--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/sketch/AlignmentThreadPool.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,118 @@
+package sketch;
+
+import java.util.ArrayList;
+import java.util.concurrent.ArrayBlockingQueue;
+import java.util.concurrent.atomic.AtomicInteger;
+
+import shared.Tools;
+
+public class AlignmentThreadPool {
+	
+	public AlignmentThreadPool(int maxThreads_) {
+		maxThreads=maxThreads_;
+		assert(maxThreads>0);
+		tlist=new ArrayList<AlignmentThread>(maxThreads);
+	}
+	
+	public void addJobs(ArrayList<Comparison> list, int maxRecords){
+		if(list==null || list.isEmpty() || maxRecords<1){return;}
+		final int limit=Tools.min(list.size(), maxRecords);
+		ArrayBlockingQueue<Comparison> dest=new ArrayBlockingQueue<Comparison>(limit);
+		int added=0;
+		for(int i=0; i<limit; i++){
+			Comparison c=list.get(i);
+			if(c.needsAlignment()){
+				addJob(c, dest);
+				added++;
+			}
+		}
+		for(int i=0; i<added; i++){
+			take(dest);
+		}
+	}
+	
+	public void addJob(Comparison c, ArrayBlockingQueue<Comparison> dest){
+		if(tlist.size()<maxThreads){spawnThread();}
+		assert(!poisoned);
+		AlignmentJob job=new AlignmentJob(c, dest);
+		put(job);
+	}
+	
+	private synchronized void spawnThread(){
+		final int size=tlist.size();
+		if(size<maxThreads && busy.get()>=size){
+//			AlignmentThread alt=new AlignmentThread(source, busy);
+			AlignmentThread alt=new AlignmentThread();
+			tlist.add(alt);
+			alt.start();
+		}
+	}
+	
+	synchronized void poison(){
+		assert(!poisoned);
+		if(poisoned){return;}
+		put(poison);
+		poisoned=true;
+	}
+	
+	private void put(AlignmentJob job){
+		busy.incrementAndGet();
+		boolean success=false;
+		while(!success){
+			try {
+				source.put(job);
+				success=true;
+			} catch (InterruptedException e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
+			}
+		}
+	}
+	
+	private final <X> X take(ArrayBlockingQueue<X> queue){
+		X x=null;
+		while(x==null){
+			try {
+				x=queue.take();
+			} catch (InterruptedException e1) {
+				// TODO Auto-generated catch block
+				e1.printStackTrace();
+			}
+		}
+		return x;
+	}
+	
+	private class AlignmentThread extends Thread {
+		
+		AlignmentThread(){}
+		
+		private final AlignmentJob next(){
+			return take(source);
+		}
+		
+		@Override
+		public void run(){
+			AlignmentJob job=null;
+			for(job=next(); !job.isPoison(); job=next()){
+				job.doWork();
+				busy.decrementAndGet();
+			}
+			put(poison);
+		}
+		
+//		private final ArrayBlockingQueue<AlignmentJob> source;
+//		private final AtomicInteger busy;
+//
+//		private static final AlignmentJob poison=new AlignmentJob(null, null);
+		
+	}
+	
+	final ArrayList<AlignmentThread> tlist;
+	final int maxThreads;
+	final AtomicInteger busy=new AtomicInteger(0);
+	private boolean poisoned=false;
+
+	private static final AlignmentJob poison=new AlignmentJob(null, null);
+	private static final ArrayBlockingQueue<AlignmentJob> source=new ArrayBlockingQueue<AlignmentJob>(4096);
+	
+}