads[0]==(activeThreads[1]+activeThreads[2]) && activeThreads[0]>=0 && activeThreads[1]>=0 &&
74 activeThreads[2]>=0 && activeThreads[2]<=lim) : Arrays.toString(activeThreads);
75
76 if(activeThreads[2]==0 || (activeThreads[2]<lim && activeThreads[1]>0)){activeThreads.notify();}
77 // System.err.println(activeThreads[2]);
78 // try {
79 // activeThreads.wait(5000);
80 // } catch (InterruptedException e) {
81 // // TODO Auto-generated catch block
82 // e.printStackTrace();
83 // }
84 return activeThreads[2];
85 }
86 }
87
88 public static final int countActiveThreads(){
89 final int lim=(Shared.LOW_MEMORY ? 1 : LIMIT);
90 synchronized(activeThreads){
91 assert(activeThreads[0]==(activeThreads[1]+activeThreads[2]) && activeThreads[0]>=0 && activeThreads[1]>=0 &&
92 activeThreads[2]>=0 && activeThreads[2]<=lim) : Arrays.toString(activeThreads);
93 return activeThreads[0];
94 }
95 }
96
97 public static final void waitForReadingToFinish(){
98 final int lim=(Shared.LOW_MEMORY ? 1 : LIMIT);
99 synchronized(activeThreads){
100 while(activeThreads[0]>0){
101 assert(activeThreads[0]==(activeThreads[1]+activeThreads[2]) && activeThreads[0]>=0 && activeThreads[1]>=0 &&
102 activeThreads[2]>=0 && activeThreads[2]<=lim) : Arrays.toString(activeThreads);
103 try {
104 activeThreads.wait(8000);
105 } catch (InterruptedException e) {
106 // TODO Auto-generated catch block
107 e.printStackTrace();
108 }
109 if(activeThreads[2]==0 || (activeThreads[2]<lim && activeThreads[1]>0)){activeThreads.notify();}
110 }
111 }
112 }
113
114 public final void waitForThisToFinish(){
115 if(output==null){
116 while(this.getState()!=State.TERMINATED){
117 try {
118 this.join();
119 } catch (InterruptedException e) {
120 // TODO Auto-generated catch block
121 e.printStackTrace();
122 }
123 }
124 }
125 }
126
127 /** {active, waiting, running} <br>
128 * Active means running or waiting.
129 */
130 public static int[] activeThreads={0, 0, 0};
131
132 private final String fname;
133 private final Class<X> c;
134 public X output=null;
135
136 private static final int[] RUNNING=new int[1];
137 public static int LIMIT=Tools.min(12, Tools.max(Shared.threads(), 1));
138
139 }