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

Example 26 with IsotopePattern

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

the class FormulaPredictionPeakListTask method checkConstraints.

private boolean checkConstraints(IMolecularFormula cdkFormula, PeakListRow peakListRow) {
    // Check elemental ratios
    if (checkRatios) {
        boolean check = ElementalHeuristicChecker.checkFormula(cdkFormula, ratiosParameters);
        if (!check) {
            return false;
        }
    }
    Double rdbeValue = RDBERestrictionChecker.calculateRDBE(cdkFormula);
    // Check RDBE condition
    if (checkRDBE && (rdbeValue != null)) {
        boolean check = RDBERestrictionChecker.checkRDBE(rdbeValue, rdbeParameters);
        if (!check) {
            return false;
        }
    }
    // Calculate isotope similarity score
    IsotopePattern detectedPattern = peakListRow.getBestIsotopePattern();
    IsotopePattern predictedIsotopePattern = null;
    Double isotopeScore = null;
    if ((checkIsotopes) && (detectedPattern != null)) {
        String stringFormula = MolecularFormulaManipulator.getString(cdkFormula);
        String adjustedFormula = FormulaUtils.ionizeFormula(stringFormula, ionType, charge);
        final double isotopeNoiseLevel = isotopeParameters.getParameter(IsotopePatternScoreParameters.isotopeNoiseLevel).getValue();
        final double detectedPatternHeight = detectedPattern.getHighestDataPoint().getIntensity();
        final double minPredictedAbundance = isotopeNoiseLevel / detectedPatternHeight;
        predictedIsotopePattern = IsotopePatternCalculator.calculateIsotopePattern(adjustedFormula, minPredictedAbundance, charge, ionType.getPolarity());
        isotopeScore = IsotopePatternScoreCalculator.getSimilarityScore(detectedPattern, predictedIsotopePattern, isotopeParameters);
        final double minScore = isotopeParameters.getParameter(IsotopePatternScoreParameters.isotopePatternScoreThreshold).getValue();
        if (isotopeScore < minScore) {
            return false;
        }
    }
    // MS/MS evaluation is slowest, so let's do it last
    Double msmsScore = null;
    Feature bestPeak = peakListRow.getBestPeak();
    RawDataFile dataFile = bestPeak.getDataFile();
    int msmsScanNumber = bestPeak.getMostIntenseFragmentScanNumber();
    if ((checkMSMS) && (msmsScanNumber > 0)) {
        Scan msmsScan = dataFile.getScan(msmsScanNumber);
        String massListName = msmsParameters.getParameter(MSMSScoreParameters.massList).getValue();
        MassList ms2MassList = msmsScan.getMassList(massListName);
        if (ms2MassList == null) {
            setStatus(TaskStatus.ERROR);
            setErrorMessage("The MS/MS scan #" + msmsScanNumber + " in file " + dataFile.getName() + " does not have a mass list called '" + massListName + "'");
            return false;
        }
        MSMSScore score = MSMSScoreCalculator.evaluateMSMS(cdkFormula, msmsScan, msmsParameters);
        double minMSMSScore = msmsParameters.getParameter(MSMSScoreParameters.msmsMinScore).getValue();
        if (score != null) {
            msmsScore = score.getScore();
            // Check the MS/MS condition
            if (msmsScore < minMSMSScore) {
                return false;
            }
        }
    }
    return true;
}

Example 27 with IsotopePattern

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

the class AdapMgfExportTask method exportPeakList.

private void exportPeakList(PeakList peakList, FileWriter writer) throws IOException {
    for (PeakListRow row : peakList.getRows()) {
        IsotopePattern ip = row.getBestIsotopePattern();
        if (ip == null)
            continue;
        exportRow(writer, row, ip);
        finishedRows++;
    }
}

Example 28 with IsotopePattern

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

the class PeakListSaveHandler method fillPeakElement.

/**
 * Add the peaks information into the XML document
 *
 * @param peak
 * @param element
 * @param dataFileID
 * @throws IOException
 */
private void fillPeakElement(Feature peak, TransformerHandler hd) throws SAXException, IOException {
    AttributesImpl atts = new AttributesImpl();
    // <REPRESENTATIVE_SCAN>
    hd.startElement("", "", PeakListElementName.REPRESENTATIVE_SCAN.getElementName(), atts);
    hd.characters(String.valueOf(peak.getRepresentativeScanNumber()).toCharArray(), 0, String.valueOf(peak.getRepresentativeScanNumber()).length());
    hd.endElement("", "", PeakListElementName.REPRESENTATIVE_SCAN.getElementName());
    // <FRAGMENT_SCAN>
    hd.startElement("", "", PeakListElementName.FRAGMENT_SCAN.getElementName(), atts);
    hd.characters(String.valueOf(peak.getMostIntenseFragmentScanNumber()).toCharArray(), 0, String.valueOf(peak.getMostIntenseFragmentScanNumber()).length());
    hd.endElement("", "", PeakListElementName.FRAGMENT_SCAN.getElementName());
    // <ALL_MS2_FRAGMENT_SCANS>
    fillAllMS2FragmentScanNumbers(peak.getAllMS2FragmentScanNumbers(), hd);
    int[] scanNumbers = peak.getScanNumbers();
    // <ISOTOPE_PATTERN>
    IsotopePattern isotopePattern = peak.getIsotopePattern();
    if (isotopePattern != null) {
        atts.addAttribute("", "", PeakListElementName.STATUS.getElementName(), "CDATA", String.valueOf(isotopePattern.getStatus()));
        atts.addAttribute("", "", PeakListElementName.DESCRIPTION.getElementName(), "CDATA", isotopePattern.getDescription());
        hd.startElement("", "", PeakListElementName.ISOTOPE_PATTERN.getElementName(), atts);
        atts.clear();
        fillIsotopePatternElement(isotopePattern, hd);
        hd.endElement("", "", PeakListElementName.ISOTOPE_PATTERN.getElementName());
    }
    // <MZPEAK>
    atts.addAttribute("", "", PeakListElementName.QUANTITY.getElementName(), "CDATA", String.valueOf(scanNumbers.length));
    hd.startElement("", "", PeakListElementName.MZPEAKS.getElementName(), atts);
    atts.clear();
    // <SCAN_ID> <MASS> <HEIGHT>
    ByteArrayOutputStream byteScanStream = new ByteArrayOutputStream();
    DataOutputStream dataScanStream = new DataOutputStream(byteScanStream);
    ByteArrayOutputStream byteMassStream = new ByteArrayOutputStream();
    DataOutputStream dataMassStream = new DataOutputStream(byteMassStream);
    ByteArrayOutputStream byteHeightStream = new ByteArrayOutputStream();
    DataOutputStream dataHeightStream = new DataOutputStream(byteHeightStream);
    float mass, height;
    for (int scan : scanNumbers) {
        dataScanStream.writeInt(scan);
        dataScanStream.flush();
        DataPoint mzPeak = peak.getDataPoint(scan);
        if (mzPeak != null) {
            mass = (float) mzPeak.getMZ();
            height = (float) mzPeak.getIntensity();
        } else {
            mass = 0f;
            height = 0f;
        }
        dataMassStream.writeFloat(mass);
        dataMassStream.flush();
        dataHeightStream.writeFloat(height);
        dataHeightStream.flush();
    }
    byte[] bytes = Base64.encode(byteScanStream.toByteArray());
    hd.startElement("", "", PeakListElementName.SCAN_ID.getElementName(), atts);
    String sbytes = new String(bytes);
    hd.characters(sbytes.toCharArray(), 0, sbytes.length());
    hd.endElement("", "", PeakListElementName.SCAN_ID.getElementName());
    bytes = Base64.encode(byteMassStream.toByteArray());
    hd.startElement("", "", PeakListElementName.MZ.getElementName(), atts);
    sbytes = new String(bytes);
    hd.characters(sbytes.toCharArray(), 0, sbytes.length());
    hd.endElement("", "", PeakListElementName.MZ.getElementName());
    bytes = Base64.encode(byteHeightStream.toByteArray());
    hd.startElement("", "", PeakListElementName.HEIGHT.getElementName(), atts);
    sbytes = new String(bytes);
    hd.characters(sbytes.toCharArray(), 0, sbytes.length());
    hd.endElement("", "", PeakListElementName.HEIGHT.getElementName());
    hd.endElement("", "", PeakListElementName.MZPEAKS.getElementName());
}

Example 29 with IsotopePattern

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

the class SpectraVisualizerWindow method actionPerformed.

@Override
public void actionPerformed(ActionEvent event) {
    String command = event.getActionCommand();
    if (command.equals("PEAKLIST_CHANGE")) {
        // If no scan is loaded yet, ignore
        if (currentScan == null)
            return;
        PeakList selectedPeakList = bottomPanel.getSelectedPeakList();
        loadPeaks(selectedPeakList);
    }
    if (command.equals("PREVIOUS_SCAN")) {
        if (dataFile == null)
            return;
        int msLevel = currentScan.getMSLevel();
        int[] scanNumbers = dataFile.getScanNumbers(msLevel);
        int scanIndex = Arrays.binarySearch(scanNumbers, currentScan.getScanNumber());
        if (scanIndex > 0) {
            final int prevScanIndex = scanNumbers[scanIndex - 1];
            Runnable newThreadRunnable = new Runnable() {

                @Override
                public void run() {
                    loadRawData(dataFile.getScan(prevScanIndex));
                }
            };
            Thread newThread = new Thread(newThreadRunnable);
            newThread.start();
        }
    }
    if (command.equals("NEXT_SCAN")) {
        if (dataFile == null)
            return;
        int msLevel = currentScan.getMSLevel();
        int[] scanNumbers = dataFile.getScanNumbers(msLevel);
        int scanIndex = Arrays.binarySearch(scanNumbers, currentScan.getScanNumber());
        if (scanIndex < (scanNumbers.length - 1)) {
            final int nextScanIndex = scanNumbers[scanIndex + 1];
            Runnable newThreadRunnable = new Runnable() {

                @Override
                public void run() {
                    loadRawData(dataFile.getScan(nextScanIndex));
                }
            };
            Thread newThread = new Thread(newThreadRunnable);
            newThread.start();
        }
    }
    if (command.equals("SHOW_MSMS")) {
        String selectedScanString = (String) bottomPanel.getMSMSSelector().getSelectedItem();
        if (selectedScanString == null)
            return;
        int sharpIndex = selectedScanString.indexOf('#');
        int commaIndex = selectedScanString.indexOf(',');
        selectedScanString = selectedScanString.substring(sharpIndex + 1, commaIndex);
        int selectedScan = Integer.valueOf(selectedScanString);
        SpectraVisualizerModule.showNewSpectrumWindow(dataFile, selectedScan);
    }
    if (command.equals("TOGGLE_PLOT_MODE")) {
        if (spectrumPlot.getPlotMode() == MassSpectrumType.CENTROIDED) {
            spectrumPlot.setPlotMode(MassSpectrumType.PROFILE);
            toolBar.setCentroidButton(MassSpectrumType.PROFILE);
        } else {
            spectrumPlot.setPlotMode(MassSpectrumType.CENTROIDED);
            toolBar.setCentroidButton(MassSpectrumType.CENTROIDED);
        }
    }
    if (command.equals("SHOW_DATA_POINTS")) {
        spectrumPlot.switchDataPointsVisible();
    }
    if (command.equals("SHOW_ANNOTATIONS")) {
        spectrumPlot.switchItemLabelsVisible();
    }
    if (command.equals("SHOW_PICKED_PEAKS")) {
        spectrumPlot.switchPickedPeaksVisible();
    }
    if (command.equals("SHOW_ISOTOPE_PEAKS")) {
        spectrumPlot.switchIsotopePeaksVisible();
    }
    if (command.equals("SETUP_AXES")) {
        AxesSetupDialog dialog = new AxesSetupDialog(this, spectrumPlot.getXYPlot());
        dialog.setVisible(true);
    }
    // library entry creation
    if (command.equals("CREATE_LIBRARY_ENTRY")) {
        // open window with all selected rows
        MSMSLibrarySubmissionWindow libraryWindow = new MSMSLibrarySubmissionWindow();
        libraryWindow.setData(currentScan);
        libraryWindow.setVisible(true);
    }
    if (command.equals("EXPORT_SPECTRA")) {
        ExportScansModule.showSetupDialog(currentScan);
    }
    if (command.equals("ADD_ISOTOPE_PATTERN")) {
        IsotopePattern newPattern = IsotopePatternCalculator.showIsotopePredictionDialog(this, true);
        if (newPattern == null)
            return;
        loadIsotopes(newPattern);
    }
    if ((command.equals("ZOOM_IN")) || (command.equals("ZOOM_IN_BOTH_COMMAND"))) {
        spectrumPlot.getXYPlot().getDomainAxis().resizeRange(1 / zoomCoefficient);
    }
    if ((command.equals("ZOOM_OUT")) || (command.equals("ZOOM_OUT_BOTH_COMMAND"))) {
        spectrumPlot.getXYPlot().getDomainAxis().resizeRange(zoomCoefficient);
    }
    if (command.equals("SET_SAME_RANGE")) {
        // Get current axes range
        NumberAxis xAxis = (NumberAxis) spectrumPlot.getXYPlot().getDomainAxis();
        NumberAxis yAxis = (NumberAxis) spectrumPlot.getXYPlot().getRangeAxis();
        double xMin = xAxis.getRange().getLowerBound();
        double xMax = xAxis.getRange().getUpperBound();
        double xTick = xAxis.getTickUnit().getSize();
        double yMin = yAxis.getRange().getLowerBound();
        double yMax = yAxis.getRange().getUpperBound();
        double yTick = yAxis.getTickUnit().getSize();
        // Get all frames of my class
        Window[] spectraFrames = JFrame.getWindows();
        // Set the range of these frames
        for (Window frame : spectraFrames) {
            if (!(frame instanceof SpectraVisualizerWindow))
                continue;
            SpectraVisualizerWindow spectraFrame = (SpectraVisualizerWindow) frame;
            spectraFrame.setAxesRange(xMin, xMax, xTick, yMin, yMax, yTick);
        }
    }
    if (command.equals("ONLINEDATABASESEARCH")) {
        SwingUtilities.invokeLater(new Runnable() {

            @Override
            public void run() {
                OnlineDBSpectraSearchModule.showSpectraIdentificationDialog(currentScan, spectrumPlot);
            }
        });
    }
    if (command.equals("CUSTOMDATABASESEARCH")) {
        SwingUtilities.invokeLater(new Runnable() {

            @Override
            public void run() {
                CustomDBSpectraSearchModule.showSpectraIdentificationDialog(currentScan, spectrumPlot);
            }
        });
    }
    if (command.equals("LIPIDSEARCH")) {
        SwingUtilities.invokeLater(new Runnable() {

            @Override
            public void run() {
                LipidSpectraSearchModule.showSpectraIdentificationDialog(currentScan, spectrumPlot);
            }
        });
    }
    if (command.equals("SUMFORMULA")) {
        SwingUtilities.invokeLater(new Runnable() {

            @Override
            public void run() {
                SumFormulaSpectraSearchModule.showSpectraIdentificationDialog(currentScan, spectrumPlot);
            }
        });
    }
    if (command.equals("SPECTRALDATABASESEARCH")) {
        SwingUtilities.invokeLater(new Runnable() {

            @Override
            public void run() {
                SpectraIdentificationSpectralDatabaseModule.showSpectraIdentificationDialog(currentScan, spectrumPlot);
            }
        });
    }
    if (command.equals("SET_PROCESSING_PARAMETERS")) {
        SwingUtilities.invokeLater(new Runnable() {

            @Override
            public void run() {
                if (!dppmWindowOpen) {
                    dppmWindowOpen = true;
                    ExitCode exitCode = DataPointProcessingManager.getInst().getParameters().showSetupDialog(MZmineCore.getDesktop().getMainWindow(), true);
                    dppmWindowOpen = false;
                    if (exitCode == ExitCode.OK && DataPointProcessingManager.getInst().isEnabled()) {
                        // if processing was run before, this removes the previous results.
                        getSpectrumPlot().removeDataPointProcessingResultDataSets();
                        getSpectrumPlot().checkAndRunController();
                    }
                }
            }
        });
    }
    if (command.equals("ENABLE_PROCESSING")) {
        SwingUtilities.invokeLater(new Runnable() {

            @Override
            public void run() {
                DataPointProcessingManager inst = DataPointProcessingManager.getInst();
                inst.setEnabled(!inst.isEnabled());
                bottomPanel.updateProcessingButton();
                getSpectrumPlot().checkAndRunController();
                // if the tick is removed, set the data back to default
                if (!inst.isEnabled()) {
                    getSpectrumPlot().removeDataPointProcessingResultDataSets();
                // loadRawData(currentScan);
                }
            }
        });
    }
}

Example 30 with IsotopePattern

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

the class PseudoSpectrum method createDataSet.

public static PseudoSpectrumDataSet createDataSet(PeakListRow[] group, RawDataFile raw, boolean sum) {
    // data
    PseudoSpectrumDataSet series = new PseudoSpectrumDataSet(true, "pseudo");
    // add all isotopes as a second series:
    XYSeries isoSeries = new XYSeries("Isotopes", true);
    // raw isotopes in a different color
    XYSeries rawIsoSeries = new XYSeries("Raw isotope pattern", true);
    // for each row
    for (PeakListRow row : group) {
        String annotation = null;
        // sum -> heighest peak
        if (sum)
            series.addDP(row.getAverageMZ(), row.getBestPeak().getHeight(), annotation);
        else {
            Feature f = raw == null ? row.getBestPeak() : row.getPeak(raw);
            if (f != null)
                series.addDP(f.getMZ(), f.getHeight(), null);
        }
        // add isotopes
        IsotopePattern pattern = row.getBestIsotopePattern();
        if (pattern != null) {
            for (DataPoint dp : pattern.getDataPoints()) isoSeries.add(dp.getMZ(), dp.getIntensity());
        }
    }
    series.addSeries(isoSeries);
    series.addSeries(rawIsoSeries);
    return series;
}