Examples of Precursor

Examples of com.compomics.util.experiment.massspectrometry.Precursor

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        if (runError == null) {
            throw new IllegalArgumentException("No m/z deviation statistics found for spectrum file " + fileName + ".");
        }

        MSnSpectrum spectrum = (MSnSpectrum) spectrumFactory.getSpectrum(fileName, spectrumTitle);
        Precursor precursor = spectrum.getPrecursor();
        double precursorMz = precursor.getMz();
        double precursorRT = precursor.getRt();
        double correction = 0.0;

        if (recalibratePrecursor) {
            correction = runError.getPrecursorMzCorrection(precursorMz, precursorRT);
        }

        Precursor newPrecursor = spectrum.getPrecursor().getRecalibratedPrecursor(correction, 0.0);
        HashMap<Double, Peak> peakList = spectrum.getPeakMap();

        if (recalibrateFragmentIons) {
            peakList = runError.recalibratePeakList(precursorRT, spectrum.getPeakMap());
        }
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Examples of com.compomics.util.experiment.massspectrometry.Precursor

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                    SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);
                    PeptideAssumption peptideAssumption = spectrumMatch.getBestPeptideAssumption();

                    if (peptideAssumption != null) {

                        Precursor precursor = spectrumFactory.getPrecursor(spectrumKey);
                        double precursorMzError = peptideAssumption.getDeltaMass(precursor.getMz(), searchParameters.isPrecursorAccuracyTypePpm());
                        precursorMzDeviations.add(precursorMzError);
                        Integer charge = peptideAssumption.getIdentificationCharge().value;

                        if (!charges.contains(charge)) {
                            charges.add(charge);
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Examples of uk.ac.ebi.pride.jaxb.model.Precursor

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                    && spectrum.getSpectrumDesc().getPrecursorList().getPrecursor().size() > 0) {

                bw.write("BEGIN IONS" + System.getProperty("line.separator"));
                bw.write("TITLE=" + spectrum.getId() + System.getProperty("line.separator"));

                Precursor precursor = spectrum.getSpectrumDesc().getPrecursorList().getPrecursor().get(0); // get the first precursor
                List<CvParam> precursorCvParams = precursor.getIonSelection().getCvParam();
                Double precursorMz = null, precursorIntensity = null;
                String precursorRt = null;
                Integer precursorCharge = null;

                for (CvParam cvParam : precursorCvParams) {
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