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

Example 51 with PeakListRow

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

the class FormulaPredictionPeakListTask method run.

/**
 * @see java.lang.Runnable#run()
 */
@Override
public void run() {
    setStatus(TaskStatus.PROCESSING);
    totalRows = peakList.getNumberOfRows();
    for (PeakListRow row : peakList.getRows()) {
        if (row.getPeakIdentities().length > 0) {
            continue;
        }
        this.searchedMass = (row.getAverageMZ() - ionType.getAddedMass()) * charge;
        message = "Formula prediction for " + MZmineCore.getConfiguration().getMZFormat().format(searchedMass);
        massRange = mzTolerance.getToleranceRange(searchedMass);
        IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
        generator = new MolecularFormulaGenerator(builder, massRange.lowerEndpoint(), massRange.upperEndpoint(), elementCounts);
        IMolecularFormula cdkFormula;
        // create a map to store ResultFormula and relative mass deviation for sorting
        Map<Double, String> possibleFormulas = new TreeMap<>();
        while ((cdkFormula = generator.getNextFormula()) != null) {
            if (isCanceled())
                return;
            // Mass is ok, so test other constraints
            if (checkConstraints(cdkFormula, row) == true) {
                String formula = MolecularFormulaManipulator.getString(cdkFormula);
                // calc rel mass deviation
                Double relMassDev = ((searchedMass - (FormulaUtils.calculateExactMass(formula))) / searchedMass) * 1000000;
                // write to map
                possibleFormulas.put(relMassDev, formula);
            }
        }
        if (isCanceled())
            return;
        // create a map to store ResultFormula and relative mass deviation for sorting
        Map<Double, String> possibleFormulasSorted = new TreeMap<>((Comparator<Double>) (o1, o2) -> Double.compare(Math.abs(o1), Math.abs(o2)));
        possibleFormulasSorted.putAll(possibleFormulas);
        // Add the new formula entry top results
        int ctr = 0;
        for (Map.Entry<Double, String> entry : possibleFormulasSorted.entrySet()) {
            if (ctr < maxBestFormulasPerPeak) {
                SimplePeakIdentity newIdentity = new SimplePeakIdentity(entry.getValue(), entry.getValue(), this.getClass().getName(), null, null);
                row.addPeakIdentity(newIdentity, false);
                ctr++;
            }
        }
        if (isCanceled())
            return;
        finishedRows++;
    }
    if (isCanceled())
        return;
    logger.finest("Finished formula search for all the peaks");
    setStatus(TaskStatus.FINISHED);
}

Example 52 with PeakListRow

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

the class FragmentSearchTask method run.

/**
 * @see java.lang.Runnable#run()
 */
public void run() {
    setStatus(TaskStatus.PROCESSING);
    logger.info("Starting fragments search in " + peakList);
    PeakListRow[] rows = peakList.getRows();
    totalRows = rows.length;
    // Start with the highest peaks
    Arrays.sort(rows, new PeakListRowSorter(SortingProperty.Height, SortingDirection.Descending));
    // Compare each two rows against each other
    for (int i = 0; i < totalRows; i++) {
        for (int j = i + 1; j < rows.length; j++) {
            // Task canceled?
            if (isCanceled())
                return;
            // smaller one may be a fragment
            if (rows[i].getAverageMZ() > rows[j].getAverageMZ()) {
                if (checkFragment(rows[i], rows[j]))
                    addFragmentInfo(rows[i], rows[j]);
            } else {
                if (checkFragment(rows[j], rows[i]))
                    addFragmentInfo(rows[j], rows[i]);
            }
        }
        finishedRows++;
    }
    // Add task description to peakList
    ((SimplePeakList) peakList).addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod("Identification of fragments", parameters));
    // Repaint the window to reflect the change in the feature list
    Desktop desktop = MZmineCore.getDesktop();
    if (!(desktop instanceof HeadLessDesktop))
        desktop.getMainWindow().repaint();
    setStatus(TaskStatus.FINISHED);
    logger.info("Finished fragments search in " + peakList);
}

Example 53 with PeakListRow

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

the class NistMsSearchTask method groupPeakRows.

/**
 * 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 Map<PeakListRow, Set<PeakListRow>> groupPeakRows() {
    // Determine contemporaneity.
    final int numRows = peakList.getNumberOfRows();
    final Map<PeakListRow, Set<PeakListRow>> rowHoods = new HashMap<PeakListRow, Set<PeakListRow>>(numRows);
    for (int i = 0; i < numRows; i++) {
        // Get this row's neighbours list - create it if necessary.
        final PeakListRow row1 = peakList.getRow(i);
        if (!rowHoods.containsKey(row1)) {
            rowHoods.put(row1, new HashSet<PeakListRow>(4));
        }
        // Holds neighbours.
        final Set<PeakListRow> neighbours = rowHoods.get(row1);
        // Contemporaneous with self.
        neighbours.add(row1);
        // Find contemporaneous peaks.
        final double rt = row1.getAverageRT();
        for (int j = i + 1; j < numRows; j++) {
            // Are peak rows contemporaneous?
            final PeakListRow row2 = peakList.getRow(j);
            if (rtTolerance.checkWithinTolerance(rt, row2.getAverageRT()) && (!sameIds || checkSameIds(row1, row2))) {
                // Add rows to each others' neighbours lists.
                neighbours.add(row2);
                if (!rowHoods.containsKey(row2)) {
                    rowHoods.put(row2, new HashSet<PeakListRow>(4));
                }
                rowHoods.get(row2).add(row1);
            }
        }
    }
    return rowHoods;
}

Example 54 with PeakListRow

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

the class Ms2SearchTask method run.

/**
 * @see java.lang.Runnable#run()
 */
public void run() {
    setStatus(TaskStatus.PROCESSING);
    logger.info("Starting MS2 similarity search between " + peakList1 + " and " + peakList2 + " with mz tolerance:" + mzTolerance.getPpmTolerance());
    Ms2SearchResult searchResult;
    PeakListRow[] rows1 = peakList1.getRows();
    PeakListRow[] rows2 = peakList2.getRows();
    int rows1Length = rows1.length;
    int rows2Length = rows2.length;
    totalRows = rows1Length;
    for (int i = 0; i < rows1Length; i++) {
        for (int j = 0; j < rows2Length; j++) {
            Feature featureA = rows1[i].getBestPeak();
            Feature featureB = rows2[j].getBestPeak();
            // Complication. The "best" peak, may not have the "best" fragmentation
            Scan scanA = rows1[i].getBestFragmentation();
            Scan scanB = rows2[j].getBestFragmentation();
            searchResult = simpleMS2similarity(scanA, scanB, intensityThreshold, mzTolerance, massListName);
            // Report the final score to the peaklist identity
            if (searchResult != null && searchResult.getScore() > scoreThreshold && searchResult.getNumIonsMatched() >= minimumIonsMatched)
                this.addMS2Identity(rows1[i], featureA, featureB, searchResult);
            if (isCanceled())
                return;
        }
        // Update progress bar
        finishedRows++;
    }
    // Add task description to peakList
    ((SimplePeakList) peakList1).addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod("Identification of similar MS2s", parameters));
    // Repaint the window to reflect the change in the feature list
    Desktop desktop = MZmineCore.getDesktop();
    if (!(desktop instanceof HeadLessDesktop))
        desktop.getMainWindow().repaint();
    setStatus(TaskStatus.FINISHED);
    logger.info("Finished MS2 similarity search for " + peakList1 + "against" + peakList2);
}

Example 55 with PeakListRow

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

the class PeakListTablePopupMenu method show.

@Override
public void show(final Component invoker, final int x, final int y) {
    // Select the row where clicked?
    final Point clickedPoint = new Point(x, y);
    final int clickedRow = table.rowAtPoint(clickedPoint);
    if (table.getSelectedRowCount() < 2) {
        ListSelectionModel selectionModel = table.getSelectionModel();
        selectionModel.setSelectionInterval(clickedRow, clickedRow);
    }
    // First, disable all the Show... items
    show2DItem.setEnabled(false);
    show3DItem.setEnabled(false);
    manuallyDefineItem.setEnabled(false);
    showMSMSItem.setEnabled(false);
    showMSMSMirrorItem.setEnabled(false);
    showSpectralDBResults.setEnabled(false);
    showAllMSMSItem.setEnabled(false);
    showIsotopePatternItem.setEnabled(false);
    showPeakRowSummaryItem.setEnabled(false);
    exportIsotopesItem.setEnabled(false);
    exportMSMSItem.setEnabled(false);
    exportMenu.setEnabled(false);
    // Enable row items if applicable
    final int[] selectedRows = table.getSelectedRows();
    final boolean rowsSelected = selectedRows.length > 0;
    deleteRowsItem.setEnabled(rowsSelected);
    clearIdsItem.setEnabled(rowsSelected);
    pasteIdsItem.setEnabled(rowsSelected && copiedId != null);
    plotRowsItem.setEnabled(rowsSelected);
    showMenu.setEnabled(rowsSelected);
    idsMenu.setEnabled(rowsSelected);
    exportIsotopesItem.setEnabled(rowsSelected);
    exportToSirius.setEnabled(rowsSelected);
    exportMSMSLibrary.setEnabled(rowsSelected);
    exportMS1Library.setEnabled(rowsSelected);
    exportMenu.setEnabled(rowsSelected);
    final boolean oneRowSelected = selectedRows.length == 1;
    searchMenu.setEnabled(true);
    // search methods for single rows
    onlineDbSearchItem.setEnabled(oneRowSelected);
    nistSearchItem.setEnabled(oneRowSelected);
    formulaItem.setEnabled(oneRowSelected);
    siriusItem.setEnabled(oneRowSelected);
    // search methods for single and multiple rows
    spectralDbSearchItem.setEnabled(true);
    // Find the row and column where the user clicked
    clickedDataFile = null;
    final int clickedColumn = columnModel.getColumn(table.columnAtPoint(clickedPoint)).getModelIndex();
    if (clickedRow >= 0 && clickedColumn >= 0) {
        final int rowIndex = table.convertRowIndexToModel(clickedRow);
        clickedPeakListRow = getPeakListRow(rowIndex);
        allClickedPeakListRows = new PeakListRow[selectedRows.length];
        for (int i = 0; i < selectedRows.length; i++) {
            allClickedPeakListRows[i] = getPeakListRow(table.convertRowIndexToModel(selectedRows[i]));
        }
        // Enable items.
        show2DItem.setEnabled(oneRowSelected);
        show3DItem.setEnabled(oneRowSelected);
        showPeakRowSummaryItem.setEnabled(oneRowSelected);
        if (clickedPeakListRow.getBestPeak() != null) {
            exportMSMSItem.setEnabled(oneRowSelected && clickedPeakListRow.getBestPeak().getMostIntenseFragmentScanNumber() > 0);
        }
        // If we clicked on data file columns, check the peak
        if (clickedColumn >= CommonColumnType.values().length) {
            // Enable manual peak picking
            manuallyDefineItem.setEnabled(oneRowSelected);
            // Find the actual peak, if we have it.
            clickedDataFile = peakList.getRawDataFile((clickedColumn - CommonColumnType.values().length) / DataFileColumnType.values().length);
            final Feature clickedPeak = getPeakListRow(table.convertRowIndexToModel(clickedRow)).getPeak(clickedDataFile);
            // If we have the peak, enable Show... items
            if (clickedPeak != null && oneRowSelected) {
                showIsotopePatternItem.setEnabled(clickedPeak.getIsotopePattern() != null);
            }
        } else {
            showIsotopePatternItem.setEnabled(clickedPeakListRow.getBestIsotopePattern() != null && oneRowSelected);
        }
        long nRowsWithFragmentation = Arrays.stream(allClickedPeakListRows).filter(r -> r.getBestFragmentation() != null).count();
        // always show for multi MSMS window
        showMSMSItem.setEnabled((oneRowSelected && getSelectedPeakForMSMS() != null && getSelectedPeakForMSMS().getMostIntenseFragmentScanNumber() > 0) || (selectedRows.length > 1 && nRowsWithFragmentation > 1));
        // always show if at least one fragmentation is available
        showAllMSMSItem.setEnabled(clickedPeakListRow.getBestFragmentation() != null && oneRowSelected);
        // only show if selected rows == 2 and both have MS2
        boolean bothMS2 = selectedRows.length == 2 && nRowsWithFragmentation == 2;
        showMSMSMirrorItem.setEnabled(bothMS2);
        // has identity of spectral database match
        showSpectralDBResults.setEnabled(hasSpectralDBIdentities(clickedPeakListRow));
        // open id url if available
        PeakIdentity pi = clickedPeakListRow.getPreferredPeakIdentity();
        String url = null;
        if (pi != null)
            url = pi.getPropertyValue(PeakIdentity.PROPERTY_URL);
        openCompoundIdUrl.setEnabled(url != null && !url.isEmpty());
    }
    copyIdsItem.setEnabled(oneRowSelected && allClickedPeakListRows[0].getPreferredPeakIdentity() != null);
    super.show(invoker, x, y);
}