--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/java-genomics-toolkit/gui/edu/unc/genomics/ToolRunnerFrame.java	Mon Feb 13 21:55:55 2012 -0500
@@ -0,0 +1,328 @@
+package edu.unc.genomics;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.Font;
+
+import javax.swing.JFrame;
+import javax.swing.JPanel;
+
+import javax.swing.BorderFactory;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.JMenuBar;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JButton;
+import javax.swing.JOptionPane;
+import javax.swing.JPopupMenu;
+import javax.swing.JScrollPane;
+import javax.swing.SwingConstants;
+
+import javax.swing.JProgressBar;
+import javax.swing.JSplitPane;
+import javax.swing.BoxLayout;
+import javax.swing.JTabbedPane;
+import javax.swing.JTextPane;
+
+import javax.swing.event.TreeSelectionListener;
+import javax.swing.event.TreeSelectionEvent;
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.apache.log4j.Logger;
+import org.simplericity.macify.eawt.Application;
+import org.simplericity.macify.eawt.ApplicationEvent;
+import org.simplericity.macify.eawt.ApplicationListener;
+import org.simplericity.macify.eawt.DefaultApplication;
+import org.xml.sax.SAXException;
+
+import com.beust.jcommander.JCommander;
+
+import java.awt.event.ActionListener;
+import java.awt.event.ActionEvent;
+import java.io.IOException;
+
+/**
+ * The main ToolRunner window
+ * and controller for creating, running, and managing Jobs
+ * 
+ * @author timpalpant
+ *
+ */
+public class ToolRunnerFrame extends JFrame implements ApplicationListener {
+	
+	private static final long serialVersionUID = 6454774196137357898L;
+	private static final Logger log = Logger.getLogger(ToolRunnerFrame.class);
+	
+	private final Application application = new DefaultApplication();
+	
+	private final JPanel contentPane = new JPanel();
+	private final JSplitPane splitPane = new JSplitPane();
+	private final JPanel mainPane = new JPanel();
+	private final JProgressBar progressBar = new JProgressBar();
+	private final JTabbedPane tabbedPane = new JTabbedPane(SwingConstants.TOP);
+	private final JobConfigPanel configurationPanel = new JobConfigPanel();
+	private final JTextPane helpTextPanel = new JTextPane();
+	private final ToolsTree toolsTree = new ToolsTree();
+		
+	private final JobQueue queue = new JobQueue();
+	private final JobQueueManager queueManager = new JobQueueManager(queue);
+	private final JList<SubmittedJob> queueList = new JList<>(queue);
+
+	/**
+	 * Create the frame.
+	 */
+	public ToolRunnerFrame() {
+    //application.addPreferencesMenuItem();
+    //application.setEnabledPreferencesMenu(true);
+    application.addApplicationListener(this);
+		
+    // set OS X-specific properties
+    if (application.isMac()) {
+    	setDefaultCloseOperation(JFrame.HIDE_ON_CLOSE);
+    	//toolsTree.putClientProperty("Quaqua.Tree.style", "sourceList");
+    } else {
+    	setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+    }
+		setTitle("Genomics Toolkit Tool Runner");
+		setBounds(100, 100, 1000, 600);
+		
+		contentPane.setBorder(BorderFactory.createEmptyBorder());
+		contentPane.setLayout(new BorderLayout(0, 0));
+		setContentPane(contentPane);
+		
+		initializeChildren();
+		initializeMenuBar();
+	}
+	
+	private void initializeChildren() {
+		splitPane.setBorder(BorderFactory.createEmptyBorder());
+		contentPane.add(splitPane, BorderLayout.CENTER);
+		
+		initializeQueuePanel();
+		initializeToolsTree();
+		
+		mainPane.setLayout(new BorderLayout(0, 0));
+		mainPane.setBorder(BorderFactory.createLineBorder(Color.LIGHT_GRAY));
+		mainPane.add(tabbedPane, BorderLayout.CENTER);
+		
+		JPanel runPanel = new JPanel();
+		runPanel.setBorder(BorderFactory.createEmptyBorder(0, 5, 0, 0));
+		runPanel.setLayout(new BoxLayout(runPanel, BoxLayout.X_AXIS));
+		runPanel.add(progressBar);
+		JButton btnRun = new JButton("Run");
+		btnRun.addActionListener(new ActionListener() {
+			public void actionPerformed(ActionEvent e) {
+				addJobToQueue();
+			}
+		});
+		runPanel.add(btnRun);
+		mainPane.add(runPanel, BorderLayout.SOUTH);
+		splitPane.setRightComponent(mainPane);
+		
+		initializeConfigurationPanel();
+		initializeHelpPanel();
+	}
+	
+	private void initializeMenuBar() {
+		JMenuBar menuBar = new JMenuBar();
+		setJMenuBar(menuBar);
+
+		JMenu mnFileMenu = new JMenu("File");
+		menuBar.add(mnFileMenu);
+		
+		JMenuItem mntmAssemblyManager = new JMenuItem("Assembly manager");
+		mntmAssemblyManager.addActionListener(new ActionListener() {
+			public void actionPerformed(ActionEvent e) {
+				JMenuItem menuItem = (JMenuItem) e.getSource();  
+        JPopupMenu popupMenu = (JPopupMenu) menuItem.getParent();  
+        Component invoker = popupMenu.getInvoker(); //this is the JMenu (in my code)  
+        JComponent invokerAsJComponent = (JComponent) invoker;  
+        Container topLevel = invokerAsJComponent.getTopLevelAncestor();
+				AssemblyManagerDialog dialog = new AssemblyManagerDialog((JFrame) topLevel);
+				//dialog.getRootPane().putClientProperty("Window.style", "small");
+				dialog.setVisible(true);
+			}
+		});
+		mnFileMenu.add(mntmAssemblyManager);
+		
+		JMenu mnHelpMenu = new JMenu("Help");
+		menuBar.add(mnHelpMenu);
+		
+		JMenuItem mntmHelpContents = new JMenuItem("Help Contents");
+		mnHelpMenu.add(mntmHelpContents);
+		
+		if (!application.isMac()) {
+			JMenuItem mntmAbout = new JMenuItem("About");
+			mnHelpMenu.add(mntmAbout);
+			mnHelpMenu.addActionListener(new ActionListener() {
+				public void actionPerformed(ActionEvent e) {
+					handleAbout(null);
+				}
+			});
+		}
+	}
+	
+	private void initializeQueuePanel() {
+		JPanel queuePanel = new JPanel();
+		queuePanel.setLayout(new BoxLayout(queuePanel, BoxLayout.PAGE_AXIS));
+		queuePanel.setBorder(BorderFactory.createEmptyBorder());
+		contentPane.add(queuePanel, BorderLayout.EAST);
+		
+		JLabel queueLabel = new JLabel("Job Queue");
+		queueLabel.setBorder(BorderFactory.createEmptyBorder(5, 0, 5, 0));
+		queueLabel.setAlignmentX(JLabel.CENTER_ALIGNMENT);
+		queuePanel.add(queueLabel);
+
+		queueList.setBackground(contentPane.getBackground());
+		queueList.setCellRenderer(new JobQueueCellRenderer());
+		JScrollPane queueListScrollPane = new JScrollPane(queueList);
+		queueListScrollPane.setBorder(BorderFactory.createEmptyBorder());
+		queueListScrollPane.setBackground(contentPane.getBackground());
+		queueListScrollPane.setPreferredSize(new Dimension(200, Integer.MAX_VALUE));
+		queuePanel.add(queueListScrollPane);
+	}
+	
+	private void initializeConfigurationPanel() {		
+		JScrollPane configScrollPane = new JScrollPane(configurationPanel);
+		configScrollPane.setBorder(BorderFactory.createEmptyBorder());
+		tabbedPane.addTab("Tool Configuration", null, configScrollPane, "Configure tool");
+	}
+	
+	private void initializeHelpPanel() {
+		JPanel helpPanel = new JPanel();
+		tabbedPane.addTab("Help", null, helpPanel, null);
+		helpPanel.setLayout(new BorderLayout(0, 0));
+		
+		helpTextPanel.setEditable(false);
+		helpTextPanel.setBackground(tabbedPane.getBackground());
+		Font mono = new Font("Monospaced", helpTextPanel.getFont().getStyle(), helpTextPanel.getFont().getSize());
+		helpTextPanel.setFont(mono);
+		JScrollPane helpScrollPane = new JScrollPane(helpTextPanel);
+		helpScrollPane.setBorder(BorderFactory.createEmptyBorder());
+		helpPanel.add(helpScrollPane);
+	}
+		
+	private void initializeToolsTree() {
+		try {
+			ToolsTreeModel model = ToolsTreeModel.loadDefaultConfig();
+			toolsTree.setModel(model);
+		} catch (ParserConfigurationException | SAXException | IOException e1) {
+			log.error("Error loading tool configuration file");
+			e1.printStackTrace();
+			System.exit(-1);
+		} catch (ClassNotFoundException e) {
+			log.error("Error loading tool: " + e.getMessage());
+			e.printStackTrace();
+			System.exit(-1);
+		}
+
+		toolsTree.addTreeSelectionListener(new TreeSelectionListener() {
+			public void valueChanged(TreeSelectionEvent e) {
+				changeTool();
+			}
+		});
+		
+		JScrollPane toolsTreeScrollPane = new JScrollPane(toolsTree);
+		toolsTreeScrollPane.setBorder(BorderFactory.createMatteBorder(0, 0, 0, 1, Color.LIGHT_GRAY));
+		splitPane.setLeftComponent(toolsTreeScrollPane);
+	}
+
+	/**
+	 * Change the configuration panel to the currently selected tool
+	 * to configure a new Job
+	 */
+	private void changeTool() {
+		// Returns the last path element of the selection.
+    Object node = toolsTree.getLastSelectedPathComponent();
+    // Nothing is selected
+    if (node == null) {   
+    	return;
+    }
+
+    if (node instanceof ToolsTreeNode) {
+    	ToolsTreeNode toolNode = (ToolsTreeNode) node;
+			try {
+	      Class<? extends CommandLineTool> tool = toolNode.getClazz();
+	      
+	      // Set up the configuration panel to configure this tool
+				Job job = new Job(tool);
+	      configurationPanel.setJob(job);
+	      // Set the help text to the usage
+	      helpTextPanel.setText(job.getUsageText());
+			} catch (InstantiationException | IllegalAccessException e) {
+				log.error("Error initializing Job");
+				e.printStackTrace();
+				JOptionPane.showMessageDialog(this, "Error initializing job", "Job Initialization Error", JOptionPane.ERROR_MESSAGE);
+			}
+
+    }
+	}
+	
+	private void addJobToQueue() {
+		Job currentJob = configurationPanel.getJob();
+		if (currentJob == null) return;
+		
+		// Validate the required parameters
+		log.info("Validating parameters for tool");
+		if (!currentJob.validateArguments()) {
+			configurationPanel.highlightInvalidArguments();
+			return;
+		}
+		
+		// Add the job to the queue
+		try {
+			queueManager.submitJob(currentJob);
+			configurationPanel.setJob(null);
+		} catch (JobException e) {
+			log.error("Error adding Job to queue");
+			e.printStackTrace();
+			JOptionPane.showMessageDialog(this, "Error adding job to queue", "Job Queue Error", JOptionPane.ERROR_MESSAGE);
+		}
+	}
+	
+	public void handleAbout(ApplicationEvent event) {
+		JOptionPane.showMessageDialog(this, "Java Genomics Toolkit v1.0");
+		if (event != null) {
+			event.setHandled(true);
+		}
+	}
+
+	public void handleOpenApplication(ApplicationEvent event) {
+		// Application was opened
+	}
+
+	public void handleOpenFile(ApplicationEvent event) {
+		//JOptionPane.showMessageDialog(frmToolRunner, "OS X told us to open " + event.getFilename());
+	}
+
+	public void handlePreferences(ApplicationEvent event) {
+		//JOptionPane.showMessageDialog(frmToolRunner, "No preferences available");
+	}
+
+	public void handlePrintFile(ApplicationEvent event) {
+		//JOptionPane.showMessageDialog(frmToolRunner, "OS X told us to print " + event.getFilename());
+	}
+
+	public void handleQuit(ApplicationEvent event) {
+		boolean confirm = true;
+		if (queueManager.isRunning()) {
+			int result = JOptionPane.showConfirmDialog(this, "Jobs are currently running. Are you sure you want to quit?", "Confirm Quit", JOptionPane.OK_CANCEL_OPTION);
+			confirm = (result == JOptionPane.OK_OPTION);
+		}
+		
+		if (confirm) {
+			dispose();
+			System.exit(0);
+		}
+	}
+
+	public void handleReOpenApplication(ApplicationEvent event) {
+		//JOptionPane.showMessageDialog(frmToolRunner, "OS X told the application was reopened");
+		setVisible(true);
+	}
+}