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1 package kmer;
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2
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3 import java.util.concurrent.atomic.AtomicInteger;
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4
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5 import shared.Shared;
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6 import shared.Tools;
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7 import structures.SuperLongList;
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8
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9 public final class HistogramMaker {
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10
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11
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12 public static long[] fillHistogram(final AbstractKmerTable[] tables, final int histMax) {
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13 if(Shared.threads()>2){
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14 return fillHistogram_MT(tables, histMax);
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15 }else{
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16 return fillHistogram_ST(tables, histMax);
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17 }
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18 }
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19
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20 private static long[] fillHistogram_ST(final AbstractKmerTable[] tables, final int histMax) {
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21 long[] ca=new long[histMax+1];
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22 for(AbstractKmerTable set : tables){
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23 set.fillHistogram(ca, histMax);
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24 }
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25 return ca;
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26 }
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27
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28 private static long[] fillHistogram_MT(final AbstractKmerTable[] tables, final int histMax) {
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29 boolean errorState=false;
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30 int threads=Shared.threads();
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31 threads=Tools.min((threads>20 ? threads/2 : threads), (tables.length+1)/2, 32);
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32 if(threads<2){return fillHistogram_ST(tables, histMax);}
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33
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34 final FillThread[] array=new FillThread[threads];
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35 final AtomicInteger next=new AtomicInteger(0);
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36 for(int i=0; i<threads; i++){array[i]=new FillThread(tables, histMax, next);}
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37 for(int i=0; i<threads; i++){array[i].start();}
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38
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39 //Wait for completion of all threads
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40 final long[] ca=new long[histMax+1];
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41 boolean success=true;
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42 for(FillThread pt : array){
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43
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44 //Wait until this thread has terminated
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45 while(pt.getState()!=Thread.State.TERMINATED){
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46 try {
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47 //Attempt a join operation
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48 pt.join();
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49 } catch (InterruptedException e) {
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50 //Potentially handle this, if it is expected to occur
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51 e.printStackTrace();
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52 }
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53 }
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54
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55 //Accumulate per-thread statistics
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56
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57 pt.sll.addTo(ca);
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58 pt.sll=null;
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59 }
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60
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61 //Track whether any threads failed
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62 if(!success){errorState=true;}
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63
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64 return ca;
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65 }
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66
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67 private static class FillThread extends Thread{
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68
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69 FillThread(final AbstractKmerTable[] tables_, int histMax_, AtomicInteger next_){
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70 tables=tables_;
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71 next=next_;
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72 sll=new SuperLongList(Tools.mid(5000, histMax_, 100000));
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73 }
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74
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75 @Override
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76 public void run(){
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77 for(int tnum=next.getAndIncrement(); tnum<tables.length; tnum=next.getAndIncrement()){
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78 tables[tnum].fillHistogram(sll);
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79 }
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80 }
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81
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82 final AbstractKmerTable[] tables;
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83 final AtomicInteger next;
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84 SuperLongList sll;
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85
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86 }
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87
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88 }
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