use of net.sf.mzmine.desktop.impl.projecttree.RawDataTreeModel in project mzmine2 by mzmine.
the class StorableScan method removeMassList.
@Override
public synchronized void removeMassList(@Nonnull final MassList massList) {
// Remove the mass list
massLists.remove(massList);
if (massList instanceof StorableMassList) {
StorableMassList storableMassList = (StorableMassList) massList;
storableMassList.removeStoredData();
}
// Remove from the tree model
MZmineProjectImpl project = (MZmineProjectImpl) MZmineCore.getProjectManager().getCurrentProject();
// Check if we are using the current project
if (Arrays.asList(project.getDataFiles()).contains(rawDataFile)) {
final RawDataTreeModel treeModel = project.getRawDataTreeModel();
Runnable swingCode = new Runnable() {
@Override
public void run() {
treeModel.removeObject(massList);
}
};
SwingUtilities.invokeLater(swingCode);
}
}
use of net.sf.mzmine.desktop.impl.projecttree.RawDataTreeModel in project mzmine2 by mzmine.
the class MassDetectionTask method run.
/**
* @see Runnable#run()
*/
public void run() {
// make arrays to contain everything you need
ArrayList<Integer> pointsInScans = new ArrayList<>();
ArrayList<Double> allMZ = new ArrayList<>();
ArrayList<Double> allIntensities = new ArrayList<>();
// idecies of full mass list where scan starts?
ArrayList<Integer> startIndex = new ArrayList<>();
ArrayList<Double> scanAcquisitionTime = new ArrayList<>();
// XCMS needs this one
ArrayList<Double> totalIntensity = new ArrayList<>();
double curTotalIntensity;
int lastPointCount = 0;
startIndex.add(0);
try {
setStatus(TaskStatus.PROCESSING);
logger.info("Started mass detector on " + dataFile);
final Scan[] scans = scanSelection.getMatchingScans(dataFile);
totalScans = scans.length;
// Process scans one by one
for (Scan scan : scans) {
if (isCanceled())
return;
MassDetector detector = massDetector.getModule();
DataPoint[] mzPeaks = detector.getMassValues(scan, massDetector.getParameterSet());
SimpleMassList newMassList = new SimpleMassList(name, scan, mzPeaks);
// Add new mass list to the scan
scan.addMassList(newMassList);
if (this.saveToCDF) {
curTotalIntensity = 0;
for (int a = 0; a < mzPeaks.length; a++) {
DataPoint curMzPeak = mzPeaks[a];
allMZ.add(curMzPeak.getMZ());
allIntensities.add(curMzPeak.getIntensity());
curTotalIntensity += curMzPeak.getIntensity();
}
scanAcquisitionTime.add(scan.getRetentionTime());
pointsInScans.add(0);
startIndex.add(mzPeaks.length + lastPointCount);
totalIntensity.add(curTotalIntensity);
lastPointCount = mzPeaks.length + lastPointCount;
}
processedScans++;
}
// Update the GUI with all new mass lists
MZmineProjectImpl project = (MZmineProjectImpl) MZmineCore.getProjectManager().getCurrentProject();
final RawDataTreeModel treeModel = project.getRawDataTreeModel();
treeModel.updateGUIWithNewObjects();
;
if (this.saveToCDF) {
// ************** write mass list *******************************
final String outFileNamePath = outFilename.getPath();
logger.info("Saving mass detector results to netCDF file " + outFileNamePath);
NetcdfFileWriter writer = NetcdfFileWriter.createNew(NetcdfFileWriter.Version.netcdf3, outFileNamePath, null);
Dimension dim_massValues = writer.addDimension(null, "mass_values", allMZ.size());
Dimension dim_intensityValues = writer.addDimension(null, "intensity_values", allIntensities.size());
Dimension dim_scanIndex = writer.addDimension(null, "scan_index", startIndex.size() - 1);
Dimension dim_scanAcquisitionTime = writer.addDimension(null, "scan_acquisition_time", scanAcquisitionTime.size());
Dimension dim_totalIntensity = writer.addDimension(null, "total_intensity", totalIntensity.size());
Dimension dim_pointsInScans = writer.addDimension(null, "point_count", pointsInScans.size());
// add dimensions to list
List<Dimension> dims = new ArrayList<>();
dims.add(dim_massValues);
dims.add(dim_intensityValues);
dims.add(dim_scanIndex);
dims.add(dim_scanAcquisitionTime);
dims.add(dim_totalIntensity);
dims.add(dim_pointsInScans);
// make the variables that contain the actual data I think.
Variable var_massValues = writer.addVariable(null, "mass_values", DataType.DOUBLE, "mass_values");
Variable var_intensityValues = writer.addVariable(null, "intensity_values", DataType.DOUBLE, "intensity_values");
Variable var_scanIndex = writer.addVariable(null, "scan_index", DataType.INT, "scan_index");
Variable var_scanAcquisitionTime = writer.addVariable(null, "scan_acquisition_time", DataType.DOUBLE, "scan_acquisition_time");
Variable var_totalIntensity = writer.addVariable(null, "total_intensity", DataType.DOUBLE, "total_intensity");
Variable var_pointsInScans = writer.addVariable(null, "point_count", DataType.INT, "point_count");
var_massValues.addAttribute(new Attribute("units", "M/Z"));
var_intensityValues.addAttribute(new Attribute("units", "Arbitrary Intensity Units"));
var_scanIndex.addAttribute(new Attribute("units", "index"));
var_scanAcquisitionTime.addAttribute(new Attribute("units", "seconds"));
var_totalIntensity.addAttribute(new Attribute("units", "Arbitrary Intensity Units"));
var_pointsInScans.addAttribute(new Attribute("units", "count"));
var_massValues.addAttribute(new Attribute("scale_factor", 1.0));
var_intensityValues.addAttribute(new Attribute("scale_factor", 1.0));
var_scanIndex.addAttribute(new Attribute("scale_factor", 1.0));
var_scanAcquisitionTime.addAttribute(new Attribute("scale_factor", 1.0));
var_totalIntensity.addAttribute(new Attribute("scale_factor", 1.0));
var_pointsInScans.addAttribute(new Attribute("scale_factor", 1.0));
// create file
writer.create();
ArrayDouble.D1 arr_massValues = new ArrayDouble.D1(dim_massValues.getLength());
ArrayDouble.D1 arr_intensityValues = new ArrayDouble.D1(dim_intensityValues.getLength());
ArrayDouble.D1 arr_scanIndex = new ArrayDouble.D1(dim_scanIndex.getLength());
ArrayDouble.D1 arr_scanAcquisitionTime = new ArrayDouble.D1(dim_scanAcquisitionTime.getLength());
ArrayDouble.D1 arr_totalIntensity = new ArrayDouble.D1(dim_totalIntensity.getLength());
ArrayDouble.D1 arr_pointsInScans = new ArrayDouble.D1(dim_pointsInScans.getLength());
for (int i = 0; i < allMZ.size(); i++) {
arr_massValues.set(i, allMZ.get(i));
arr_intensityValues.set(i, allIntensities.get(i));
}
int i = 0;
for (; i < scanAcquisitionTime.size(); i++) {
arr_scanAcquisitionTime.set(i, scanAcquisitionTime.get(i) * 60);
arr_pointsInScans.set(i, pointsInScans.get(i));
arr_scanIndex.set(i, startIndex.get(i));
arr_totalIntensity.set(i, totalIntensity.get(i));
}
// arr_scanIndex.set(i,startIndex.get(i));
// For tiny test file
// arr_intensityValues .set(0,200);
// arr_scanIndex .set(0,0);
// arr_scanAcquisitionTime .set(0,10);
// arr_totalIntensity .set(0,200);
// arr_pointsInScans .set(0,0);
// arr_intensityValues .set(1,300);
// arr_scanIndex .set(1,1);
// arr_scanAcquisitionTime .set(1,20);
// arr_totalIntensity .set(1,300);
// arr_pointsInScans .set(1,0);
writer.write(var_massValues, arr_massValues);
writer.write(var_intensityValues, arr_intensityValues);
writer.write(var_scanIndex, arr_scanIndex);
writer.write(var_scanAcquisitionTime, arr_scanAcquisitionTime);
writer.write(var_totalIntensity, arr_totalIntensity);
writer.write(var_pointsInScans, arr_pointsInScans);
writer.close();
}
} catch (Exception e) {
e.printStackTrace();
setErrorMessage(e.getMessage());
setStatus(TaskStatus.ERROR);
}
setStatus(TaskStatus.FINISHED);
logger.info("Finished mass detector on " + dataFile);
}
use of net.sf.mzmine.desktop.impl.projecttree.RawDataTreeModel in project mzmine2 by mzmine.
the class SortDataFilesModule method runModule.
@Override
@Nonnull
public ExitCode runModule(@Nonnull MZmineProject project, @Nonnull ParameterSet parameters, @Nonnull Collection<Task> tasks) {
List<RawDataFile> dataFiles = Arrays.asList(parameters.getParameter(SortDataFilesParameters.dataFiles).getValue().getMatchingRawDataFiles());
RawDataTreeModel model = null;
if (project instanceof MZmineProjectImpl) {
model = ((MZmineProjectImpl) project).getRawDataTreeModel();
} else if (MZmineCore.getDesktop() instanceof MainWindow) {
ProjectTree tree = ((MainWindow) MZmineCore.getDesktop()).getMainPanel().getRawDataTree();
model = (RawDataTreeModel) tree.getModel();
}
if (model == null)
throw new MSDKRuntimeException("Cannot find raw data file tree model for sorting. Different MZmine project impl?");
final DefaultMutableTreeNode rootNode = model.getRoot();
// Get all tree nodes that represent selected data files, and remove
// them from
final ArrayList<DefaultMutableTreeNode> selectedNodes = new ArrayList<DefaultMutableTreeNode>();
for (int row = 0; row < rootNode.getChildCount(); row++) {
DefaultMutableTreeNode selectedNode = (DefaultMutableTreeNode) rootNode.getChildAt(row);
Object selectedObject = selectedNode.getUserObject();
if (dataFiles.contains(selectedObject)) {
selectedNodes.add(selectedNode);
}
}
// Get the index of the first selected item
final ArrayList<Integer> positions = new ArrayList<Integer>();
for (DefaultMutableTreeNode node : selectedNodes) {
int nodeIndex = rootNode.getIndex(node);
if (nodeIndex != -1)
positions.add(nodeIndex);
}
if (positions.isEmpty())
return ExitCode.ERROR;
int insertPosition = Collections.min(positions);
// Sort the data files by name
Collections.sort(selectedNodes, new Comparator<DefaultMutableTreeNode>() {
@Override
public int compare(DefaultMutableTreeNode o1, DefaultMutableTreeNode o2) {
return o1.getUserObject().toString().compareTo(o2.getUserObject().toString());
}
});
// Reorder the nodes in the tree model
for (DefaultMutableTreeNode node : selectedNodes) {
model.removeNodeFromParent(node);
model.insertNodeInto(node, rootNode, insertPosition);
insertPosition++;
}
return ExitCode.OK;
}
use of net.sf.mzmine.desktop.impl.projecttree.RawDataTreeModel in project mzmine2 by mzmine.
the class StorableScan method addMassList.
@Override
public synchronized void addMassList(@Nonnull final MassList massList) {
// Remove all mass lists with same name, if there are any
MassList[] currentMassLists = massLists.toArray(new MassList[0]);
for (MassList ml : currentMassLists) {
if (ml.getName().equals(massList.getName()))
removeMassList(ml);
}
StorableMassList storedMassList;
if (massList instanceof StorableMassList) {
storedMassList = (StorableMassList) massList;
} else {
DataPoint[] massListDataPoints = massList.getDataPoints();
try {
int mlStorageID = rawDataFile.storeDataPoints(massListDataPoints);
storedMassList = new StorableMassList(rawDataFile, mlStorageID, massList.getName(), this);
} catch (IOException e) {
logger.severe("Could not write data to temporary file " + e.toString());
return;
}
}
// Add the new mass list
massLists.add(storedMassList);
// Add the mass list to the tree model
MZmineProjectImpl project = (MZmineProjectImpl) MZmineCore.getProjectManager().getCurrentProject();
// Check if we are adding to the current project
if (Arrays.asList(project.getDataFiles()).contains(rawDataFile)) {
final RawDataTreeModel treeModel = project.getRawDataTreeModel();
treeModel.addObjectWithoutGUIUpdate(storedMassList);
}
}
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