jpayne@68: package kmer;
jpayne@68: 
jpayne@68: import java.util.concurrent.atomic.AtomicInteger;
jpayne@68: 
jpayne@68: import shared.Shared;
jpayne@68: import shared.Tools;
jpayne@68: import structures.SuperLongList;
jpayne@68: 
jpayne@68: public final class HistogramMaker {
jpayne@68: 
jpayne@68: 	
jpayne@68: 	public static long[] fillHistogram(final AbstractKmerTable[] tables, final int histMax) {
jpayne@68: 		if(Shared.threads()>2){
jpayne@68: 			return fillHistogram_MT(tables, histMax);
jpayne@68: 		}else{
jpayne@68: 			return fillHistogram_ST(tables, histMax);
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private static long[] fillHistogram_ST(final AbstractKmerTable[] tables, final int histMax) {
jpayne@68: 		long[] ca=new long[histMax+1];
jpayne@68: 		for(AbstractKmerTable set : tables){
jpayne@68: 			set.fillHistogram(ca, histMax);
jpayne@68: 		}
jpayne@68: 		return ca;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private static long[] fillHistogram_MT(final AbstractKmerTable[] tables, final int histMax) {
jpayne@68: 		boolean errorState=false;
jpayne@68: 		int threads=Shared.threads();
jpayne@68: 		threads=Tools.min((threads>20 ? threads/2 : threads), (tables.length+1)/2, 32);
jpayne@68: 		if(threads<2){return fillHistogram_ST(tables, histMax);}
jpayne@68: 		
jpayne@68: 		final FillThread[] array=new FillThread[threads];
jpayne@68: 		final AtomicInteger next=new AtomicInteger(0);
jpayne@68: 		for(int i=0; i<threads; i++){array[i]=new FillThread(tables, histMax, next);}
jpayne@68: 		for(int i=0; i<threads; i++){array[i].start();}
jpayne@68: 		
jpayne@68: 		//Wait for completion of all threads
jpayne@68: 		final long[] ca=new long[histMax+1];
jpayne@68: 		boolean success=true;
jpayne@68: 		for(FillThread pt : array){
jpayne@68: 
jpayne@68: 			//Wait until this thread has terminated
jpayne@68: 			while(pt.getState()!=Thread.State.TERMINATED){
jpayne@68: 				try {
jpayne@68: 					//Attempt a join operation
jpayne@68: 					pt.join();
jpayne@68: 				} catch (InterruptedException e) {
jpayne@68: 					//Potentially handle this, if it is expected to occur
jpayne@68: 					e.printStackTrace();
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 
jpayne@68: 			//Accumulate per-thread statistics
jpayne@68: 			
jpayne@68: 			pt.sll.addTo(ca);
jpayne@68: 			pt.sll=null;
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		//Track whether any threads failed
jpayne@68: 		if(!success){errorState=true;}
jpayne@68: 		
jpayne@68: 		return ca;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private static class FillThread extends Thread{
jpayne@68: 		
jpayne@68: 		FillThread(final AbstractKmerTable[] tables_, int histMax_, AtomicInteger next_){
jpayne@68: 			tables=tables_;
jpayne@68: 			next=next_;
jpayne@68: 			sll=new SuperLongList(Tools.mid(5000, histMax_, 100000));
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		@Override
jpayne@68: 		public void run(){
jpayne@68: 			for(int tnum=next.getAndIncrement(); tnum<tables.length; tnum=next.getAndIncrement()){
jpayne@68: 				tables[tnum].fillHistogram(sll);
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		final AbstractKmerTable[] tables;
jpayne@68: 		final AtomicInteger next;
jpayne@68: 		SuperLongList sll;
jpayne@68: 		
jpayne@68: 	}
jpayne@68: 	
jpayne@68: }