/** * <p> * getIntensityValues. * </p> * * @return an array of float. */ @Nonnull default float[] getIntensityValues() { return getIntensityValues(null); }
@Nonnull float[] getRetentionTimes(@Nullable float array[]);
/** * <p> * getMzValues. * </p> * * @return an array of double. */ @Nullable default double[] getMzValues() { return getMzValues(null); }
xmlStreamWriter.writeStartElement(MzMLTags.TAG_CHROMATOGRAM); xmlStreamWriter.writeAttribute(MzMLTags.ATTR_INDEX, String.valueOf(parsedChromatograms)); xmlStreamWriter.writeAttribute(MzMLTags.ATTR_ID, chromatogram.getChromatogramType().name()); xmlStreamWriter.writeAttribute(MzMLTags.ATTR_DEFAULT_ARRAY_LENGTH, String.valueOf(chromatogram.getNumberOfDataPoints())); switch (chromatogram.getChromatogramType()) { case BPC: writeCVParam(xmlStreamWriter, if (!chromatogram.getIsolations().isEmpty()) { IsolationInfo isolationInfo = chromatogram.getIsolations().get(0); if (chromatogram.getMz() != null) { Double mz = chromatogram.getMz(); writeCVParam(xmlStreamWriter, new MzMLCVParam(MzMLCV.cvIsolationWindowTarget, String.valueOf(mz), "isolation window target m/z", MzMLCV.cvMz)); rtBuffer = MzMLPeaksEncoder.encodeFloat(chromatogram.getRetentionTimes(null), floatArrayCompression); xmlStreamWriter.writeStartElement(MzMLTags.TAG_BINARY_DATA_ARRAY); MzMLPeaksEncoder.encodeFloat(chromatogram.getIntensityValues(), floatArrayCompression); xmlStreamWriter.writeStartElement(MzMLTags.TAG_BINARY_DATA_ARRAY); xmlStreamWriter.writeAttribute(MzMLTags.ATTR_ENCODED_LENGTH, chromatograms.get(i).getChromatogramType().name()); xmlStreamWriter.writeCharacters(String.valueOf(chromatogramIndices.get(i)));
if (chromatogram.getChromatogramType() != ChromatogramType.MRM_SRM) { parsed++; continue;
/** * <p> * getNextChromatogramNumber. * </p> * * @param rawDataFile a {@link io.github.msdk.datamodel.RawDataFile} object. * @return a {@link java.lang.Integer} object. */ @Nonnull static public Integer getNextChromatogramNumber(RawDataFile rawDataFile) { int chromatogramNumber = 1; List<Chromatogram> chromatograms = rawDataFile.getChromatograms(); for (Chromatogram chromatogram : chromatograms) { int currentChromatogramNumber = chromatogram.getChromatogramNumber(); if (currentChromatogramNumber > chromatogramNumber) chromatogramNumber = currentChromatogramNumber; } return chromatogramNumber; } }
xmlStreamWriter.writeStartElement(MzMLTags.TAG_CHROMATOGRAM); xmlStreamWriter.writeAttribute(MzMLTags.ATTR_INDEX, String.valueOf(parsedChromatograms)); xmlStreamWriter.writeAttribute(MzMLTags.ATTR_ID, chromatogram.getChromatogramType().name()); xmlStreamWriter.writeAttribute(MzMLTags.ATTR_DEFAULT_ARRAY_LENGTH, String.valueOf(chromatogram.getNumberOfDataPoints())); switch (chromatogram.getChromatogramType()) { case BPC: writeCVParam(xmlStreamWriter, if (!chromatogram.getIsolations().isEmpty()) { IsolationInfo isolationInfo = chromatogram.getIsolations().get(0); if (chromatogram.getMz() != null) { Double mz = chromatogram.getMz(); writeCVParam(xmlStreamWriter, new MzMLCVParam(MzMLCV.cvIsolationWindowTarget, String.valueOf(mz), "isolation window target m/z", MzMLCV.cvMz)); rtBuffer = MzMLPeaksEncoder.encodeFloat(chromatogram.getRetentionTimes(null), floatArrayCompression); xmlStreamWriter.writeStartElement(MzMLTags.TAG_BINARY_DATA_ARRAY); MzMLPeaksEncoder.encodeFloat(chromatogram.getIntensityValues(), floatArrayCompression); xmlStreamWriter.writeStartElement(MzMLTags.TAG_BINARY_DATA_ARRAY); xmlStreamWriter.writeAttribute(MzMLTags.ATTR_ENCODED_LENGTH, chromatograms.get(i).getChromatogramType().name()); xmlStreamWriter.writeCharacters(String.valueOf(chromatogramIndices.get(i)));
if (chromatogram.getChromatogramType() != ChromatogramType.MRM_SRM) { parsed++; continue;
/** * <p> * getNextChromatogramNumber. * </p> * * @param rawDataFile a {@link io.github.msdk.datamodel.RawDataFile} object. * @return a {@link java.lang.Integer} object. */ @Nonnull static public Integer getNextChromatogramNumber(RawDataFile rawDataFile) { int chromatogramNumber = 1; List<Chromatogram> chromatograms = rawDataFile.getChromatograms(); for (Chromatogram chromatogram : chromatograms) { int currentChromatogramNumber = chromatogram.getChromatogramNumber(); if (currentChromatogramNumber > chromatogramNumber) chromatogramNumber = currentChromatogramNumber; } return chromatogramNumber; } }
/** * <p> * getIntensityValues. * </p> * * @return an array of float. */ @Nonnull default float[] getIntensityValues() { return getIntensityValues(null); }
@Nonnull float[] getRetentionTimes(@Nullable float array[]);
/** * <p> * getMzValues. * </p> * * @return an array of double. */ @Nullable default double[] getMzValues() { return getMzValues(null); }