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

Example 6 with MassList

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

the class ScanSelectPanel method getFilteredDataPointsRemoved.

/**
 * Removed data points
 *
 * @return
 */
@Nullable
public DataPoint[] getFilteredDataPointsRemoved() {
    if (scans != null && !scans.isEmpty()) {
        Scan scan = scans.get(selectedScanI);
        MassList massList = ScanUtils.getMassListOrFirst(scan, massListName);
        if (massList != null)
            return ScanUtils.getBelowThreshold(massList.getDataPoints(), noiseLevel);
    }
    return null;
}

Example 7 with MassList

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

the class SQLExportTask method exportPeakListRow.

private void exportPeakListRow(PeakListRow row) throws SQLException {
    // Cancel?
    if (isCanceled()) {
        return;
    }
    // Value for looping through raw data files
    boolean loopDataFiles = false;
    StringBuilder sql = new StringBuilder();
    sql.append("INSERT INTO ");
    sql.append(tableName);
    sql.append(" (");
    for (int i = 0; i < exportColumns.getRowCount(); i++) {
        sql.append(exportColumns.getValueAt(i, 0));
        if (i < exportColumns.getRowCount() - 1)
            sql.append(",");
    }
    sql.append(" ) VALUES (");
    for (int i = 0; i < exportColumns.getRowCount(); i++) {
        sql.append("?");
        if (i < exportColumns.getRowCount() - 1)
            sql.append(",");
    }
    sql.append(")");
    PreparedStatement statement = dbConnection.prepareStatement(sql.toString());
    if (row == null) {
        for (int i = 0; i < exportColumns.getRowCount(); i++) {
            SQLExportDataType dataType = (SQLExportDataType) exportColumns.getValueAt(i, 1);
            String dataValue = (String) exportColumns.getValueAt(i, 2);
            switch(dataType) {
                case CONSTANT:
                    statement.setString(i + 1, dataValue);
                    break;
                case RAWFILE:
                    RawDataFile[] rawdatafiles = peakList.getRawDataFiles();
                    statement.setString(i + 1, rawdatafiles[0].getName());
                    break;
                default:
                    statement.setString(i + 1, null);
                    break;
            }
        }
        statement.executeUpdate();
    } else {
        for (RawDataFile rawDataFile : row.getRawDataFiles()) {
            Feature peak = row.getPeak(rawDataFile);
            for (int i = 0; i < exportColumns.getRowCount(); i++) {
                SQLExportDataType dataType = (SQLExportDataType) exportColumns.getValueAt(i, 1);
                String dataValue = (String) exportColumns.getValueAt(i, 2);
                switch(dataType) {
                    case CONSTANT:
                        statement.setString(i + 1, dataValue);
                        break;
                    case MZ:
                        statement.setDouble(i + 1, row.getAverageMZ());
                        break;
                    case RT:
                        statement.setDouble(i + 1, row.getAverageRT());
                        break;
                    case ID:
                        statement.setInt(i + 1, row.getID());
                        break;
                    case PEAKCHARGE:
                        statement.setDouble(i + 1, peak.getCharge());
                        loopDataFiles = true;
                        break;
                    case PEAKDURATION:
                        statement.setDouble(i + 1, RangeUtils.rangeLength(peak.getRawDataPointsRTRange()));
                        loopDataFiles = true;
                        break;
                    case PEAKSTATUS:
                        statement.setString(i + 1, peak.getFeatureStatus().name());
                        loopDataFiles = true;
                        break;
                    case PEAKMZ:
                        statement.setDouble(i + 1, peak.getMZ());
                        loopDataFiles = true;
                        break;
                    case PEAKRT:
                        statement.setDouble(i + 1, peak.getRT());
                        loopDataFiles = true;
                        break;
                    case PEAKRT_START:
                        statement.setDouble(i + 1, peak.getRawDataPointsRTRange().lowerEndpoint());
                        loopDataFiles = true;
                        break;
                    case PEAKRT_END:
                        statement.setDouble(i + 1, peak.getRawDataPointsRTRange().upperEndpoint());
                        loopDataFiles = true;
                        break;
                    case PEAKHEIGHT:
                        statement.setDouble(i + 1, peak.getHeight());
                        loopDataFiles = true;
                        break;
                    case PEAKAREA:
                        statement.setDouble(i + 1, peak.getArea());
                        loopDataFiles = true;
                        break;
                    case DATAPOINTS:
                        statement.setDouble(i + 1, peak.getScanNumbers().length);
                        loopDataFiles = true;
                        break;
                    case FWHM:
                        statement.setDouble(i + 1, peak.getFWHM());
                        loopDataFiles = true;
                        break;
                    case TAILINGFACTOR:
                        statement.setDouble(i + 1, peak.getTailingFactor());
                        loopDataFiles = true;
                        break;
                    case ASYMMETRYFACTOR:
                        statement.setDouble(i + 1, peak.getAsymmetryFactor());
                        loopDataFiles = true;
                        break;
                    case RAWFILE:
                        statement.setString(i + 1, rawDataFile.getName());
                        loopDataFiles = true;
                        break;
                    case HEIGHT:
                        statement.setDouble(i + 1, row.getAverageHeight());
                        break;
                    case AREA:
                        statement.setDouble(i + 1, row.getAverageArea());
                        break;
                    case COMMENT:
                        statement.setString(i + 1, row.getComment());
                        break;
                    case IDENTITY:
                        PeakIdentity id = row.getPreferredPeakIdentity();
                        if (id != null) {
                            statement.setString(i + 1, id.getName());
                        } else {
                            statement.setNull(i + 1, Types.VARCHAR);
                        }
                        break;
                    case ISOTOPEPATTERN:
                        IsotopePattern isotopes = row.getBestIsotopePattern();
                        if (isotopes == null) {
                            statement.setNull(i + 1, Types.BLOB);
                            break;
                        }
                        DataPoint[] dataPoints = isotopes.getDataPoints();
                        byte[] bytes = ScanUtils.encodeDataPointsToBytes(dataPoints);
                        ByteArrayInputStream is = new ByteArrayInputStream(bytes);
                        statement.setBlob(i + 1, is);
                        break;
                    case MSMS:
                        int msmsScanNum = row.getBestPeak().getMostIntenseFragmentScanNumber();
                        // Check if there is any MS/MS scan
                        if (msmsScanNum <= 0) {
                            statement.setNull(i + 1, Types.BLOB);
                            break;
                        }
                        RawDataFile dataFile = row.getBestPeak().getDataFile();
                        Scan msmsScan = dataFile.getScan(msmsScanNum);
                        MassList msmsMassList = msmsScan.getMassList(dataValue);
                        // Check if there is a masslist for the scan
                        if (msmsMassList == null) {
                            statement.setNull(i + 1, Types.BLOB);
                            break;
                        }
                        dataPoints = msmsMassList.getDataPoints();
                        bytes = ScanUtils.encodeDataPointsToBytes(dataPoints);
                        is = new ByteArrayInputStream(bytes);
                        statement.setBlob(i + 1, is);
                        break;
                    default:
                        break;
                }
            }
            statement.executeUpdate();
            // data files in feature list
            if (!loopDataFiles) {
                break;
            }
        }
    }
}

Example 8 with MassList

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

the class Candidates method getAvgPeakHeights.

/**
 * @param ID
 * @return avg heights of all with the ids, but only if they are contained in same scans and mass
 *         lists
 */
private double[] getAvgPeakHeights(int[] ID) {
    PeakListRow[] rows = plh.getRowsByID(ID);
    RawDataFile[] raws = rows[0].getRawDataFiles();
    if (raws.length < 1)
        return null;
    double[] mzs = new double[ID.length];
    for (int i = 0; i < rows.length; i++) mzs[i] = rows[i].getAverageMZ();
    double[] avgHeights = new double[ID.length];
    int pointsAdded = 0;
    for (RawDataFile raw : raws) {
        if (!raw.getDataMZRange().contains(rows[0].getAverageMZ()))
            continue;
        int[] scanNums = raw.getScanNumbers();
        for (int i = 0; i < scanNums.length; i++) {
            Scan scan = raw.getScan(scanNums[i]);
            MassList list = scan.getMassList(massListName);
            if (list == null || !massListContainsEveryMZ(list, mzs, minHeight))
                continue;
            double[] avgBuffer = new double[mzs.length];
            boolean allFound = true;
            for (int j = 0; j < mzs.length; j++) {
                DataPoint[] points = getMassListDataPointsByMass(list, mzTolerance.getToleranceRange(mzs[j]));
                if (points.length == 0)
                    continue;
                DataPoint dp = getClosestDataPoint(points, rows[j].getAverageMZ(), minHeight);
                if (// yes the list contained something close to every datapoint that was over
                dp == null) // minHeight, BUT
                {
                    // the closest might not have been. Check is done inside getClosestDataPoint();
                    allFound = false;
                    break;
                }
                avgBuffer[j] = dp.getIntensity();
            }
            if (allFound) {
                pointsAdded++;
                for (int j = 0; j < mzs.length; j++) avgHeights[j] += avgBuffer[j];
            }
        }
    }
    if (pointsAdded == 0) {
        logger.warning("Error: Peaks with ids: " + Arrays.toString(ID) + " were not in same scans at all. Please update the parameters.");
        return null;
    }
    for (int i = 0; i < avgHeights.length; i++) avgHeights[i] /= (pointsAdded);
    return avgHeights;
}

Example 9 with MassList

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

the class RawDataFileSaveHandler method fillScanElement.

/**
 * Create the part of the XML document related to the scans
 *
 * @param scan
 * @param element
 */
private void fillScanElement(Scan scan, TransformerHandler hd) throws SAXException, IOException {
    // <SCAN_ID>
    AttributesImpl atts = new AttributesImpl();
    hd.startElement("", "", RawDataElementName.SCAN_ID.getElementName(), atts);
    hd.characters(String.valueOf(scan.getScanNumber()).toCharArray(), 0, String.valueOf(scan.getScanNumber()).length());
    hd.endElement("", "", RawDataElementName.SCAN_ID.getElementName());
    // <MS_LEVEL>
    hd.startElement("", "", RawDataElementName.MS_LEVEL.getElementName(), atts);
    hd.characters(String.valueOf(scan.getMSLevel()).toCharArray(), 0, String.valueOf(scan.getMSLevel()).length());
    hd.endElement("", "", RawDataElementName.MS_LEVEL.getElementName());
    if (scan.getMSLevel() >= 2) {
        // <PRECURSOR_MZ>
        hd.startElement("", "", RawDataElementName.PRECURSOR_MZ.getElementName(), atts);
        hd.characters(String.valueOf(scan.getPrecursorMZ()).toCharArray(), 0, String.valueOf(scan.getPrecursorMZ()).length());
        hd.endElement("", "", RawDataElementName.PRECURSOR_MZ.getElementName());
        // <PRECURSOR_CHARGE>
        hd.startElement("", "", RawDataElementName.PRECURSOR_CHARGE.getElementName(), atts);
        hd.characters(String.valueOf(scan.getPrecursorCharge()).toCharArray(), 0, String.valueOf(scan.getPrecursorCharge()).length());
        hd.endElement("", "", RawDataElementName.PRECURSOR_CHARGE.getElementName());
    }
    // <RETENTION_TIME>
    hd.startElement("", "", RawDataElementName.RETENTION_TIME.getElementName(), atts);
    // In the project file, retention time is represented in seconds, for
    // historical reasons
    double rt = scan.getRetentionTime() * 60d;
    hd.characters(String.valueOf(rt).toCharArray(), 0, String.valueOf(rt).length());
    hd.endElement("", "", RawDataElementName.RETENTION_TIME.getElementName());
    // <CENTROIDED>
    hd.startElement("", "", RawDataElementName.CENTROIDED.getElementName(), atts);
    hd.characters(String.valueOf(scan.getSpectrumType()).toCharArray(), 0, String.valueOf(scan.getSpectrumType()).length());
    hd.endElement("", "", RawDataElementName.CENTROIDED.getElementName());
    // <QUANTITY_DATAPOINTS>
    hd.startElement("", "", RawDataElementName.QUANTITY_DATAPOINTS.getElementName(), atts);
    hd.characters(String.valueOf((scan.getNumberOfDataPoints())).toCharArray(), 0, String.valueOf((scan.getNumberOfDataPoints())).length());
    hd.endElement("", "", RawDataElementName.QUANTITY_DATAPOINTS.getElementName());
    // <FRAGMENT_SCAN>
    if (scan.getFragmentScanNumbers() != null) {
        int[] fragmentScans = scan.getFragmentScanNumbers();
        atts.addAttribute("", "", RawDataElementName.QUANTITY.getElementName(), "CDATA", String.valueOf(fragmentScans.length));
        hd.startElement("", "", RawDataElementName.QUANTITY_FRAGMENT_SCAN.getElementName(), atts);
        atts.clear();
        for (int i : fragmentScans) {
            hd.startElement("", "", RawDataElementName.FRAGMENT_SCAN.getElementName(), atts);
            hd.characters(String.valueOf(i).toCharArray(), 0, String.valueOf(i).length());
            hd.endElement("", "", RawDataElementName.FRAGMENT_SCAN.getElementName());
        }
        hd.endElement("", "", RawDataElementName.QUANTITY_FRAGMENT_SCAN.getElementName());
    }
    // <MASS_LIST>
    MassList[] massLists = scan.getMassLists();
    for (MassList massList : massLists) {
        StorableMassList stMassList = (StorableMassList) massList;
        atts.addAttribute("", "", RawDataElementName.NAME.getElementName(), "CDATA", stMassList.getName());
        atts.addAttribute("", "", RawDataElementName.STORAGE_ID.getElementName(), "CDATA", String.valueOf(stMassList.getStorageID()));
        hd.startElement("", "", RawDataElementName.MASS_LIST.getElementName(), atts);
        atts.clear();
        hd.endElement("", "", RawDataElementName.MASS_LIST.getElementName());
    }
    // <POLARITY>
    hd.startElement("", "", RawDataElementName.POLARITY.getElementName(), atts);
    String pol = scan.getPolarity().toString();
    hd.characters(pol.toCharArray(), 0, pol.length());
    hd.endElement("", "", RawDataElementName.POLARITY.getElementName());
    // <SCAN_DESCRIPTION>
    hd.startElement("", "", RawDataElementName.SCAN_DESCRIPTION.getElementName(), atts);
    String scanDesc = scan.getScanDefinition();
    hd.characters(scanDesc.toCharArray(), 0, scanDesc.length());
    hd.endElement("", "", RawDataElementName.SCAN_DESCRIPTION.getElementName());
    // <SCAN_MZ_RANGE>
    hd.startElement("", "", RawDataElementName.SCAN_MZ_RANGE.getElementName(), atts);
    Range<Double> mzRange = scan.getScanningMZRange();
    String mzRangeStr = mzRange.lowerEndpoint() + "-" + mzRange.upperEndpoint();
    hd.characters(mzRangeStr.toCharArray(), 0, mzRangeStr.length());
    hd.endElement("", "", RawDataElementName.SCAN_MZ_RANGE.getElementName());
}

Example 10 with MassList

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

the class ShoulderPeaksFilterSetupDialog method loadPreview.

/**
 * This function set all the information into the plot chart
 *
 * @param scanNumber
 */
protected void loadPreview(SpectraPlot spectrumPlot, Scan previewScan) {
    // Remove previous data sets
    spectrumPlot.removeAllDataSets();
    // Add scan data set
    ScanDataSet scanDataSet = new ScanDataSet(previewScan);
    spectrumPlot.addDataSet(scanDataSet, SpectraVisualizerWindow.scanColor, false);
    // If the scan is centroided, switch to centroid mode
    spectrumPlot.setPlotMode(previewScan.getSpectrumType());
    // If the parameters are not complete, exit
    ArrayList<String> errors = new ArrayList<String>();
    boolean paramsOK = parameters.checkParameterValues(errors);
    if (!paramsOK)
        return;
    // Get mass list
    String massListName = parameters.getParameter(ShoulderPeaksFilterParameters.massList).getValue();
    MassList massList = previewScan.getMassList(massListName);
    if (massList == null)
        return;
    // Perform filtering
    DataPoint[] mzValues = massList.getDataPoints();
    DataPoint[] remainingMzValues = ShoulderPeaksFilter.filterMassValues(mzValues, parameters);
    Vector<DataPoint> removedPeaks = new Vector<DataPoint>();
    removedPeaks.addAll(Arrays.asList(mzValues));
    removedPeaks.removeAll(Arrays.asList(remainingMzValues));
    DataPoint[] removedMzValues = removedPeaks.toArray(new DataPoint[0]);
    // Add mass list data sets
    DataPointsDataSet removedPeaksDataSet = new DataPointsDataSet("Removed peaks", removedMzValues);
    DataPointsDataSet remainingPeaksDataSet = new DataPointsDataSet("Remaining peaks", remainingMzValues);
    spectrumPlot.addDataSet(removedPeaksDataSet, removedPeaksColor, false);
    spectrumPlot.addDataSet(remainingPeaksDataSet, SpectraVisualizerWindow.peaksColor, false);
}