Examples with MissingMassListException net.sf.mzmine.util.exceptions.MissingMassListException used on opensource projects

Example 1 with MissingMassListException

use of net.sf.mzmine.util.exceptions.MissingMassListException 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);
}

Example 2 with MissingMassListException

use of net.sf.mzmine.util.exceptions.MissingMassListException in project mzmine2 by mzmine.

the class SiriusThread method run.

@Override
public void run() {
    List<MsSpectrum> ms1list = new ArrayList<>(), ms2list = new ArrayList<>();
    try {
        Scan ms1Scan = peakListRow.getBestPeak().getRepresentativeScan();
        Collection<Scan> top10ms2Scans = ScanUtils.selectBestMS2Scans(peakListRow, massListName, 10);
        // Convert to MSDK data model
        ms1list.add(new MZmineToMSDKMsScan(ms1Scan));
        for (Scan s : top10ms2Scans) {
            ms2list.add(new MZmineToMSDKMsScan(s));
        }
    } catch (MissingMassListException f) {
        releaseResources();
        task.remoteCancel("Scan does not have requested Mass List name [" + massListName + "]");
        return;
    }
    FormulaConstraints constraints = ConstraintsGenerator.generateConstraint(range);
    IonType siriusIon = IonTypeUtil.createIonType(ionType.toString());
    List<IonAnnotation> siriusResults = null;
    SiriusIdentificationMethod siriusMethod = null;
    /*
     * Code block below gives SiriusMethod specific amount of time to be executed, if it expires ->
     * log error and continue
     */
    try {
        final SiriusIdentificationMethod method = new SiriusIdentificationMethod(ms1list, ms2list, peakListRow.getAverageMZ(), siriusIon, siriusCandidates, constraints, deviationPpm);
        // On some spectra it may never stop (halting problem), that's why interruptable thread is
        // used
        final Future<List<IonAnnotation>> f = service.submit(() -> {
            return method.execute();
        });
        siriusResults = f.get(siriusTimer, TimeUnit.SECONDS);
        siriusMethod = method;
        if (ms2list.isEmpty()) {
            /* If no MSMS spectra - add sirius results */
            addSiriusCompounds(siriusResults, peakListRow, siriusCandidates);
        } else {
            /* Initiate FingerId processing */
            Ms2Experiment experiment = siriusMethod.getExperiment();
            for (int index = 0; index < siriusCandidates; index++) {
                SiriusIonAnnotation annotation = (SiriusIonAnnotation) siriusResults.get(index);
                try {
                    FingerIdWebMethodTask task = new FingerIdWebMethodTask(annotation, experiment, fingeridCandidates, peakListRow);
                    MZmineCore.getTaskController().addTask(task, TaskPriority.NORMAL);
                    Thread.sleep(1000);
                } catch (InterruptedException interrupt) {
                    logger.error("Processing of FingerWebMethods were interrupted");
                    /* If interrupted, store last item */
                    List<IonAnnotation> lastItem = new LinkedList<>();
                    lastItem.add(annotation);
                    addSiriusCompounds(lastItem, peakListRow, 1);
                }
            }
        }
    } catch (InterruptedException | TimeoutException ie) {
        logger.error("Timeout on Sirius method expired, abort. Row id = {}", peakListRow.getID());
    } catch (ExecutionException ce) {
        logger.error("Concurrency error during Sirius method.  Row id = {}", peakListRow.getID());
    } finally {
        // Do not forget to release resources!
        releaseResources();
    }
}

Example 3 with MissingMassListException

use of net.sf.mzmine.util.exceptions.MissingMassListException in project mzmine2 by mzmine.

the class SingleRowIdentificationTask method run.

/**
 * @see Runnable#run()
 */
public void run() {
    setStatus(TaskStatus.PROCESSING);
    NumberFormat massFormater = MZmineCore.getConfiguration().getMZFormat();
    ResultWindow window = new ResultWindow(peakListRow, this);
    window.setTitle("SIRIUS/CSI-FingerID identification of " + massFormater.format(parentMass) + " m/z");
    window.setVisible(true);
    List<MsSpectrum> ms1list = new ArrayList<>(), ms2list = new ArrayList<>();
    try {
        Scan ms1Scan = peakListRow.getBestPeak().getRepresentativeScan();
        Collection<Scan> top10ms2Scans = ScanUtils.selectBestMS2Scans(peakListRow, massListName, 10);
        logger.debug("Adding MS1 scan " + ScanUtils.scanToString(ms1Scan, true) + " for SIRIUS identification");
        // Convert to MSDK data model
        ms1list.add(buildMSDKSpectrum(ms1Scan, massListName));
        for (Scan ms2Scan : top10ms2Scans) {
            logger.debug("Adding MS/MS scan " + ScanUtils.scanToString(ms2Scan, true) + " for SIRIUS identification");
            ms2list.add(buildMSDKSpectrum(ms2Scan, massListName));
        }
    } catch (MissingMassListException f) {
        showError(window, "Scan does not contain Mass List with requested name. [" + massListName + "]");
        return;
    }
    // Use executor to run Sirius Identification Method as an Interruptable thread.
    // Otherwise it may compute for too long (or even forever).
    final ExecutorService service = Executors.newSingleThreadExecutor();
    SiriusIdentificationMethod siriusMethod = null;
    List<IonAnnotation> siriusResults = null;
    /* Sirius processing */
    try {
        FormulaConstraints constraints = ConstraintsGenerator.generateConstraint(range);
        IonType type = IonTypeUtil.createIonType(ionType.toString());
        final SiriusIdentificationMethod method = new SiriusIdentificationMethod(ms1list, ms2list, parentMass, type, siriusCandidates, constraints, deviationPpm);
        final Future<List<IonAnnotation>> f = service.submit(() -> {
            return method.execute();
        });
        siriusResults = f.get(timer, TimeUnit.SECONDS);
        siriusMethod = method;
    } catch (InterruptedException | TimeoutException ie) {
        logger.error("Timeout on Sirius method expired, abort.");
        showError(window, String.format("Processing of the peaklist with mass %.2f by Sirius module expired.\n", parentMass) + "Reinitialize the task with larger Sirius Timer value.");
        return;
    } catch (ExecutionException ce) {
        ce.printStackTrace();
        logger.error("Concurrency error during Sirius method: " + ce.getMessage());
        showError(window, String.format("Sirius failed to predict compounds from row with id = %d", peakListRow.getID()));
        return;
    }
    /* FingerId processing */
    if (!ms2list.isEmpty()) {
        try {
            latch = new CountDownLatch(siriusResults.size());
            Ms2Experiment experiment = siriusMethod.getExperiment();
            fingerTasks = new LinkedList<>();
            /* Create a new FingerIdWebTask for each Sirius result */
            for (IonAnnotation ia : siriusResults) {
                SiriusIonAnnotation annotation = (SiriusIonAnnotation) ia;
                FingerIdWebMethodTask task = new FingerIdWebMethodTask(annotation, experiment, fingerCandidates, window);
                task.setLatch(latch);
                fingerTasks.add(task);
                MZmineCore.getTaskController().addTask(task, TaskPriority.NORMAL);
            }
            // Sleep for not overloading boecker-labs servers
            Thread.sleep(1000);
        } catch (InterruptedException interrupt) {
            logger.error("Processing of FingerWebMethods were interrupted");
        }
    } else {
        /* MS/MS spectrum is not present */
        window.addListofItems(siriusMethod.getResult());
    }
    // If there was a FingerId processing, wait until subtasks finish
    try {
        if (latch != null)
            latch.await();
    } catch (InterruptedException e) {
    }
    setStatus(TaskStatus.FINISHED);
}

Example 4 with MissingMassListException

use of net.sf.mzmine.util.exceptions.MissingMassListException 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);
}

Example 5 with MissingMassListException

use of net.sf.mzmine.util.exceptions.MissingMassListException in project mzmine2 by mzmine.

the class ScanUtils method listAllScans.

/**
 * List of all scans with n signals >= noiseLevel in the specified or first massList, if none was
 * specified
 *
 * @param massListName the name or null/empty to always use the first masslist
 * @param noiseLevel
 * @param minNumberOfSignals
 * @return
 */
@Nonnull
public static List<Scan> listAllScans(Scan[] scans, @Nullable String massListName, double noiseLevel, int minNumberOfSignals) throws MissingMassListException {
    List<Scan> filtered = new ArrayList<>();
    for (Scan scan : scans) {
        // find mass list: with name or first
        final MassList massList = getMassListOrFirst(scan, massListName);
        if (massList == null)
            throw new MissingMassListException("", massListName);
        // minimum number of signals >= noiseLevel
        int signals = 0;
        for (DataPoint dp : massList.getDataPoints()) if (dp.getIntensity() >= noiseLevel)
            signals++;
        if (signals >= minNumberOfSignals)
            filtered.add(scan);
    }
    return filtered;
}