--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gui/edu/unc/genomics/ToolsTreeModel.java	Mon Feb 13 22:12:06 2012 -0500
@@ -0,0 +1,82 @@
+package edu.unc.genomics;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+
+import javax.swing.tree.DefaultMutableTreeNode;
+import javax.swing.tree.DefaultTreeModel;
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.apache.log4j.Logger;
+import org.w3c.dom.Document;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+import org.xml.sax.SAXException;
+
+/**
+ * Model for the ToolsTree
+ * Essentially just a DefaultTreeModel, but provides methods for
+ * loading the available tools from a configuration file
+ * 
+ * @author timpalpant
+ *
+ */
+public class ToolsTreeModel extends DefaultTreeModel {
+	
+	public static final Path DEFAULT_CONFIGURATION_FILE = Paths.get("toolConf.xml");
+	
+	private static final Logger log = Logger.getLogger(ToolsTreeModel.class);
+
+	private static final long serialVersionUID = -6587614270922489960L;
+
+	public ToolsTreeModel() {
+		super(new DefaultMutableTreeNode("Tools"));
+	}
+	
+	public static ToolsTreeModel loadDefaultConfig() throws ClassNotFoundException, ParserConfigurationException, SAXException, IOException {
+		return loadConfig(ResourceManager.getResourceDirectory().resolve(DEFAULT_CONFIGURATION_FILE));
+	}
+	
+	public static ToolsTreeModel loadConfig(Path p) throws ParserConfigurationException, SAXException, IOException, ClassNotFoundException {
+		ToolsTreeModel model = new ToolsTreeModel();
+		DefaultMutableTreeNode root = (DefaultMutableTreeNode) model.getRoot();
+		
+		// Populate the TreeModel with the tools in the default configuration file
+		log.debug("Loading tools from: " + DEFAULT_CONFIGURATION_FILE.toAbsolutePath());
+		DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
+		DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
+		Document doc = dBuilder.parse(p.toFile());
+		
+		// Iterate over the sections
+		NodeList sections = doc.getElementsByTagName("section");
+		log.debug("Found "+sections.getLength()+" sections");
+		for (int i = 0; i < sections.getLength(); i++) {
+			Node section = sections.item(i);
+			String sectionName = section.getAttributes().getNamedItem("name").getNodeValue();
+			log.debug("Loading section: " + sectionName);
+			DefaultMutableTreeNode sectionNode = new DefaultMutableTreeNode(sectionName);
+			root.add(sectionNode);
+			NodeList tools = section.getChildNodes();
+			
+			// Iterate over the tools in each section
+			for (int j = 0; j < tools.getLength(); j++) {
+				Node tool = tools.item(j);
+				if (tool.getNodeType() == Node.ELEMENT_NODE && tool.getNodeName().equalsIgnoreCase("tool")) {
+					String toolName = tool.getAttributes().getNamedItem("name").getNodeValue();
+					log.debug("Loading tool: " + toolName);
+					String toolClassName = tool.getAttributes().getNamedItem("class").getNodeValue();
+					Class<? extends CommandLineTool> toolClass = (Class<? extends CommandLineTool>) Class.forName(toolClassName);
+					ToolsTreeNode toolNode = new ToolsTreeNode(toolName, toolClass);
+					sectionNode.add(toolNode);
+				}
+			}
+		}
+		
+		return model;
+	}
+
+}