--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/fileIO/LoadThread.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,139 @@
+package fileIO;
+
+import java.util.Arrays;
+
+import shared.Shared;
+import shared.Tools;
+
+/**
+ * @author Brian Bushnell
+ * @date Jan 2, 2013
+ *
+ */
+public class LoadThread<X> extends Thread{
+	
+	public static <Y> LoadThread<Y> load(String fname, Class<Y> c){
+		LoadThread<Y> lt=new LoadThread<Y>(fname, c);
+		lt.start();
+		return lt;
+	}
+	
+	private LoadThread(String fname_, Class<X> c_){
+		fname=fname_;
+		c=c_;
+		addThread(1);
+	}
+	
+	@Override
+	public void run(){
+		addRunningThread(1);
+		output=ReadWrite.read(c, fname, false);
+		addRunningThread(-1);
+		synchronized(this){this.notify();}
+	}
+	
+	
+	private static final int addThread(int x){
+		final int lim=(Shared.LOW_MEMORY ? 1 : LIMIT);
+		synchronized(activeThreads){
+			assert(x!=0);
+			if(x>0){
+				activeThreads[0]+=x;
+				activeThreads[1]+=x;
+			}else{
+				addRunningThread(x);
+			}
+			assert(activeThreads[0]==(activeThreads[1]+activeThreads[2]) && activeThreads[0]>=0 && activeThreads[1]>=0 &&
+					activeThreads[2]>=0 && activeThreads[2]<=lim) : Arrays.toString(activeThreads);
+					
+			return activeThreads[0];
+		}
+	}
+	
+	private static final int addRunningThread(int x){
+		final int lim=(Shared.LOW_MEMORY ? 1 : LIMIT);
+		synchronized(activeThreads){
+			assert(x!=0);
+			if(x>0){
+				assert(activeThreads[1]>=x);
+				while(activeThreads[2]>=lim){
+					try {
+						activeThreads.wait();
+					} catch (InterruptedException e) {
+						// TODO Auto-generated catch block
+						e.printStackTrace();
+					}
+				}
+				activeThreads[1]-=x; //Remove from waiting
+			}else{
+				activeThreads[0]+=x; //Remove from active
+			}
+			activeThreads[2]+=x; //Change number running
+			
+			assert(activeThreads[0]==(activeThreads[1]+activeThreads[2]) && activeThreads[0]>=0 && activeThreads[1]>=0 &&
+					activeThreads[2]>=0 && activeThreads[2]<=lim) : Arrays.toString(activeThreads);
+			
+			if(activeThreads[2]==0 || (activeThreads[2]<lim && activeThreads[1]>0)){activeThreads.notify();}
+//			System.err.println(activeThreads[2]);
+//			try {
+//				activeThreads.wait(5000);
+//			} catch (InterruptedException e) {
+//				// TODO Auto-generated catch block
+//				e.printStackTrace();
+//			}
+			return activeThreads[2];
+		}
+	}
+	
+	public static final int countActiveThreads(){
+		final int lim=(Shared.LOW_MEMORY ? 1 : LIMIT);
+		synchronized(activeThreads){
+			assert(activeThreads[0]==(activeThreads[1]+activeThreads[2]) && activeThreads[0]>=0 && activeThreads[1]>=0 &&
+					activeThreads[2]>=0 && activeThreads[2]<=lim) : Arrays.toString(activeThreads);
+			return activeThreads[0];
+		}
+	}
+	
+	public static final void waitForReadingToFinish(){
+		final int lim=(Shared.LOW_MEMORY ? 1 : LIMIT);
+		synchronized(activeThreads){
+			while(activeThreads[0]>0){
+				assert(activeThreads[0]==(activeThreads[1]+activeThreads[2]) && activeThreads[0]>=0 && activeThreads[1]>=0 &&
+						activeThreads[2]>=0 && activeThreads[2]<=lim) : Arrays.toString(activeThreads);
+				try {
+					activeThreads.wait(8000);
+				} catch (InterruptedException e) {
+					// TODO Auto-generated catch block
+					e.printStackTrace();
+				}
+				if(activeThreads[2]==0 || (activeThreads[2]<lim && activeThreads[1]>0)){activeThreads.notify();}
+			}
+		}
+	}
+	
+	public final void waitForThisToFinish(){
+		if(output==null){
+			while(this.getState()!=State.TERMINATED){
+				try {
+					this.join();
+				} catch (InterruptedException e) {
+					// TODO Auto-generated catch block
+					e.printStackTrace();
+				}
+			}
+		}
+	}
+	
+	/** {active, waiting, running} <br>
+	 * Active means running or waiting.
+	 */
+	public static int[] activeThreads={0, 0, 0};
+	
+	private final String fname;
+	private final Class<X> c;
+	public X output=null;
+	
+	private static final int[] RUNNING=new int[1];
+	public static int LIMIT=Tools.min(12, Tools.max(Shared.threads(), 1));
+	
+}