Examples with PeakListRow net.sf.mzmine.datamodel.PeakListRow used on opensource projects

Example 96 with PeakListRow

use of net.sf.mzmine.datamodel.PeakListRow in project mzmine2 by mzmine.

the class NistMsSearchTask method findPeakRowGroup.

/**
 * Determines the contemporaneity between all pairs of non-identical peak rows.
 *
 * @return a map holding pairs of adjacent (non-identical) peak rows. (x,y) <=> (y,x)
 */
private Set<PeakListRow> findPeakRowGroup() {
    // Create neighbourhood.
    final Set<PeakListRow> neighbours = new HashSet<PeakListRow>(INITIAL_NEIGHBOURHOOD_SIZE);
    // Contemporaneous with self.
    neighbours.add(peakListRow);
    // Find neighbours.
    final double rt = peakListRow.getAverageRT();
    for (final PeakListRow row2 : peakList.getRows()) {
        // Are peak rows contemporaneous?
        if (!peakListRow.equals(row2) && rtTolerance.checkWithinTolerance(rt, row2.getAverageRT()) && (!sameIds || checkSameIds(peakListRow, row2))) {
            neighbours.add(row2);
        }
    }
    return neighbours;
}

Example 97 with PeakListRow

use of net.sf.mzmine.datamodel.PeakListRow in project mzmine2 by mzmine.

the class NistMsSearchTask method writeSpectraFile.

/**
 * Writes a search spectrum file for the given row and its neighbours.
 *
 * @param peakRow the row.
 * @param neighbourRows its neighbouring rows.
 * @return the file.
 * @throws IOException if an i/o problem occurs.
 */
private File writeSpectraFile(final PeakListRow peakRow, final Collection<PeakListRow> neighbourRows) throws IOException {
    final File spectraFile = File.createTempFile(SPECTRA_FILE_PREFIX, SPECTRA_FILE_SUFFIX);
    spectraFile.deleteOnExit();
    final BufferedWriter writer = new BufferedWriter(new FileWriter(spectraFile));
    try {
        LOG.finest("Writing spectra to file " + spectraFile);
        // Write header.
        final PeakIdentity identity = peakRow.getPreferredPeakIdentity();
        final String name = SPECTRUM_NAME_PREFIX + peakRow.getID() + (identity == null ? "" : " (" + identity + ')') + " of " + peakList.getName();
        writer.write("Name: " + name.substring(0, Math.min(SPECTRUM_NAME_MAX_LENGTH, name.length())));
        writer.newLine();
        writer.write("Num Peaks: " + neighbourRows.size());
        writer.newLine();
        for (final PeakListRow row : neighbourRows) {
            final Feature peak = row.getBestPeak();
            final int charge = peak.getCharge();
            final double mass = (peak.getMZ() - ionType.getAddedMass()) * (charge == 0 ? 1.0 : (double) charge);
            writer.write(mass + "\t" + peak.getHeight());
            writer.newLine();
        }
    } finally {
        // Close the open file.
        writer.close();
    }
    return spectraFile;
}

Example 98 with PeakListRow

use of net.sf.mzmine.datamodel.PeakListRow in project mzmine2 by mzmine.

the class PeakListIdentificationTask method run.

@Override
public void run() {
    if (!isCanceled()) {
        try {
            setStatus(TaskStatus.PROCESSING);
            // Create database gateway.
            gateway = db.getModule().getGatewayClass().newInstance();
            // Identify the feature list rows starting from the biggest peaks.
            final PeakListRow[] rows = peakList.getRows();
            Arrays.sort(rows, new PeakListRowSorter(SortingProperty.Area, SortingDirection.Descending));
            // Initialize counters.
            numItems = rows.length;
            // Process rows.
            for (finishedItems = 0; !isCanceled() && finishedItems < numItems; finishedItems++) {
                // Retrieve results for each row.
                retrieveIdentification(rows[finishedItems]);
            }
            if (!isCanceled()) {
                setStatus(TaskStatus.FINISHED);
            }
        } catch (Throwable t) {
            final String msg = "Could not search " + db;
            LOG.log(Level.WARNING, msg, t);
            setStatus(TaskStatus.ERROR);
            setErrorMessage(msg + ": " + ExceptionUtils.exceptionToString(t));
        }
    }
}

Example 99 with PeakListRow

use of net.sf.mzmine.datamodel.PeakListRow in project mzmine2 by mzmine.

the class NistMsSearchTask method trimNeighbours.

/**
 * Trims the row neighbourhoods to the specified size.
 *
 * @param neighbourhoods map from each feature list row to its neighbours.
 */
private void trimNeighbours(final Map<PeakListRow, Set<PeakListRow>> neighbourhoods) {
    if (maxPeaks > 0) {
        // Process each row's neighbour list.
        for (final Entry<PeakListRow, Set<PeakListRow>> entry : neighbourhoods.entrySet()) {
            final PeakListRow row = entry.getKey();
            final Set<PeakListRow> neighbours = entry.getValue();
            // Need trimming?
            if (neighbours.size() > maxPeaks) {
                final List<PeakListRow> keepers = new ArrayList<PeakListRow>(neighbours);
                // Exclude current row from sorting.
                keepers.remove(row);
                // Sort on RT difference (ascending) then intensity
                // (descending)
                final double rt = row.getAverageRT();
                Collections.sort(keepers, new Comparator<PeakListRow>() {

                    @Override
                    public int compare(final PeakListRow o1, final PeakListRow o2) {
                        // Compare on RT difference (ascending).
                        final int compare = Double.compare(Math.abs(rt - o1.getAverageRT()), Math.abs(rt - o2.getAverageRT()));
                        // difference.
                        return compare == 0 ? Double.compare(o2.getAverageHeight(), o1.getAverageHeight()) : compare;
                    }
                });
                // Add the current row and keepers up to maxPeaks.
                neighbours.clear();
                neighbours.add(row);
                neighbours.addAll(keepers.subList(0, maxPeaks - 1));
            }
        }
    }
}

Example 100 with PeakListRow

use of net.sf.mzmine.datamodel.PeakListRow in project mzmine2 by mzmine.

the class NistMsSearchTask method nistSearch.

/**
 * Run the NIST search.
 *
 * @throws IOException if there are i/o problems.
 */
private void nistSearch() throws IOException {
    // Waiting to get the SEMAPHORE: only one instance of NIST MS Search can
    // run at a time.
    setStatus(TaskStatus.WAITING);
    synchronized (SEMAPHORE) {
        File locatorFile2 = null;
        try {
            if (!isCanceled()) {
                setStatus(TaskStatus.PROCESSING);
                // Configure locator files.
                final File locatorFile1 = new File(nistMsSearchDir, PRIMARY_LOCATOR_FILE_NAME);
                locatorFile2 = getSecondLocatorFile(locatorFile1);
                if (locatorFile2 == null) {
                    throw new IOException("Primary locator file " + locatorFile1 + " doesn't contain the name of a valid file.");
                }
                // Is MS Search already running?
                if (locatorFile2.exists()) {
                    throw new IllegalStateException("NIST MS Search appears to be busy - please wait until it finishes its current task and then try again.  Alternatively, try manually deleting the file " + locatorFile2);
                }
            }
            // Single or multiple row search?
            final PeakListRow[] peakListRows;
            final Map<PeakListRow, Set<PeakListRow>> rowHoods;
            if (peakListRow == null) {
                peakListRows = peakList.getRows();
                rowHoods = groupPeakRows();
            } else {
                peakListRows = new PeakListRow[] { peakListRow };
                rowHoods = new HashMap<PeakListRow, Set<PeakListRow>>(1);
                rowHoods.put(peakListRow, findPeakRowGroup());
            }
            // Reduce neighbourhoods to maximum number of peaks.
            trimNeighbours(rowHoods);
            // Store search results for each neighbourhood - to avoid repeat
            // searches.
            final int numRows = peakListRows.length;
            final Map<Set<PeakListRow>, List<PeakIdentity>> rowIdentities = new HashMap<Set<PeakListRow>, List<PeakIdentity>>(numRows);
            // Search command string.
            final String command = nistMsSearchExe.getAbsolutePath() + ' ' + COMMAND_LINE_ARGS;
            // Perform searches for each feature list row..
            progress = 0;
            progressMax = numRows;
            for (final PeakListRow row : peakListRows) {
                // Get the row's neighbours.
                final Set<PeakListRow> neighbours = rowHoods.get(row);
                // Has this neighbourhood's search been run already?
                if (!rowIdentities.containsKey(neighbours)) {
                    if (!isCanceled()) {
                        // Write spectra file.
                        final File spectraFile = writeSpectraFile(row, neighbours);
                        // Write locator file.
                        writeSecondaryLocatorFile(locatorFile2, spectraFile);
                        // Run the search.
                        runNistMsSearch(command);
                        // Read the search results file and store the
                        // results.
                        rowIdentities.put(neighbours, readSearchResults(row));
                    }
                }
                // Get the search results.
                final List<PeakIdentity> identities = rowIdentities.get(neighbours);
                if (identities != null) {
                    // Add (copy of) identities to peak row.
                    int maxMatchFactor = -1;
                    for (final PeakIdentity identity : identities) {
                        // Copy the identity.
                        final PeakIdentity id = new SimplePeakIdentity((Hashtable<String, String>) identity.getAllProperties());
                        // Best match factor?
                        final boolean isPreferred;
                        final int matchFactor = Integer.parseInt(id.getPropertyValue(MATCH_FACTOR_PROPERTY));
                        if (matchFactor > maxMatchFactor) {
                            maxMatchFactor = matchFactor;
                            isPreferred = true;
                        } else {
                            isPreferred = false;
                        }
                        // Add peak identity.
                        row.addPeakIdentity(id, isPreferred);
                    }
                    // Notify the GUI about the change in the project
                    MZmineCore.getProjectManager().getCurrentProject().notifyObjectChanged(row, false);
                }
                progress++;
            }
        } finally {
            // Clean up.
            if (locatorFile2 != null) {
                locatorFile2.delete();
            }
        }
    }
}