use of net.sf.mzmine.util.spectraldb.entry.SpectralDBPeakIdentity in project mzmine2 by mzmine.
the class SpectralMatchTask method run.
/**
* @see java.lang.Runnable#run()
*/
@Override
public void run() {
// check for mass list
DataPoint[] spectraMassList;
try {
spectraMassList = getDataPoints(currentScan);
} catch (MissingMassListException e) {
// no mass list
setStatus(TaskStatus.ERROR);
setErrorMessage(MessageFormat.format("No masslist for name: {0} in scan {1} of raw file {2}", massListName, currentScan.getScanNumber(), currentScan.getDataFile().getName()));
return;
}
// remove 13C isotopes
if (removeIsotopes)
spectraMassList = removeIsotopes(spectraMassList);
setStatus(TaskStatus.PROCESSING);
try {
totalSteps = list.size();
matches = new ArrayList<>();
for (SpectralDBEntry ident : list) {
if (isCanceled()) {
logger.info("Added " + count + " spectral library matches (before being cancelled)");
repaintWindow();
return;
}
SpectralSimilarity sim = spectraDBMatch(spectraMassList, ident);
if (sim != null && (!needsIsotopePattern || checkForIsotopePattern(sim, mzToleranceSpectra, minMatchedIsoSignals))) {
count++;
// use SpectralDBPeakIdentity to store all results similar to peaklist method
matches.add(new SpectralDBPeakIdentity(currentScan, massListName, ident, sim, SpectraIdentificationSpectralDatabaseModule.MODULE_NAME));
}
// next row
finishedSteps++;
}
addIdentities(matches);
logger.info("Added " + count + " spectral library matches");
// check if no match was found
if (count == 0) {
logger.log(Level.WARNING, "No data base matches found");
setErrorMessage("No data base matches found. Spectral data base matching failed");
list = null;
return;
}
} catch (Exception e) {
setStatus(TaskStatus.ERROR);
logger.log(Level.SEVERE, "Spectral data base matching failed", e);
setErrorMessage("Spectral data base matching failed");
return;
}
// Repaint the window to reflect the change in the feature list
repaintWindow();
list = null;
setStatus(TaskStatus.FINISHED);
}
use of net.sf.mzmine.util.spectraldb.entry.SpectralDBPeakIdentity in project mzmine2 by mzmine.
the class RowsSpectralMatchTask method run.
/**
* @see java.lang.Runnable#run()
*/
@Override
public void run() {
setStatus(TaskStatus.PROCESSING);
for (PeakListRow row : rows) {
if (isCanceled()) {
logger.info("Added " + count + " spectral library matches (before being cancelled)");
repaintWindow();
return;
}
try {
// All MS2 or only best MS2 scan
// best MS1 scan
// check for MS1 or MSMS scan
List<Scan> scans = getScans(row);
List<DataPoint[]> rowMassLists = new ArrayList<>();
for (Scan scan : scans) {
// get mass list and perform deisotoping if active
DataPoint[] rowMassList = getDataPoints(scan, true);
if (removeIsotopes)
rowMassList = removeIsotopes(rowMassList);
rowMassLists.add(rowMassList);
}
// match against all library entries
for (SpectralDBEntry ident : list) {
SpectralDBPeakIdentity best = null;
// match all scans against this ident to find best match
for (int i = 0; i < scans.size(); i++) {
SpectralSimilarity sim = spectraDBMatch(row, rowMassLists.get(i), ident);
if (sim != null && (!needsIsotopePattern || SpectralMatchTask.checkForIsotopePattern(sim, mzToleranceSpectra, minMatchedIsoSignals)) && (best == null || best.getSimilarity().getScore() < sim.getScore())) {
best = new SpectralDBPeakIdentity(scans.get(i), massListName, ident, sim, METHOD);
}
}
// has match?
if (best != null) {
addIdentity(row, best);
count++;
}
}
// sort identities based on similarity score
SortSpectralDBIdentitiesTask.sortIdentities(row);
} catch (MissingMassListException e) {
logger.log(Level.WARNING, "No mass list in spectrum for rowID=" + row.getID(), e);
errorCounter++;
}
// check for max error (missing masslist)
if (errorCounter > MAX_ERROR) {
logger.log(Level.WARNING, "Data base matching failed. To many missing mass lists ");
setStatus(TaskStatus.ERROR);
setErrorMessage("Data base matching failed. To many missing mass lists ");
list = null;
return;
}
// next row
finishedRows++;
}
if (count > 0)
logger.info("Added " + count + " spectral library matches");
// Repaint the window to reflect the change in the feature list
repaintWindow();
list = null;
setStatus(TaskStatus.FINISHED);
}
use of net.sf.mzmine.util.spectraldb.entry.SpectralDBPeakIdentity in project mzmine2 by mzmine.
the class SortSpectralDBIdentitiesTask method sortIdentities.
/**
* Sort database matches by score
*
* @param row
* @param filterMinSimilarity
* @param minScore
*/
public static void sortIdentities(PeakListRow row, boolean filterMinSimilarity, double minScore) {
// get all row identities
PeakIdentity[] identities = row.getPeakIdentities();
if (identities == null || identities.length == 0)
return;
// filter for SpectralDBPeakIdentity and write to map
List<SpectralDBPeakIdentity> match = new ArrayList<>();
for (PeakIdentity identity : identities) {
if (identity instanceof SpectralDBPeakIdentity) {
row.removePeakIdentity(identity);
if (!filterMinSimilarity || ((SpectralDBPeakIdentity) identity).getSimilarity().getScore() >= minScore)
match.add((SpectralDBPeakIdentity) identity);
}
}
if (match.isEmpty())
return;
// reversed order: by similarity score
match.sort((a, b) -> {
return Double.compare(b.getSimilarity().getScore(), a.getSimilarity().getScore());
});
for (SpectralDBPeakIdentity entry : match) {
row.addPeakIdentity(entry, false);
}
row.setPreferredPeakIdentity(match.get(0));
// Notify the GUI about the change in the project
MZmineCore.getProjectManager().getCurrentProject().notifyObjectChanged(row, false);
}
use of net.sf.mzmine.util.spectraldb.entry.SpectralDBPeakIdentity in project mzmine2 by mzmine.
the class PeakListTablePopupMenu method actionPerformed.
@Override
public void actionPerformed(final ActionEvent e) {
final Object src = e.getSource();
if (deleteRowsItem.equals(src)) {
final int[] rowsToDelete = table.getSelectedRows();
final int[] unsortedIndexes = new int[rowsToDelete.length];
for (int i = rowsToDelete.length - 1; i >= 0; i--) {
unsortedIndexes[i] = table.convertRowIndexToModel(rowsToDelete[i]);
}
// sort row indexes and start removing from the last
Arrays.sort(unsortedIndexes);
// delete the rows starting from last
for (int i = unsortedIndexes.length - 1; i >= 0; i--) {
peakList.removeRow(unsortedIndexes[i]);
}
// Notify the GUI that peaklist contents have changed
updateTableGUI();
}
if (plotRowsItem.equals(src)) {
final int[] selectedTableRows = table.getSelectedRows();
final PeakListRow[] selectedRows = new PeakListRow[selectedTableRows.length];
for (int i = 0; i < selectedTableRows.length; i++) {
selectedRows[i] = getPeakListRow(table.convertRowIndexToModel(selectedTableRows[i]));
}
SwingUtilities.invokeLater(new Runnable() {
@Override
public void run() {
IntensityPlotModule.showIntensityPlot(MZmineCore.getProjectManager().getCurrentProject(), peakList, selectedRows);
}
});
}
if (showXICItem.equals(src) && allClickedPeakListRows.length != 0) {
// Map peaks to their identity labels.
final Map<Feature, String> labelsMap = new HashMap<Feature, String>(allClickedPeakListRows.length);
final RawDataFile selectedDataFile = clickedDataFile == null ? allClickedPeakListRows[0].getBestPeak().getDataFile() : clickedDataFile;
Range<Double> mzRange = null;
final List<Feature> selectedPeaks = new ArrayList<Feature>(allClickedPeakListRows.length);
for (final PeakListRow row : allClickedPeakListRows) {
for (final Feature peak : row.getPeaks()) {
if (mzRange == null) {
mzRange = peak.getRawDataPointsMZRange();
double upper = mzRange.upperEndpoint();
double lower = mzRange.lowerEndpoint();
if ((upper - lower) < 0.000001) {
// Workaround to make ultra narrow mzRanges (e.g. from imported mzTab peaklist),
// a more reasonable default for a HRAM instrument (~5ppm)
double fiveppm = (upper * 5E-6);
mzRange = Range.closed(lower - fiveppm, upper + fiveppm);
}
} else {
mzRange = mzRange.span(peak.getRawDataPointsMZRange());
}
}
final Feature filePeak = row.getPeak(selectedDataFile);
if (filePeak != null) {
selectedPeaks.add(filePeak);
// Label the peak with the row's preferred identity.
final PeakIdentity identity = row.getPreferredPeakIdentity();
if (identity != null) {
labelsMap.put(filePeak, identity.getName());
}
}
}
ScanSelection scanSelection = new ScanSelection(selectedDataFile.getDataRTRange(1), 1);
TICVisualizerModule.showNewTICVisualizerWindow(new RawDataFile[] { selectedDataFile }, selectedPeaks.toArray(new Feature[selectedPeaks.size()]), labelsMap, scanSelection, TICPlotType.BASEPEAK, mzRange);
}
if (showXICSetupItem.equals(src) && allClickedPeakListRows.length != 0) {
// Map peaks to their identity labels.
final Map<Feature, String> labelsMap = new HashMap<Feature, String>(allClickedPeakListRows.length);
final RawDataFile[] selectedDataFiles = clickedDataFile == null ? peakList.getRawDataFiles() : new RawDataFile[] { clickedDataFile };
Range<Double> mzRange = null;
final ArrayList<Feature> allClickedPeaks = new ArrayList<Feature>(allClickedPeakListRows.length);
final ArrayList<Feature> selectedClickedPeaks = new ArrayList<Feature>(allClickedPeakListRows.length);
for (final PeakListRow row : allClickedPeakListRows) {
// Label the peak with the row's preferred identity.
final PeakIdentity identity = row.getPreferredPeakIdentity();
for (final Feature peak : row.getPeaks()) {
allClickedPeaks.add(peak);
if (peak.getDataFile() == clickedDataFile) {
selectedClickedPeaks.add(peak);
}
if (mzRange == null) {
mzRange = peak.getRawDataPointsMZRange();
} else {
mzRange = mzRange.span(peak.getRawDataPointsMZRange());
}
if (identity != null) {
labelsMap.put(peak, identity.getName());
}
}
}
ScanSelection scanSelection = new ScanSelection(selectedDataFiles[0].getDataRTRange(1), 1);
TICVisualizerModule.setupNewTICVisualizer(MZmineCore.getProjectManager().getCurrentProject().getDataFiles(), selectedDataFiles, allClickedPeaks.toArray(new Feature[allClickedPeaks.size()]), selectedClickedPeaks.toArray(new Feature[selectedClickedPeaks.size()]), labelsMap, scanSelection, mzRange);
}
if (show2DItem.equals(src)) {
final Feature showPeak = getSelectedPeak();
if (showPeak != null) {
TwoDVisualizerModule.show2DVisualizerSetupDialog(showPeak.getDataFile(), getPeakMZRange(showPeak), getPeakRTRange(showPeak));
}
}
if (show3DItem.equals(src)) {
final Feature showPeak = getSelectedPeak();
if (showPeak != null) {
Fx3DVisualizerModule.setupNew3DVisualizer(showPeak.getDataFile(), getPeakMZRange(showPeak), getPeakRTRange(showPeak), showPeak);
}
}
if (manuallyDefineItem.equals(src)) {
// ManualPeakPickerModule.runManualDetection(clickedDataFile, clickedPeakListRow, peakList,
// table);
XICManualPickerModule.runManualDetection(clickedDataFile, clickedPeakListRow, peakList, table);
}
if (showSpectrumItem.equals(src)) {
final Feature showPeak = getSelectedPeak();
if (showPeak != null) {
SpectraVisualizerModule.showNewSpectrumWindow(showPeak.getDataFile(), showPeak.getRepresentativeScanNumber(), showPeak);
}
}
if (openCompoundIdUrl.equals(src)) {
if (clickedPeakListRow != null && clickedPeakListRow.getPreferredPeakIdentity() != null) {
String url = clickedPeakListRow.getPreferredPeakIdentity().getPropertyValue(PeakIdentity.PROPERTY_URL);
if (url != null && !url.isEmpty() && Desktop.isDesktopSupported()) {
try {
Desktop.getDesktop().browse(new URI(url));
} catch (IOException | URISyntaxException e1) {
}
}
}
}
if (showMSMSItem.equals(src)) {
if (allClickedPeakListRows != null && allClickedPeakListRows.length > 1) {
// show multi msms window of multiple rows
MultiMSMSWindow multi = new MultiMSMSWindow();
multi.setData(allClickedPeakListRows, peakList.getRawDataFiles(), clickedDataFile, true, SortingProperty.MZ, SortingDirection.Ascending);
multi.setVisible(true);
} else {
Feature showPeak = getSelectedPeakForMSMS();
if (showPeak != null) {
final int scanNumber = showPeak.getMostIntenseFragmentScanNumber();
if (scanNumber > 0) {
SpectraVisualizerModule.showNewSpectrumWindow(showPeak.getDataFile(), scanNumber);
} else {
MZmineCore.getDesktop().displayMessage(window, "There is no fragment for " + MZmineCore.getConfiguration().getMZFormat().format(showPeak.getMZ()) + " m/z in the current raw data.");
}
}
}
}
// mirror of the two best fragment scans
if (showMSMSMirrorItem.equals(src)) {
if (allClickedPeakListRows != null && allClickedPeakListRows.length == 2) {
PeakListRow a = allClickedPeakListRows[0];
PeakListRow b = allClickedPeakListRows[1];
Scan scan = a.getBestFragmentation();
Scan mirror = b.getBestFragmentation();
if (scan != null && mirror != null) {
// show mirror msms window of two rows
MirrorScanWindow mirrorWindow = new MirrorScanWindow();
mirrorWindow.setScans(scan, mirror);
mirrorWindow.setVisible(true);
}
}
}
// show spectral db matches
if (showSpectralDBResults.equals(src)) {
List<SpectralDBPeakIdentity> spectralID = Arrays.stream(clickedPeakListRow.getPeakIdentities()).filter(pi -> pi instanceof SpectralDBPeakIdentity).map(pi -> ((SpectralDBPeakIdentity) pi)).collect(Collectors.toList());
if (!spectralID.isEmpty()) {
SpectraIdentificationResultsWindow window = new SpectraIdentificationResultsWindow();
window.addMatches(spectralID);
window.setTitle("Matched " + spectralID.size() + " compounds for feature list row" + clickedPeakListRow.getID());
window.setVisible(true);
}
}
if (showAllMSMSItem.equals(src)) {
final Feature showPeak = getSelectedPeakForMSMS();
RawDataFile raw = clickedPeakListRow.getBestFragmentation().getDataFile();
if (showPeak != null && showPeak.getMostIntenseFragmentScanNumber() != 0)
raw = showPeak.getDataFile();
if (clickedPeakListRow.getBestFragmentation() != null) {
MultiSpectraVisualizerWindow multiSpectraWindow = new MultiSpectraVisualizerWindow(clickedPeakListRow, raw);
multiSpectraWindow.setVisible(true);
} else {
MZmineCore.getDesktop().displayMessage(window, "There is no fragment for " + MZmineCore.getConfiguration().getMZFormat().format(showPeak.getMZ()) + " m/z in the current raw data.");
}
}
if (showIsotopePatternItem.equals(src)) {
final Feature showPeak = getSelectedPeak();
if (showPeak != null && showPeak.getIsotopePattern() != null) {
SwingUtilities.invokeLater(new Runnable() {
@Override
public void run() {
SpectraVisualizerModule.showNewSpectrumWindow(showPeak.getDataFile(), showPeak.getRepresentativeScanNumber(), showPeak.getIsotopePattern());
}
});
}
}
if (formulaItem != null && formulaItem.equals(src)) {
SwingUtilities.invokeLater(new Runnable() {
@Override
public void run() {
FormulaPredictionModule.showSingleRowIdentificationDialog(clickedPeakListRow);
}
});
}
// peak.
if (siriusItem != null && siriusItem.equals(src)) {
SwingUtilities.invokeLater(new Runnable() {
@Override
public void run() {
SiriusProcessingModule.showSingleRowIdentificationDialog(clickedPeakListRow);
}
});
}
if (onlineDbSearchItem != null && onlineDbSearchItem.equals(src)) {
SwingUtilities.invokeLater(new Runnable() {
@Override
public void run() {
OnlineDBSearchModule.showSingleRowIdentificationDialog(clickedPeakListRow);
}
});
}
if (spectralDbSearchItem != null && spectralDbSearchItem.equals(src)) {
SwingUtilities.invokeLater(new Runnable() {
@Override
public void run() {
LocalSpectralDBSearchModule.showSelectedRowsIdentificationDialog(allClickedPeakListRows, table);
}
});
}
if (nistSearchItem != null && nistSearchItem.equals(src)) {
NistMsSearchModule.singleRowSearch(peakList, clickedPeakListRow);
}
if (addNewRowItem.equals(src)) {
// find maximum ID and add 1
int newID = 1;
for (final PeakListRow row : peakList.getRows()) {
if (row.getID() >= newID) {
newID = row.getID() + 1;
}
}
// create a new row
final PeakListRow newRow = new SimplePeakListRow(newID);
ManualPeakPickerModule.runManualDetection(peakList.getRawDataFiles(), newRow, peakList, table);
}
if (showPeakRowSummaryItem.equals(src)) {
PeakSummaryVisualizerModule.showNewPeakSummaryWindow(clickedPeakListRow);
}
if (exportIsotopesItem.equals(src)) {
IsotopePatternExportModule.exportIsotopePattern(clickedPeakListRow);
}
if (exportToSirius.equals(src)) {
// export all selected rows
SiriusExportModule.exportSingleRows(allClickedPeakListRows);
}
if (exportMSMSLibrary.equals(src)) {
// open window with all selected rows
MSMSLibrarySubmissionWindow libraryWindow = new MSMSLibrarySubmissionWindow();
libraryWindow.setData(allClickedPeakListRows, SortingProperty.MZ, SortingDirection.Ascending, true);
libraryWindow.setVisible(true);
}
if (exportMS1Library.equals(src)) {
// open window with all selected rows
MSMSLibrarySubmissionWindow libraryWindow = new MSMSLibrarySubmissionWindow();
libraryWindow.setData(allClickedPeakListRows, SortingProperty.MZ, SortingDirection.Ascending, false);
libraryWindow.setVisible(true);
}
if (exportMSMSItem.equals(src)) {
MSMSExportModule.exportMSMS(clickedPeakListRow);
}
if (clearIdsItem.equals(src)) {
// Delete identities of selected rows.
for (final PeakListRow row : allClickedPeakListRows) {
// Selected row index.
for (final PeakIdentity id : row.getPeakIdentities()) {
// Remove id.
row.removePeakIdentity(id);
}
}
// Update table GUI.
updateTableGUI();
}
if (copyIdsItem.equals(src) && allClickedPeakListRows.length > 0) {
final PeakIdentity id = allClickedPeakListRows[0].getPreferredPeakIdentity();
if (id != null) {
copiedId = (PeakIdentity) id.clone();
}
}
if (pasteIdsItem.equals(src) && copiedId != null) {
// Paste identity into selected rows.
for (final PeakListRow row : allClickedPeakListRows) {
row.setPreferredPeakIdentity((PeakIdentity) copiedId.clone());
}
// Update table GUI.
updateTableGUI();
}
}
use of net.sf.mzmine.util.spectraldb.entry.SpectralDBPeakIdentity in project mzmine2 by mzmine.
the class SpectralMatchTask method addIdentities.
private void addIdentities(List<SpectralDBPeakIdentity> matches) {
for (SpectralDBPeakIdentity match : matches) {
try {
// TODO put into separate method and add comments
// get data points of matching scans
DataPoint[] spectraMassList = getDataPoints(currentScan);
List<DataPoint[]> alignedDataPoints = ScanAlignment.align(mzToleranceSpectra, match.getEntry().getDataPoints(), spectraMassList);
alignedSignals = ScanAlignment.removeUnaligned(alignedDataPoints);
// add new mass list to the spectra for match
DataPoint[] dataset = new DataPoint[alignedSignals.size()];
for (int i = 0; i < dataset.length; i++) {
dataset[i] = alignedSignals.get(i)[1];
}
String compoundName = match.getEntry().getField(DBEntryField.NAME).toString();
String shortName = compoundName;
// TODO remove or specify more - special naming format?
int start = compoundName.indexOf("[");
int end = compoundName.indexOf("]");
if (start != -1 && start + 1 < compoundName.length() && end != -1 && end < compoundName.length())
shortName = compoundName.substring(start + 1, end);
DataPointsDataSet detectedCompoundsDataset = new DataPointsDataSet(shortName + " " + "Score: " + COS_FORM.format(match.getSimilarity().getScore()), dataset);
spectraPlot.addDataSet(detectedCompoundsDataset, new Color((int) (Math.random() * 0x1000000)), true);
} catch (MissingMassListException e) {
logger.log(Level.WARNING, "No mass list for the selected spectrum", e);
errorCounter++;
}
}
resultWindow.addMatches(matches);
resultWindow.revalidate();
resultWindow.repaint();
setStatus(TaskStatus.FINISHED);
}
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