/** @see java.lang.Runnable#run() */
public void run() {
Task actualTask = wrappedTask.getActualTask();
logger.finest("Starting processing of task: " + actualTask.getTaskDescription());
try {
// Process the actual task
actualTask.run();
// Check if task finished with an error
if (actualTask.getStatus() == TaskStatus.ERROR) {
logger.severe("Task error: " + actualTask.getErrorMessage());
String errorMsg = actualTask.getErrorMessage();
if (errorMsg == null) errorMsg = "Unspecified error";
MZmineCore.getDesktop()
.displayErrorMessage("Error of task " + actualTask.getTaskDescription(), errorMsg);
}
/*
* This is important to allow the garbage collector to remove the
* task, while keeping the task description in the
* "Tasks in progress" window
*/
wrappedTask.removeTaskReference();
} catch (Throwable e) {
/*
* This should never happen, it means the task did not handle its
* exception properly, or there was some severe error, like
* OutOfMemoryError
*/
logger.log(
Level.SEVERE,
"Unhandled exception " + e + " while processing task " + actualTask.getTaskDescription(),
e);
e.printStackTrace();
MZmineCore.getDesktop()
.displayErrorMessage(
"Unhandled exception in task "
+ actualTask.getTaskDescription()
+ ": "
+ ExceptionUtils.exceptionToString(e));
}
/*
* Mark this thread as finished
*/
finished = true;
}
@Override
@Nonnull
public ExitCode runModule(@Nonnull ParameterSet parameters, @Nonnull Collection<Task> tasks) {
final RawDataFile[] dataFiles =
parameters.getParameter(TICVisualizerParameters.DATA_FILES).getValue();
final int msLevel = parameters.getParameter(TICVisualizerParameters.MS_LEVEL).getValue();
final Range rtRange = parameters.getParameter(TICVisualizerParameters.RT_RANGE).getValue();
final Range mzRange = parameters.getParameter(TICVisualizerParameters.MZ_RANGE).getValue();
final PlotType plotType = parameters.getParameter(TICVisualizerParameters.PLOT_TYPE).getValue();
final ChromatographicPeak[] selectionPeaks =
parameters.getParameter(TICVisualizerParameters.PEAKS).getValue();
if (dataFiles == null || dataFiles.length == 0) {
MZmineCore.getDesktop().displayErrorMessage("Please select raw data file(s)");
} else {
// Add the window to the desktop only if we actually have any raw
// data to show.
boolean weHaveData = false;
for (int i = 0, dataFilesLength = dataFiles.length; !weHaveData && i < dataFilesLength; i++) {
weHaveData = dataFiles[i].getScanNumbers(msLevel, rtRange).length > 0;
}
if (weHaveData) {
MZmineCore.getDesktop()
.addInternalFrame(
new TICVisualizerWindow(
dataFiles,
plotType,
msLevel,
rtRange,
mzRange,
selectionPeaks,
((TICVisualizerParameters) parameters).getPeakLabelMap()));
} else {
MZmineCore.getDesktop()
.displayErrorMessage(
"No scans found at MS level " + msLevel + " within given retention time range.");
}
}
return ExitCode.OK;
}
public ExitCode showSetupDialog() {
JFileChooser chooser = new JFileChooser();
for (FileFilter filter : filters) chooser.setFileFilter(filter);
chooser.setFileFilter(filters[0]);
File lastFiles[] = getParameter(fileNames).getValue();
if ((lastFiles != null) && (lastFiles.length > 0)) {
File currentDir = lastFiles[0].getParentFile();
if ((currentDir != null) && (currentDir.exists())) chooser.setCurrentDirectory(currentDir);
}
chooser.setMultiSelectionEnabled(true);
int returnVal = chooser.showOpenDialog(MZmineCore.getDesktop().getMainWindow());
if (returnVal != JFileChooser.APPROVE_OPTION) return ExitCode.CANCEL;
File selectedFiles[] = chooser.getSelectedFiles();
getParameter(fileNames).setValue(selectedFiles);
return ExitCode.OK;
}
public MsMsVisualizerWindow(
RawDataFile dataFile,
Range<Double> rtRange,
Range<Double> mzRange,
IntensityType intensityType,
NormalizationType normalizationType,
Double minPeakInt,
ParameterSet parameters) {
super("MS/MS visualizer: [" + dataFile.getName() + "]");
setDefaultCloseOperation(DISPOSE_ON_CLOSE);
setBackground(Color.white);
this.dataFile = dataFile;
this.tooltipMode = true;
dataset =
new MsMsDataSet(
dataFile, rtRange, mzRange, intensityType, normalizationType, minPeakInt, this);
toolBar = new MsMsToolBar(this);
add(toolBar, BorderLayout.EAST);
IDAPlot = new MsMsPlot(this, dataFile, this, dataset, rtRange, mzRange);
add(IDAPlot, BorderLayout.CENTER);
bottomPanel = new MsMsBottomPanel(this, dataFile, parameters);
add(bottomPanel, BorderLayout.SOUTH);
updateTitle();
// After we have constructed everything, load the peak lists into the
// bottom panel
bottomPanel.rebuildPeakListSelector();
MZmineCore.getDesktop().addPeakListTreeListener(bottomPanel);
// Add the Windows menu
JMenuBar menuBar = new JMenuBar();
menuBar.add(new WindowsMenu());
setJMenuBar(menuBar);
pack();
// get the window settings parameter
ParameterSet paramSet =
MZmineCore.getConfiguration().getModuleParameters(MsMsVisualizerModule.class);
WindowSettingsParameter settings = paramSet.getParameter(MsMsParameters.windowSettings);
// update the window and listen for changes
settings.applySettingsToWindow(this);
this.addComponentListener(settings);
}
public static void showNewTICVisualizerWindow(
final RawDataFile[] dataFiles,
final ChromatographicPeak[] selectionPeaks,
final Map<ChromatographicPeak, String> peakLabels,
final int msLevel,
final PlotType plotType,
final Range rtRange,
final Range mzRange) {
MZmineCore.getDesktop()
.addInternalFrame(
new TICVisualizerWindow(
dataFiles, plotType, msLevel, rtRange, mzRange, selectionPeaks, peakLabels));
}
public void dispose() {
super.dispose();
MZmineCore.getDesktop().removePeakListTreeListener(bottomPanel);
}