final MsFunction msFunction = MSDKObjectBuilder.getMsFunction(1); MsScan scan = MSDKObjectBuilder.getMsScan(dataStore, scanNumber, msFunction); .getChromatographyInfo1D(SeparationType.UNKNOWN, scanRetentionTimes[scanIndex]);
private static FeatureTableRow copyRow(@Nonnull FeatureTableRow row, @Nonnull FeatureTable result) { // Create a new row with the common feature data final FeatureTableRow newRow = MSDKObjectBuilder.getFeatureTableRow(result, row.getId()); FeatureTableUtil.copyCommonValues(row, newRow, false); // Copy the feature data for the samples for (Sample sample : row.getFeatureTable().getSamples()) { FeatureTableUtil.copyFeatureValues(row, newRow, sample); } return newRow; }
FeatureTableColumn<Integer> idColumn = MSDKObjectBuilder.getIdFeatureTableColumn(); FeatureTableColumn<Double> mzColumn = MSDKObjectBuilder.getMzFeatureTableColumn(); FeatureTableColumn<Double> ppmColumn = MSDKObjectBuilder.getPpmFeatureTableColumn(); FeatureTableColumn<ChromatographyInfo> chromatographyInfoColumn = MSDKObjectBuilder .getChromatographyInfoFeatureTableColumn(); FeatureTableColumn<IonAnnotation> ionAnnotationColumn = MSDKObjectBuilder .getIonAnnotationFeatureTableColumn(); featureTable.addColumn(idColumn); featureTable.addColumn(mzColumn); FeatureTableColumn<?> column = featureTable.getColumn(columnName.getName(), sample); if (column == null) { column = MSDKObjectBuilder.getFeatureTableColumn(columnName, sample); featureTable.addColumn(column);
private void addCommonColumns(@Nonnull FeatureTable featureTable) { // Common columns // Only add common columns if the feature table is empty if (featureTable.getColumns().isEmpty()) { FeatureTableColumn<Integer> idColumn = MSDKObjectBuilder.getIdFeatureTableColumn(); FeatureTableColumn<Double> mzColumn = MSDKObjectBuilder.getMzFeatureTableColumn(); FeatureTableColumn<Double> ppmColumn = MSDKObjectBuilder.getPpmFeatureTableColumn(); FeatureTableColumn<Float> rtColumn = MSDKObjectBuilder.getRetentionTimeFeatureTableColumn(); FeatureTableColumn<List<SimpleIonAnnotation>> ionAnnotationColumn = MSDKObjectBuilder.getIonAnnotationFeatureTableColumn(); featureTable.addColumn(idColumn); featureTable.addColumn(mzColumn); featureTable.addColumn(ppmColumn); featureTable.addColumn(rtColumn); featureTable.addColumn(ionAnnotationColumn); } }
MsFunction msFunction = MSDKObjectBuilder.getMsFunction(msLevel); MsScan newScan = MSDKObjectBuilder.getMsScan(dataStore, scanNumber, msFunction); .getChromatographyInfo1D(SeparationType.UNKNOWN, retentionTime); newScan.setChromatographyInfo(chromInfo); IsolationInfo isolation = MSDKObjectBuilder.getIsolationInfo( Range.singleton(precursorMz), null, precursorMz, precursorCharge, null);
.getIdFeatureTableColumn(); FeatureTableColumn<Double> mzColumn = MSDKObjectBuilder .getMzFeatureTableColumn(); FeatureTableColumn<ChromatographyInfo> chromatographyInfoColumn = MSDKObjectBuilder .getChromatographyInfoFeatureTableColumn(); FeatureTableColumn<IonAnnotation> ionAnnotationColumn = MSDKObjectBuilder .getIonAnnotationFeatureTableColumn(); FeatureTableColumn<Integer> chargeColumn = MSDKObjectBuilder .getChargeFeatureTableColumn(); newFeatureTable.addColumn(idColumn); newFeatureTable.addColumn(mzColumn); Sample sample = MSDKObjectBuilder.getSimpleSample(fileName); int msRunKey = entry.getKey(); column = MSDKObjectBuilder.getFeatureTableColumn(ColumnName.AREA, sample); newFeatureTable.addColumn(column);
FeatureTableColumn column; FeatureTableRow currentRow = MSDKObjectBuilder .getFeatureTableRow(featureTable, parsedRows); .getChromatographyInfo1D(SeparationType.UNKNOWN, rtAverageValue); .getSimpleIonAnnotation(); ionAnnotation.setAnnotationId(database); ionAnnotation.setDescription(description); Float rtValue = Float.parseFloat(orgValue); ChromatographyInfo ciValue = MSDKObjectBuilder .getChromatographyInfo1D( SeparationType.UNKNOWN, rtValue); currentRow.setData(column, ciValue);
HighestDataPointConnector(double minimumTimeSpan, double minimumHeight, MZTolerance mzTolerance) { this.mzTolerance = mzTolerance; this.minimumHeight = minimumHeight; this.minimumTimeSpan = minimumTimeSpan; // Create the data structure dataPoints = MSDKObjectBuilder.getMsSpectrumDataPointList(); // We use LinkedHashSet to maintain a reproducible ordering. If we use // plain HashSet, the resulting peak list row IDs will have different // order every time the method is invoked. buildingChromatograms = new LinkedHashSet<BuildingChromatogram>(); connectedChromatograms = new LinkedHashSet<BuildingChromatogram>(); }
/** {@inheritDoc} */ @Override public MsFunction getMsFunction() { Integer msLevel = 1; String value = getCVValue(MzMLCV.cvMSLevel); if (!Strings.isNullOrEmpty(value)) msLevel = Integer.parseInt(value); return MSDKObjectBuilder.getMsFunction(msLevel); }
.getChromatographyInfo1D(SeparationType.UNKNOWN, retentionTime); return chromInfo;
activationInfo = MSDKObjectBuilder.getActivationInfo( precursorActivationEnergy, precursorActivation); isolationInfo = MSDKObjectBuilder.getIsolationInfo( Range.singleton(precursorIsolationMz), null, precursorIsolationMz, null, activationInfo); isolationInfo = MSDKObjectBuilder.getIsolationInfo( Range.singleton(productIsolationMz), null, productIsolationMz, null, null);
@Nullable @SuppressWarnings("null") private FeatureTableColumn<?> getFeatureTableColumn( @Nonnull String mzTabColumnName, @Nonnull Sample sample, int msRunKey) { if (mzTabColumnName.contains("[" + msRunKey + "]_")) { String[] nameArray = mzTabColumnName.split("]_"); @Nonnull String name = nameArray[1]; ColumnName columnName = mzTabNameToColumnName(name); if (columnName == null) { return MSDKObjectBuilder.getFeatureTableColumn(name, String.class, sample); } else { return MSDKObjectBuilder.getFeatureTableColumn(columnName, sample); } } else { return null; } }
IsolationInfo isolation = MSDKObjectBuilder.getIsolationInfo( Range.singleton(precursorMz), null, precursorMz, precursorCharge, null);
MsFunction msFunction = MSDKObjectBuilder.getMsFunction(msLevel); MsScan newScan = MSDKObjectBuilder.getMsScan(dataStore, scanNumber, msFunction); .getChromatographyInfo1D(SeparationType.UNKNOWN, retentionTime); newScan.setChromatographyInfo(chromInfo); IsolationInfo isolation = MSDKObjectBuilder.getIsolationInfo( Range.singleton(precursorMz), null, precursorMz, precursorCharge, null);
/** {@inheritDoc} */ @Override public MsScan execute() throws MSDKException { logger.info("Started wavelet centroider on scan #" + inputScan.getScanNumber()); // Copy all scan properties this.newScan = MsScanUtil.clone(dataPointStore, inputScan, false); // Create data structures final MsSpectrumDataPointList inputDataPoints = MSDKObjectBuilder .getMsSpectrumDataPointList(); final MsSpectrumDataPointList newDataPoints = MSDKObjectBuilder .getMsSpectrumDataPointList(); // Load data points inputScan.getDataPoints(inputDataPoints); // If there are no data points, just return the scan if (inputDataPoints.getSize() == 0) { newScan.setDataPoints(inputDataPoints); methodProgress = 1f; return newScan; } float waveletIntensities[] = performCWT(inputDataPoints); getMzPeaks(inputDataPoints, waveletIntensities, newDataPoints); // Store the new data points newScan.setDataPoints(newDataPoints); // Finish methodProgress = 1f; logger.info("Finished wavelet centroider on scan #" + inputScan.getScanNumber()); return newScan; }
@Nonnull MsFunction extractMsFunction(Spectrum spectrum) { Integer msLevel = 1; // Browse the spectrum parameters List<CVParam> cvParams = spectrum.getCvParam(); if (cvParams != null) { for (CVParam param : cvParams) { String accession = param.getAccession(); String value = param.getValue(); if ((accession == null) || (value == null)) continue; // MS level MS:1000511 if (accession.equals("MS:1000511")) { msLevel = Integer.parseInt(value); } } } return MSDKObjectBuilder.getMsFunction(msLevel); }
static void extractDataPoints( uk.ac.ebi.jmzml.model.mzml.Chromatogram jmzChromatogram, ChromatogramDataPointList dataPointList) { dataPointList.clear(); BinaryDataArrayList dataList = jmzChromatogram.getBinaryDataArrayList(); if ((dataList == null) || (dataList.getCount().equals(0))) return; // Obtain the data arrays from spectrum final BinaryDataArray rtArray = dataList.getBinaryDataArray().get(0); final BinaryDataArray intensityArray = dataList.getBinaryDataArray() .get(1); final Number rtValues[] = rtArray.getBinaryDataAsNumberArray(); final Number intensityValues[] = intensityArray .getBinaryDataAsNumberArray(); // Allocate space for the data points dataPointList.allocate(rtValues.length); final ChromatographyInfo rtBuffer[] = dataPointList.getRtBuffer(); final float intensityBuffer[] = dataPointList.getIntensityBuffer(); // Copy the actual data point values for (int i = 0; i < rtValues.length; i++) { final float rt = rtValues[i].floatValue(); final float intensity = intensityValues[i].floatValue(); final ChromatographyInfo chromatographyInfo = MSDKObjectBuilder .getChromatographyInfo1D(SeparationType.UNKNOWN, rt); rtBuffer[i] = chromatographyInfo; intensityBuffer[i] = intensity; } // Commit the changes dataPointList.setSize(rtValues.length); }
FeatureTableColumn<Object> column = featureTable.getColumn(columnName, sample); if (column == null) { column = MSDKObjectBuilder.getFeatureTableColumn(columnName, sample); featureTable.addColumn(column);
.getMsSpectrumDataPointList(); final MsSpectrumDataPointList newDataPoints = MSDKObjectBuilder .getMsSpectrumDataPointList();
for (Chromatogram chromatogram : chromatograms) { lastID++; FeatureTableRow newRow = MSDKObjectBuilder.getFeatureTableRow(featureTable, lastID);