public void saveConfiguration(File file) throws IOException {
try {
DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
Document configuration = dBuilder.newDocument();
Element configRoot = configuration.createElement("configuration");
configuration.appendChild(configRoot);
Element prefElement = configuration.createElement("preferences");
configRoot.appendChild(prefElement);
preferences.saveValuesToXML(prefElement);
Element modulesElement = configuration.createElement("modules");
configRoot.appendChild(modulesElement);
// traverse modules
for (MZmineModule module : MZmineStarter.getAllModules()) {
String className = module.getClass().getName();
Element moduleElement = configuration.createElement("module");
moduleElement.setAttribute("class", className);
modulesElement.appendChild(moduleElement);
Element paramElement = configuration.createElement("parameters");
moduleElement.appendChild(paramElement);
ParameterSet moduleParameters = getModuleParameters(module.getClass());
moduleParameters.saveValuesToXML(paramElement);
}
TransformerFactory transfac = TransformerFactory.newInstance();
Transformer transformer = transfac.newTransformer();
transformer.setOutputProperty(OutputKeys.METHOD, "xml");
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
transformer.setOutputProperty(OutputKeys.ENCODING, "UTF-8");
transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "4");
StreamResult result = new StreamResult(new FileOutputStream(file));
DOMSource source = new DOMSource(configuration);
transformer.transform(source, result);
logger.info("Saved configuration to file " + file);
} catch (Exception e) {
throw new IOException(e);
}
}
public void loadConfiguration(File file) throws IOException {
try {
DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
Document configuration = dBuilder.parse(file);
XPathFactory factory = XPathFactory.newInstance();
XPath xpath = factory.newXPath();
logger.info("Loading desktop configuration");
XPathExpression expr = xpath.compile("//configuration/preferences");
NodeList nodes = (NodeList) expr.evaluate(configuration, XPathConstants.NODESET);
if (nodes.getLength() == 1) {
Element preferencesElement = (Element) nodes.item(0);
preferences.loadValuesFromXML(preferencesElement);
}
logger.info("Loading modules configuration");
for (MZmineModule module : MZmineStarter.getAllModules()) {
String className = module.getClass().getName();
expr =
xpath.compile("//configuration/modules/module[@class='" + className + "']/parameters");
nodes = (NodeList) expr.evaluate(configuration, XPathConstants.NODESET);
if (nodes.getLength() != 1) continue;
Element moduleElement = (Element) nodes.item(0);
ParameterSet moduleParameters = getModuleParameters(module.getClass());
moduleParameters.loadValuesFromXML(moduleElement);
}
logger.info("Loaded configuration from file " + file);
} catch (Exception e) {
throw new IOException(e);
}
}
public DecimalFormat getMZFormat() {
return preferences.getParameter(MZminePreferences.mzFormat).getValue();
}
public DecimalFormat getIntensityFormat() {
return preferences.getParameter(MZminePreferences.intensityFormat).getValue();
}
public Boolean getSendStatistics() {
return preferences.getParameter(MZminePreferences.sendStatistics).getValue();
}