/** {@inheritDoc} */ @Override @Nonnull public Chromatogram clone(@Nonnull DataPointStore newStore) { Preconditions.checkNotNull(newStore); Chromatogram newChromatogram = MSDKObjectBuilder.getChromatogram( newStore, getChromatogramNumber(), getChromatogramType(), getSeparationType()); final ChromatogramDataPointList dataPointList = MSDKObjectBuilder .getChromatogramDataPointList(); getDataPoints(dataPointList); final RawDataFile rawDataFile2 = getRawDataFile(); if (rawDataFile2 != null) { newChromatogram.setRawDataFile(rawDataFile2); } newChromatogram.getIsolations().addAll(getIsolations()); newChromatogram.setDataPoints(dataPointList); return newChromatogram; }
ChromatogramDataPointList dataPoints = buildingChromatogram .getDataPoints(); newChromatogram.setDataPoints(dataPoints); newChromatogram.setMz(mz);
rtBuffer = chromatogram.getRetentionTimes(); intensityBuffer = chromatogram.getIntensityValues(intensityBuffer); int numOfDataPoints = chromatogram.getNumberOfDataPoints(); if (chromatogram.getIonAnnotation() != null) { column = featureTable.getColumn(ColumnName.IONANNOTATION, null); List<IonAnnotation> ionAnnotations = (List<IonAnnotation>) row.getData(column); if (ionAnnotations == null) ionAnnotations = new ArrayList<IonAnnotation>(); ionAnnotations.add(chromatogram.getIonAnnotation()); row.setData(column, ionAnnotations); row.setData(column, chromatogram); Double mz = chromatogram.getMz(); column = tableColumns.get(ColumnName.MZ); if (mz != null)
if (chromatogram.getChromatogramType() == ChromatogramType.MRM_SRM) { List<IsolationInfo> isolations = chromatogram.getIsolations(); Double mzQ1 = isolations.get(0).getPrecursorMz(); Double mzQ3 = isolations.get(1).getPrecursorMz();
newRow.setData(column, chromatogram.getIonAnnotation()); double mz = chromatogram.getMz(); column = tableColumns.get(ColumnName.MZ.getName()); newRow.setData(column, mz);
if (chromatogram.getChromatogramType() != ChromatogramType.MRM_SRM) { parsed++; continue;