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 void setModuleParameters(
Class<? extends MZmineModule> moduleClass, ParameterSet parameters) {
assert moduleClass != null;
assert parameters != null;
MZmineModule moduleInstance = MZmineStarter.getModuleInstance(moduleClass);
Class<? extends ParameterSet> parametersClass = moduleInstance.getParameterSetClass();
if (!parametersClass.isInstance(parameters)) {
throw new IllegalArgumentException(
"Given parameter set is an instance of "
+ parameters.getClass()
+ " instead of "
+ parametersClass);
}
moduleParameters.put(moduleClass, parameters);
}
@Override
public void runModule(
@Nonnull MZmineProject project,
@Nonnull ParameterSet parameters,
@Nonnull Collection<Task<?>> tasks) {
// Boolean values
Boolean filterByDuration = parameters.getParameter(FeatureFilterParameters.duration).getValue();
Boolean filterByArea = parameters.getParameter(FeatureFilterParameters.area).getValue();
Boolean filterByHeight = parameters.getParameter(FeatureFilterParameters.height).getValue();
Boolean filterByDataPoints =
parameters.getParameter(FeatureFilterParameters.dataPoints).getValue();
Boolean filterByFWHM = parameters.getParameter(FeatureFilterParameters.fwhm).getValue();
Boolean filterByTailingFactor =
parameters.getParameter(FeatureFilterParameters.tailingFactor).getValue();
Boolean filterByAsymmetryFactor =
parameters.getParameter(FeatureFilterParameters.asymmetryFactor).getValue();
// Default values
if (filterByDuration == null) filterByDuration = false;
if (filterByArea == null) filterByArea = false;
if (filterByHeight == null) filterByHeight = false;
if (filterByDataPoints == null) filterByDataPoints = false;
if (filterByFWHM == null) filterByFWHM = false;
if (filterByTailingFactor == null) filterByTailingFactor = false;
if (filterByAsymmetryFactor == null) filterByAsymmetryFactor = false;
// Embedded values
final Range<Double> durationRange =
parameters.getParameter(FeatureFilterParameters.duration).getEmbeddedParameter().getValue();
final Range<Double> areaRange =
parameters.getParameter(FeatureFilterParameters.area).getEmbeddedParameter().getValue();
final Range<Double> heightRange =
parameters.getParameter(FeatureFilterParameters.height).getEmbeddedParameter().getValue();
final Range<Integer> dataPointsRange =
parameters
.getParameter(FeatureFilterParameters.dataPoints)
.getEmbeddedParameter()
.getValue();
final Range<Double> fwhmRange =
parameters.getParameter(FeatureFilterParameters.fwhm).getEmbeddedParameter().getValue();
final Range<Double> tailingFactorRange =
parameters
.getParameter(FeatureFilterParameters.tailingFactor)
.getEmbeddedParameter()
.getValue();
final Range<Double> asymmetryFactorRange =
parameters
.getParameter(FeatureFilterParameters.asymmetryFactor)
.getEmbeddedParameter()
.getValue();
// Other values
final FeatureTablesSelection featureTables =
parameters.getParameter(FeatureFilterParameters.featureTables).getValue();
final Boolean removeOldTable =
parameters.getParameter(FeatureFilterParameters.removeOldTable).getValue();
final String nameSuffix =
parameters.getParameter(FeatureFilterParameters.nameSuffix).getValue();
if (featureTables == null || featureTables.getMatchingFeatureTables().isEmpty()) {
MZmineGUI.displayMessage("Feature filter module started with no feature table selected.");
logger.warn("Feature filter module started with no feature table selected.");
return;
}
// Check if at least one filter is selected
if (!filterByDuration
&& !filterByArea
&& !filterByHeight
&& !filterByDataPoints
&& !filterByFWHM
&& !filterByTailingFactor
&& !filterByAsymmetryFactor) {
MZmineGUI.displayMessage("Feature filter module started with no filter selected.");
logger.warn("Feature filter module started with no filter selected.");
return;
}
// Add a task for each feature table
for (FeatureTable featureTable : featureTables.getMatchingFeatureTables()) {
// Create the data structures
DataPointStore dataStore = DataPointStoreFactory.getMemoryDataStore();
// New feature filter task
FeatureFilterMethod method =
new FeatureFilterMethod(
featureTable,
dataStore,
filterByDuration,
filterByArea,
filterByHeight,
filterByDataPoints,
filterByFWHM,
filterByTailingFactor,
filterByAsymmetryFactor,
durationRange,
areaRange,
heightRange,
dataPointsRange,
fwhmRange,
tailingFactorRange,
asymmetryFactorRange,
nameSuffix);
MSDKTask newTask =
new MSDKTask("Filtering features in tables", featureTable.getName(), method);
// Add the feature table to the project
newTask.setOnSucceeded(
e -> {
FeatureTable newFeatureTable = method.getResult();
project.addFeatureTable(newFeatureTable);
// If selected, remove old feature table
if (removeOldTable != null && removeOldTable) {
project.removeFeatureTable(featureTable);
}
});
// Add the task to the queue
tasks.add(newTask);
}
}
