--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/java-genomics-toolkit/gui/edu/unc/genomics/JobQueueManager.java	Mon Feb 13 21:55:55 2012 -0500
@@ -0,0 +1,105 @@
+package edu.unc.genomics;
+
+import java.util.List;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Controller for scheduling and running jobs
+ * Wrapper for ExcecutorService, although the implementation could change
+ * 
+ * @author timpalpant
+ *
+ */
+public class JobQueueManager {
+		
+	private static final Logger log = Logger.getLogger(JobQueueManager.class);
+	
+	private final JobQueue queue;
+	private final ExecutorService exec;
+	private final Thread monitor;
+	
+	public JobQueueManager(JobQueue queue) {
+		this.queue = queue;
+		
+		int numProcessors = Runtime.getRuntime().availableProcessors();
+		log.debug("Initializing thread pool with "+numProcessors+" processors");
+		exec = Executors.newFixedThreadPool(numProcessors);
+		
+		monitor = new Thread(new JobMonitor());
+		monitor.start();
+	}
+	
+	public List<Runnable> shutdownNow() {
+		return exec.shutdownNow();
+	}
+	
+	/**
+	 * Add a Job to the queue
+	 * @param job
+	 * @throws JobException 
+	 */
+	public SubmittedJob submitJob(Job job) throws JobException {
+		// Refuse to add the Job to the queue if its arguments are not valid
+		if (!job.validateArguments()) {
+			throw new JobException("Job arguments are not valid");
+		}
+		
+		// Submit the job for execution into the thread pool
+		Future<?> future = exec.submit(job);
+		SubmittedJob submittedJob = new SubmittedJob(job, future);
+		log.info("Submitted job " + submittedJob.getId());
+		
+		// Add the SubmittedJob to the JobQueue
+		queue.add(submittedJob);
+		return submittedJob;
+	}
+	
+	/**
+	 * Are any jobs running? (not done)
+	 * @return
+	 */
+	public boolean isRunning() {
+		for (SubmittedJob job : queue) {
+			if (!job.isDone()) {
+				return true;
+			}
+		}
+		
+		return false;
+	}
+
+
+	/**
+	 * Background process for polling the status of submitted jobs
+	 * @author timpalpant
+	 *
+	 */
+	public class JobMonitor implements Runnable {
+
+		public static final int JOB_POLL_INTERVAL = 1_000;
+		
+		public void run() {
+			try {
+				while (true) {
+					// Check Job statuses every 1s
+					Thread.sleep(JOB_POLL_INTERVAL);
+					
+					for (SubmittedJob job : queue) {
+						if (job.isDone()) {
+							queue.update(job);
+						}
+					}
+				}
+			} catch (InterruptedException e) {
+				log.fatal("JobMonitor crashed");
+				e.printStackTrace();
+				throw new RuntimeException("JobMonitor crashed");
+			}
+		}
+	}
+
+}