--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gui/edu/unc/genomics/Job.java	Mon Feb 13 22:12:06 2012 -0500
@@ -0,0 +1,207 @@
+package edu.unc.genomics;
+
+import java.io.StringWriter;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+import org.apache.log4j.PatternLayout;
+import org.apache.log4j.WriterAppender;
+
+import com.beust.jcommander.JCommander;
+import com.beust.jcommander.ParameterDescription;
+
+/**
+ * A Job represents an instance of a tool configured with specific arguments
+ * Attempting to run a Job with invalid arguments will throw a RuntimeException
+ * If tool execution fails, a RuntimeException will also be thrown
+ * UncheckedExceptions should be managed by setting the Job's UncheckedExceptionManager
+ * or providing a ThreadGroup / default UncheckedExceptionManager
+ * 
+ * @author timpalpant
+ *
+ */
+public class Job implements Iterable<ParameterDescription>, Runnable {
+	
+	private static final Logger log = Logger.getLogger(Job.class);
+	
+	private final Class<? extends CommandLineTool> tool;
+	private final CommandLineTool app;
+	private final List<ParameterDescription> parameters;
+	private final String usageText;
+	private boolean isRunning = false;
+	private StringWriter writer = new StringWriter();
+	
+	/**
+	 * Arguments for running this Job
+	 */
+	private Map<ParameterDescription,String> args = new HashMap<>();
+	
+	/**
+	 * Creates a new Job model for the specified tool
+	 * @param tool
+	 * @throws IllegalAccessException 
+	 * @throws InstantiationException 
+	 */
+	public Job(final Class<? extends CommandLineTool> tool) throws InstantiationException, IllegalAccessException {
+		this.tool = tool;
+		
+		// Attempt to instantiate the tool and extract parameter information
+		app = tool.newInstance();
+		JCommander jc = new JCommander(app);
+		jc.setProgramName(tool.getSimpleName());
+		parameters = jc.getParameters();
+		StringBuilder sbuilder = new StringBuilder();
+		jc.usage(sbuilder);
+		usageText = sbuilder.toString();
+		
+		// Set default arguments
+		for (ParameterDescription param : parameters) {
+			if (param.getDefault() != null) {
+				setArgument(param, String.valueOf(param.getDefault()));
+			}
+		}
+	}
+	
+	/**
+	 * Copy-constructor
+	 * @param job
+	 */
+	public Job(final Job job) {
+		this.tool = job.tool;
+		this.app = job.app;
+		this.parameters = job.parameters;
+		this.args = job.args;
+		this.usageText = job.usageText;
+	}
+	
+	@Override
+	public void run() {
+		// Load the arguments for running the tool
+		String[] args;
+		try {
+			args = getArguments();
+		} catch (JobException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+			throw new CommandLineToolException("Job arguments are not valid");
+		}
+		
+		// Attempt to instantiate and run the tool
+		WriterAppender appender = new WriterAppender(new PatternLayout(), writer);
+		appender.addFilter(new ThreadFilter(Thread.currentThread().getName()));
+		Logger.getRootLogger().addAppender(appender);
+		isRunning = true;
+		app.toolRunnerMain(args);
+		isRunning = false;
+		Logger.getRootLogger().removeAppender(appender);
+	}
+	
+	/**
+	 * Render the arguments for running an instance of this Job
+	 * @return
+	 * @throws JobException 
+	 */
+	public String[] getArguments() throws JobException {
+		if (!validateArguments()) {
+			throw new JobException("Job Arguments are not valid");
+		}
+		
+		List<String> cmdArgs = new ArrayList<>();
+		for (ParameterDescription p : args.keySet()) {
+			cmdArgs.add(p.getLongestName());
+			cmdArgs.add(args.get(p));
+		}
+		
+		String[] ret = new String[cmdArgs.size()];
+		return cmdArgs.toArray(ret);
+	}
+	
+	public String getArgument(final ParameterDescription p) {
+		return args.get(p);
+	}
+	
+	/**
+	 * Set a value for the given parameter
+	 * @param p
+	 * @param value
+	 */
+	public void setArgument(final ParameterDescription p, final String value) {
+		if (value.length() == 0) {
+			args.remove(p);
+		} else {
+			args.put(p, value);
+		}
+	}
+	
+	/**
+	 * Remove all set arguments for this Job
+	 */
+	public void resetArguments() {
+		args.clear();
+	}
+	
+	/**
+	 * Is this parameter set?
+	 * @param p
+	 * @return
+	 */
+	public boolean isSet(final ParameterDescription p) {
+		return args.containsKey(p);
+	}
+	
+	/**
+	 * Validate that this job has all of its parameters set
+	 * and that they are all valid
+	 * @return
+	 */
+	public boolean validateArguments() {
+		// TODO: Better validation based on parameter type
+		boolean hasAllRequiredParams = true;
+		for (ParameterDescription param : parameters) {
+			if (param.getParameter().required() && !isSet(param)) {
+				log.debug("Job is missing required argument: " + param.getLongestName());
+				hasAllRequiredParams = false;
+			}
+		}
+		
+		return hasAllRequiredParams;
+	}
+	
+	public int numParameters() {
+		return parameters.size();
+	}
+
+	@Override
+	public Iterator<ParameterDescription> iterator() {
+		return parameters.iterator();
+	}
+	
+	public String getName() {
+		return tool.getSimpleName();
+	}
+	
+	public boolean isRunning() {
+		return isRunning;
+	}
+
+	/**
+	 * @return the usageText
+	 */
+	public String getUsageText() {
+		return usageText;
+	}
+
+	@Override
+	public String toString() {
+		return getName();
+	}
+	
+	public String getOutput() {
+		return writer.toString();
+	}
+	
+}