Mercurial > repos > timpalpant > java_genomics_toolkit

comparison java-genomics-toolkit/gui/edu/unc/genomics/ToolsTreeModel.java @ 0:1daf3026d231

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Upload alpha version
author timpalpant
date Mon, 13 Feb 2012 21:55:55 -0500
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1 package edu.unc.genomics;
2
3 import java.io.IOException;
4 import java.nio.file.Files;
5 import java.nio.file.Path;
6 import java.nio.file.Paths;
7
8 import javax.swing.tree.DefaultMutableTreeNode;
9 import javax.swing.tree.DefaultTreeModel;
10 import javax.xml.parsers.DocumentBuilder;
11 import javax.xml.parsers.DocumentBuilderFactory;
12 import javax.xml.parsers.ParserConfigurationException;
13
14 import org.apache.log4j.Logger;
15 import org.w3c.dom.Document;
16 import org.w3c.dom.Node;
17 import org.w3c.dom.NodeList;
18 import org.xml.sax.SAXException;
19
20 /**
21 * Model for the ToolsTree
22 * Essentially just a DefaultTreeModel, but provides methods for
23 * loading the available tools from a configuration file
24 *
25 * @author timpalpant
26 *
27 */
28 public class ToolsTreeModel extends DefaultTreeModel {
29
30 public static final Path DEFAULT_CONFIGURATION_FILE = Paths.get("toolConf.xml");
31
32 private static final Logger log = Logger.getLogger(ToolsTreeModel.class);
33
34 private static final long serialVersionUID = -6587614270922489960L;
35
36 public ToolsTreeModel() {
37 super(new DefaultMutableTreeNode("Tools"));
38 }
39
40 public static ToolsTreeModel loadDefaultConfig() throws ClassNotFoundException, ParserConfigurationException, SAXException, IOException {
41 return loadConfig(ResourceManager.getResourceDirectory().resolve(DEFAULT_CONFIGURATION_FILE));
42 }
43
44 public static ToolsTreeModel loadConfig(Path p) throws ParserConfigurationException, SAXException, IOException, ClassNotFoundException {
45 ToolsTreeModel model = new ToolsTreeModel();
46 DefaultMutableTreeNode root = (DefaultMutableTreeNode) model.getRoot();
47
48 // Populate the TreeModel with the tools in the default configuration file
49 log.debug("Loading tools from: " + DEFAULT_CONFIGURATION_FILE.toAbsolutePath());
50 DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
51 DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
52 Document doc = dBuilder.parse(p.toFile());
53
54 // Iterate over the sections
55 NodeList sections = doc.getElementsByTagName("section");
56 log.debug("Found "+sections.getLength()+" sections");
57 for (int i = 0; i < sections.getLength(); i++) {
58 Node section = sections.item(i);
59 String sectionName = section.getAttributes().getNamedItem("name").getNodeValue();
60 log.debug("Loading section: " + sectionName);
61 DefaultMutableTreeNode sectionNode = new DefaultMutableTreeNode(sectionName);
62 root.add(sectionNode);
63 NodeList tools = section.getChildNodes();
64
65 // Iterate over the tools in each section
66 for (int j = 0; j < tools.getLength(); j++) {
67 Node tool = tools.item(j);
68 if (tool.getNodeType() == Node.ELEMENT_NODE && tool.getNodeName().equalsIgnoreCase("tool")) {
69 String toolName = tool.getAttributes().getNamedItem("name").getNodeValue();
70 log.debug("Loading tool: " + toolName);
71 String toolClassName = tool.getAttributes().getNamedItem("class").getNodeValue();
72 Class<? extends CommandLineTool> toolClass = (Class<? extends CommandLineTool>) Class.forName(toolClassName);
73 ToolsTreeNode toolNode = new ToolsTreeNode(toolName, toolClass);
74 sectionNode.add(toolNode);
75 }
76 }
77 }
78
79 return model;
80 }
81
82 }