--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/kmer/HistogramMaker.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,88 @@
+package kmer;
+
+import java.util.concurrent.atomic.AtomicInteger;
+
+import shared.Shared;
+import shared.Tools;
+import structures.SuperLongList;
+
+public final class HistogramMaker {
+
+	
+	public static long[] fillHistogram(final AbstractKmerTable[] tables, final int histMax) {
+		if(Shared.threads()>2){
+			return fillHistogram_MT(tables, histMax);
+		}else{
+			return fillHistogram_ST(tables, histMax);
+		}
+	}
+	
+	private static long[] fillHistogram_ST(final AbstractKmerTable[] tables, final int histMax) {
+		long[] ca=new long[histMax+1];
+		for(AbstractKmerTable set : tables){
+			set.fillHistogram(ca, histMax);
+		}
+		return ca;
+	}
+	
+	private static long[] fillHistogram_MT(final AbstractKmerTable[] tables, final int histMax) {
+		boolean errorState=false;
+		int threads=Shared.threads();
+		threads=Tools.min((threads>20 ? threads/2 : threads), (tables.length+1)/2, 32);
+		if(threads<2){return fillHistogram_ST(tables, histMax);}
+		
+		final FillThread[] array=new FillThread[threads];
+		final AtomicInteger next=new AtomicInteger(0);
+		for(int i=0; i<threads; i++){array[i]=new FillThread(tables, histMax, next);}
+		for(int i=0; i<threads; i++){array[i].start();}
+		
+		//Wait for completion of all threads
+		final long[] ca=new long[histMax+1];
+		boolean success=true;
+		for(FillThread pt : array){
+
+			//Wait until this thread has terminated
+			while(pt.getState()!=Thread.State.TERMINATED){
+				try {
+					//Attempt a join operation
+					pt.join();
+				} catch (InterruptedException e) {
+					//Potentially handle this, if it is expected to occur
+					e.printStackTrace();
+				}
+			}
+
+			//Accumulate per-thread statistics
+			
+			pt.sll.addTo(ca);
+			pt.sll=null;
+		}
+		
+		//Track whether any threads failed
+		if(!success){errorState=true;}
+		
+		return ca;
+	}
+	
+	private static class FillThread extends Thread{
+		
+		FillThread(final AbstractKmerTable[] tables_, int histMax_, AtomicInteger next_){
+			tables=tables_;
+			next=next_;
+			sll=new SuperLongList(Tools.mid(5000, histMax_, 100000));
+		}
+		
+		@Override
+		public void run(){
+			for(int tnum=next.getAndIncrement(); tnum<tables.length; tnum=next.getAndIncrement()){
+				tables[tnum].fillHistogram(sll);
+			}
+		}
+		
+		final AbstractKmerTable[] tables;
+		final AtomicInteger next;
+		SuperLongList sll;
+		
+	}
+	
+}