How to use

de.unijena.bioinf.ChemistryBase.ms.MutableMs2Experiment

constructor

public MutableMs2Experiment makeMutable(Ms2Experiment experiment) {
  if (experiment instanceof MutableMs2Experiment) return (MutableMs2Experiment) experiment;
  else return new MutableMs2Experiment(experiment);
}

public void setExperimentInformation(Ms2Experiment exp) {
  if (exp instanceof MutableMs2Experiment) {
    this.experiment = (MutableMs2Experiment)exp;
  } else {
    this.experiment = new MutableMs2Experiment(exp);
  }
}

private List<ExperimentWithAnnotatedSpectra> extractSpectra(Ms2Dataset ms2Dataset){
  List<ExperimentWithAnnotatedSpectra> experimentsWithAnnotatedSpectra = new ArrayList<>();
  final List<Ms2Experiment> experiments = ms2Dataset.getExperiments();
  for (Ms2Experiment experiment : experiments) {
    List<Spectrum<PeakWithAnnotation>> ms1 = convert(experiment.getMs1Spectra());
    List<Spectrum<PeakWithAnnotation>> ms2 = convert(experiment.getMs2Spectra());
    experimentsWithAnnotatedSpectra.add(new ExperimentWithAnnotatedSpectra(new MutableMs2Experiment(experiment), ms1, ms2));
  }
  return experimentsWithAnnotatedSpectra;
}

  @Override
  public MutableMs2Experiment validate(Ms2Experiment originalInput, Warning warn, boolean repair) throws InvalidException {
    final MutableMs2Experiment input = new MutableMs2Experiment(originalInput);
    if (input.getMs1Spectra() == null || input.getMs1Spectra().isEmpty()) throw new InvalidException("Missing MS1 spectra");
    checkIonization(warn, repair, input);
    checkMergedMs1(warn, repair, input);
//        checkNeutralMass(warn, repair, input);
    return input;
  }

@Deprecated
public List<IdentificationResult> identifyPrecursorAndIonization(Ms2Experiment uexperiment, int numberOfCandidates, IsotopePatternHandling iso) {
  final MutableMs2Experiment exp = new MutableMs2Experiment(uexperiment);
  exp.setAnnotation(PossibleIonModes.class, PossibleIonModes.defaultFor(uexperiment.getPrecursorIonType().getCharge()));
  return identify(exp, numberOfCandidates, true, iso);
}

/**
 * Creates a Ms2Experiment object from the given MS and MS/MS spectra. A Ms2Experiment is NOT a single run or measurement, but a measurement of a concrete compound. So a MS spectrum might contain several Ms2Experiments. However, each MS/MS spectrum should have on precursor or parent mass. All MS/MS spectra with the same precursor together with the MS spectrum containing this precursor peak can be seen as one Ms2Experiment.
 *
 * @param parentMass the measured mass of the precursor ion. Can be either the MS peak or (if present) a MS/MS peak
 * @param ion        PrecursorIonType (contains ion mode as well as adducts and in-source fragmentations of the precursor ion)
 * @param ms1        the MS spectrum containing the isotope pattern of the measured compound. Might be null
 * @param ms2        a list of MS/MS spectra containing the fragmentation pattern of the measured compound
 * @return a MS2Experiment instance, ready to be analyzed by SIRIUS
 */
public Ms2Experiment getMs2Experiment(double parentMass, PrecursorIonType ion, Spectrum<Peak> ms1, Spectrum... ms2) {
  final MutableMs2Experiment mexp = new MutableMs2Experiment();
  mexp.setPrecursorIonType(ion);
  mexp.setIonMass(parentMass);
  for (Spectrum<Peak> spec : ms2) {
    mexp.getMs2Spectra().add(new MutableMs2Spectrum(spec, mexp.getIonMass(), CollisionEnergy.none(), 2));
  }
  return mexp;
}

  @Override
  public MutableMs2Experiment validate(Ms2Experiment originalInput, Warning warn, boolean repair) throws InvalidException {
    final MutableMs2Experiment input = new MutableMs2Experiment(originalInput);
    checkInchi(warn, repair, input);
    if (input.getMs2Spectra() == null)
      throw new InvalidException("Missing MS2 spectra");
    removeEmptySpectra(warn, input);
    if (input.getMs2Spectra().isEmpty() && input.getMs1Spectra().isEmpty() && input.getMergedMs1Spectrum()==null)
      throw new InvalidException("Missing MS2 and MS1 spectra");
    if (input.getMs1Spectra() == null) input.setMs1Spectra(new ArrayList<SimpleSpectrum>());

    checkIonization(warn, repair, input);
    checkMergedMs1(warn, repair, input);
    checkIonMass(warn, repair, input);
//        checkNeutralMass(warn, repair, input);
    return input;
  }

private SimpleSpectrum extractIsotopePattern(Ms2Experiment experiment) {
  Ms2Experiment experiment2;
  if (experiment.getMergedMs1Spectrum()!=null) experiment2 = experiment;
  else {
    experiment2 = new MutableMs2Experiment(experiment);
    if (experiment2.getMs1Spectra().size() > 0) {
      ((MutableMs2Experiment)experiment2).setMergedMs1Spectrum(Spectrums.mergeSpectra(experiment2.<Spectrum<Peak>>getMs1Spectra()));
    } else {
      return new SimpleSpectrum(new double[0], new double[0]);
    }
  }
  //todo again the problem with the measurementprofile?!
  return sirius.getMs1Analyzer().extractPattern(experiment2, experiment2.getIonMass());
}

MutableMs2Experiment mutableMs2Experiment = new MutableMs2Experiment(result.getExperiment());
String name = mutableMs2Experiment.getName();
List<Ms2Experiment> experimentList = nameToExperiment.get(name);

/**
 * compute {@link IsotopePattern}s. Only use if possible pattern contains precursor peak(mass)
 * @param mass
 * @param spectrum
 * @param profile
 * @param precursorMass
 * @param charge
 * @return
 */
private List<IsotopePattern> computeIsotopePatterns(double mass, MutableSpectrum<Peak> spectrum, MeasurementProfile profile, double precursorMass, int charge) {
  int absCharge = Math.abs(charge);
  boolean mergeMasses = false;
  SimpleMutableSpectrum isotopeSpec = Spectrums.extractIsotopePattern(spectrum, profile, mass, absCharge, mergeMasses);
  isotopeSpec = trimToPossiblePattern(isotopeSpec);
  //
  if (!containsMass(precursorMass, isotopeSpec)) return new ArrayList<>();
  MutableMs2Experiment mutableIsoExperiment = new MutableMs2Experiment();
  mutableIsoExperiment.setPrecursorIonType(PrecursorIonType.unknown(charge));
  mutableIsoExperiment.setIonMass(mass);
  mutableIsoExperiment.setMergedMs1Spectrum(new SimpleSpectrum(isotopeSpec));
  FormulaConstraints constraints = sirius.predictElementsFromMs1(mutableIsoExperiment);
  setUpperBounds(constraints);
  IsotopePatternAnalysis isotopePatternAnalysis = sirius.getMs1Analyzer();
  MutableMeasurementProfile mutableMeasurementProfile = new MutableMeasurementProfile(profile);
  mutableMeasurementProfile.setFormulaConstraints(constraints);
  List<IsotopePattern> isotopePatterns = isotopePatternAnalysis.deisotope(mutableIsoExperiment, mutableMeasurementProfile);
  return isotopePatterns;
}

if (!inst.hasNext()) return null;
++inst.specIndex;
final MutableMs2Experiment exp = new MutableMs2Experiment();
exp.setMs2Spectra(new ArrayList<MutableMs2Spectrum>());
exp.setMs1Spectra(new ArrayList<SimpleSpectrum>());

public FTree beautifyTree(MasterJJob<?> master, FTree tree, Ms2Experiment experiment, boolean recalibrating) {
  if (tree.getAnnotation(Beautified.class, Beautified.IS_UGGLY).isBeautiful()) return tree;
  final PrecursorIonType ionType = tree.getAnnotationOrThrow(PrecursorIonType.class);
  final MutableMs2Experiment mexp = new MutableMs2Experiment(experiment);
  mexp.setPrecursorIonType(ionType);
  final MolecularFormula formula;

MutableMs2Experiment input = new MutableMs2Experiment(originalExperiment);
Ms2Experiment exp = input;
final ProcessedInput pinput =  new ProcessedInput(new MutableMs2Experiment(exp), originalExperiment, new MutableMeasurementProfile(profile));
if (constraints==null && (originalExperiment.getAnnotation(FormulaSettings.class,null)!=null)) {
  constraints = originalExperiment.getAnnotation(FormulaSettings.class).getConstraints();

experiment = null;
if (compoundName == null) return;
final MutableMs2Experiment exp = new MutableMs2Experiment();
exp.setIonMass(parentMass);
exp.setMolecularFormula(formula);