--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/java-genomics-toolkit/gui/edu/unc/genomics/JobConfigPanel.java	Mon Feb 13 21:55:55 2012 -0500
@@ -0,0 +1,246 @@
+package edu.unc.genomics;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.FileDialog;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.lang.reflect.Field;
+import java.nio.file.Path;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.BorderFactory;
+import javax.swing.BoxLayout;
+import javax.swing.ImageIcon;
+import javax.swing.JButton;
+import javax.swing.JComboBox;
+import javax.swing.JComponent;
+import javax.swing.JFileChooser;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+import javax.swing.SpringLayout;
+import javax.swing.SwingUtilities;
+import javax.swing.event.DocumentEvent;
+import javax.swing.event.DocumentListener;
+import javax.swing.layout.SpringUtilities;
+import javax.swing.text.BadLocationException;
+import javax.swing.text.Document;
+
+import org.apache.commons.lang3.StringUtils;
+import org.apache.log4j.Logger;
+
+import com.beust.jcommander.ParameterDescription;
+
+import edu.unc.genomics.io.IntervalFile;
+import edu.unc.genomics.io.WigFile;
+
+/**
+ * View for configuring the parameters of a Job
+ * Implements databinding between a Job object and the various Swing components
+ * for configuring each parameter
+ * 
+ * @author timpalpant
+ *
+ */
+public class JobConfigPanel extends JPanel {
+
+	private static final long serialVersionUID = 3336295203155728629L;
+	private static final Logger log = Logger.getLogger(JobConfigPanel.class);
+	
+	private static final ImageIcon fileIcon = new ImageIcon(ResourceManager.getImagesDirectory().resolve("folder_page.png").toString());
+	
+	/**
+	 * Maps parameters in the Job to GUI components (forward data-binding)
+	 */
+	private Map<ParameterDescription, JComponent> guiMap = new HashMap<>();
+	
+	/**
+	 * Maps GUI components to parameters in the Job (reverse data-binding)
+	 */
+	private Map<Component, ParameterDescription> jobMap = new HashMap<>();
+	
+	/**
+	 * The model for the Job that this panel allows you to configure
+	 */
+	private Job job;
+
+	/**
+	 * Initialize a new ConfigurationPanel with no Job
+	 */
+	public JobConfigPanel() { 
+		this(null);
+	}
+	
+	/**
+	 * Initialize a new ConfigurationPanel for the given Job
+	 * @param job
+	 */
+	public JobConfigPanel(final Job job) {
+		setJob(job);
+		setLayout(new SpringLayout());
+	}
+	
+	/**
+	 * Return the Job that this ConfigurationPanel is editing
+	 * @return
+	 */
+	public Job getJob() {
+		return job;
+	}
+	
+	/**
+	 * Set the job for this Configuration panel and re-render
+	 * @param job
+	 */
+	public void setJob(final Job job) {
+		this.job = job;
+		renderJob();
+	}
+	
+	/**
+	 * Highlights fields on the Panel that are not set correctly
+	 */
+	public void highlightInvalidArguments() {
+		for (ParameterDescription param : job) {
+			JComponent guiComponent = guiMap.get(param);
+			if (param.getParameter().required() && !job.isSet(param)) {
+				guiComponent.setBorder(BorderFactory.createLineBorder(Color.RED));
+			} else {
+				guiComponent.setBorder(BorderFactory.createEmptyBorder());
+			}
+		}
+	}
+	
+	/**
+	 * Render the parameters from the Job into GUI components
+	 * and set up one-way data binding to map changes to the GUI fields
+	 * back into the Job object's parameters
+	 */
+	private void renderJob() {
+		removeAll();
+		guiMap.clear();
+		jobMap.clear();
+		if (job == null) {
+			validate();
+			repaint();
+			return;
+		}
+		
+		// Iterate through the parameters in the Job
+		// and render them appropriately based on their type
+		for (ParameterDescription paramDescription : job) {
+			// Add the parameter name to the configuration panel
+			String name = paramDescription.getLongestName();
+			while (name.startsWith("-")) {
+				name = name.substring(1);
+			}
+			name = StringUtils.capitalize(name);
+			JLabel label = new JLabel(name);
+			label.setBorder(BorderFactory.createEmptyBorder(0, 0, 0, 5));
+			add(label);
+			
+			// Add a panel for configuring the parameter
+			JPanel fieldPanel = new JPanel();
+			fieldPanel.setLayout(new BoxLayout(fieldPanel, BoxLayout.LINE_AXIS));
+			add(fieldPanel);
+			Field field = paramDescription.getField();
+			Class<?> type = field.getType();
+			if (type.equals(Assembly.class)) {
+				List<Assembly> availableAssemblies = AssemblyManager.getAvailableAssemblies();
+				Assembly[] assemblies = new Assembly[availableAssemblies.size()];
+				assemblies = availableAssemblies.toArray(assemblies);
+				final JComboBox<Assembly> cbAssemblyChooser = new JComboBox<Assembly>(assemblies);
+				cbAssemblyChooser.setPreferredSize(new Dimension(0, 25));
+				cbAssemblyChooser.setMaximumSize(new Dimension(Integer.MAX_VALUE, cbAssemblyChooser.getPreferredSize().height));
+				cbAssemblyChooser.setSelectedItem(AssemblyManager.getLastUsed());
+				cbAssemblyChooser.addActionListener(new ActionListener() {
+					public void actionPerformed(ActionEvent e) {
+						log.debug("Auto-databinding changed assembly into Job argument");
+						Assembly selectedAssembly = (Assembly) cbAssemblyChooser.getSelectedItem();
+						AssemblyManager.setLastUsed(selectedAssembly);
+						ParameterDescription param = jobMap.get(cbAssemblyChooser);
+						job.setArgument(param, selectedAssembly.toString());
+					}
+				});
+				fieldPanel.add(cbAssemblyChooser);
+				guiMap.put(paramDescription, cbAssemblyChooser);
+				jobMap.put(cbAssemblyChooser, paramDescription);
+			} else {
+				final JTextField textField = new JTextField();
+				// Set to default parameter, if it exists
+				if (job.isSet(paramDescription)) {
+					textField.setText(job.getArgument(paramDescription));
+				}
+				textField.setPreferredSize(new Dimension(0, 20));
+				textField.setMaximumSize(new Dimension(Integer.MAX_VALUE, textField.getPreferredSize().height));
+				textField.getDocument().addDocumentListener(new DocumentListener() {
+					public void changedUpdate(DocumentEvent e) {
+						pushTextToModel(e);
+					}
+					
+					public void removeUpdate(DocumentEvent e) {
+						pushTextToModel(e);
+					}
+					
+					public void insertUpdate(DocumentEvent e) {
+						pushTextToModel(e);
+					}
+					
+					private void pushTextToModel(DocumentEvent e) {
+						log.debug("Auto-databinding changed text into Job argument");
+						Document doc = (Document) e.getDocument();
+						ParameterDescription param = jobMap.get(textField);
+						try {
+							String text = doc.getText(0, doc.getLength());
+							job.setArgument(param, text);
+						} catch (BadLocationException e1) {
+							log.error("Error pushing changed text into Job model");
+							e1.printStackTrace();
+						}
+					}
+				});
+				fieldPanel.add(textField);
+				guiMap.put(paramDescription, textField);
+				jobMap.put(textField, paramDescription);
+				
+				// For input/output files, add a file chooser button
+				if (type.equals(Path.class) || type.equals(WigFile.class) || type.equals(IntervalFile.class)) {
+					// TODO Replace with file icon
+					JButton btnChooseFile = new JButton(fileIcon);
+					btnChooseFile.addActionListener(new ActionListener() {
+						public void actionPerformed(ActionEvent e) {
+							// AWT FileDialog uses native components, but seems to hang
+							//Component c = (Component) e.getSource();
+			        //JFrame frame = (JFrame) SwingUtilities.getRoot(c);
+							//FileDialog fd = new FileDialog(frame, "Choose File");
+							//fd.setVisible(true);
+							//if (fd.getFile() != null) {
+							//	textField.setText(fd.getDirectory()+fd.getFile());
+							//}
+							
+							// Swing JFileChooser
+							JFileChooser fc = new JFileChooser();
+							int retValue = fc.showDialog(getParent(), "OK");
+							if (retValue == JFileChooser.APPROVE_OPTION) {
+								textField.setText(fc.getSelectedFile().toString());
+							}
+						}
+					});
+					fieldPanel.add(btnChooseFile);
+				}
+			}
+		}
+		
+		// Lay out the panel
+		SpringUtilities.makeCompactGrid(this, job.numParameters(), 2, 5, 5, 5, 5);
+		
+		validate();
+		repaint();
+	}
+
+}