--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/java-genomics-toolkit/gui/edu/unc/genomics/AssemblyManagerDialog.java	Mon Feb 13 21:55:55 2012 -0500
@@ -0,0 +1,135 @@
+package edu.unc.genomics;
+
+import java.awt.BorderLayout;
+import java.awt.FlowLayout;
+
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JFileChooser;
+import javax.swing.JFrame;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTable;
+import javax.swing.border.EmptyBorder;
+
+import org.apache.log4j.Logger;
+
+import java.awt.event.ActionListener;
+import java.awt.event.ActionEvent;
+import java.io.IOException;
+import java.nio.file.Path;
+import java.util.zip.DataFormatException;
+
+/**
+ * View for AssemblyManager
+ * 
+ * @author timpalpant
+ *
+ */
+public class AssemblyManagerDialog extends JDialog {
+	
+	public static final int DEFAULT_WIDTH = 400;
+	public static final int DEFAULT_HEIGHT = 500;
+	
+	private static final long serialVersionUID = -1461628562713621064L;
+	private static final Logger log = Logger.getLogger(AssemblyManagerDialog.class);
+
+	private final JPanel contentPanel = new JPanel();
+	private final JFileChooser fcCustomAssembly = new JFileChooser();
+	private final JTable assembliesTable = new JTable();
+	
+	private AssemblyTableModel model;
+
+	/**
+	 * Create the dialog.
+	 */
+	public AssemblyManagerDialog(JFrame parent) {
+		super(parent, "Assembly Manager", true);
+		
+		setSize(DEFAULT_WIDTH, DEFAULT_HEIGHT);
+		int centeredX = parent.getX() + (parent.getWidth()-getWidth()) / 2;
+		int centeredY = parent.getY() + (parent.getHeight()-getHeight()) / 2;
+		setLocation(centeredX, centeredY);
+		
+		getContentPane().setLayout(new BorderLayout());
+		contentPanel.setBorder(new EmptyBorder(5, 5, 5, 5));
+		getContentPane().add(contentPanel, BorderLayout.CENTER);
+		contentPanel.setLayout(new BorderLayout(0, 0));
+
+		// Initialize the assemblies list
+		model = new AssemblyTableModel(AssemblyManager.getAvailableAssemblies());
+		assembliesTable.setModel(model);
+		assembliesTable.setRowSelectionAllowed(true);
+		JScrollPane scrollPane = new JScrollPane(assembliesTable);
+		assembliesTable.setFillsViewportHeight(true);
+		contentPanel.add(scrollPane);
+
+		JPanel buttonPane = new JPanel();
+		buttonPane.setLayout(new FlowLayout(FlowLayout.RIGHT));
+		getContentPane().add(buttonPane, BorderLayout.SOUTH);
+		
+		JButton removeAssemblyButton = new JButton("Remove");
+		removeAssemblyButton.setActionCommand("RemoveAssembly");
+		removeAssemblyButton.addActionListener(new ActionListener() {
+			public void actionPerformed(ActionEvent e) {
+				removeCustomAssembly();
+			}
+		});
+		buttonPane.add(removeAssemblyButton);
+		
+		JButton loadAssemblyButton = new JButton("Load Custom Assembly");
+		loadAssemblyButton.setActionCommand("LoadAssembly");
+		loadAssemblyButton.addActionListener(new ActionListener() {
+			public void actionPerformed(ActionEvent e) {
+				loadCustomAssembly();
+			}
+		});
+		buttonPane.add(loadAssemblyButton);
+		
+		JButton doneButton = new JButton("Done");
+		doneButton.setActionCommand("Done");
+		doneButton.addActionListener(new ActionListener() {
+			public void actionPerformed(ActionEvent e) {
+				closeDialog();
+			}
+		});
+		buttonPane.add(doneButton);
+		getRootPane().setDefaultButton(doneButton);
+	}
+	
+	private void removeCustomAssembly() {
+		for (int row : assembliesTable.getSelectedRows()) {
+			try {
+				Assembly a = model.getRow(row);
+				AssemblyManager.deleteAssembly(a);
+				model.removeRow(row);
+			} catch (IOException e) {
+				log.error("Error deleting Assembly");
+				e.printStackTrace();
+				JOptionPane.showMessageDialog(this, "Error deleting assembly", "Assembly Manager Error", JOptionPane.ERROR_MESSAGE);
+			}
+		}
+	}
+	
+	private void loadCustomAssembly() {
+		int returnVal = fcCustomAssembly.showOpenDialog(this);
+		if (returnVal == JFileChooser.APPROVE_OPTION) {
+			Path assemblyFile = fcCustomAssembly.getSelectedFile().toPath();
+			try {
+				Assembly a = AssemblyManager.loadCustomAssembly(assemblyFile);
+				// Add it to the assemblies list model
+				model.addAssembly(a);
+			} catch (IOException | DataFormatException e) {
+				log.error("Error loading custom assembly: " + assemblyFile);
+				e.printStackTrace();
+				JOptionPane.showMessageDialog(this, "Error loading custom assembly", "Assembly Manager Error", JOptionPane.ERROR_MESSAGE);
+			}
+		}
+	}
+	
+	private void closeDialog() {
+		this.dispose();
+	}
+
+}