List of recalibrateSpectrum() Examples

Examples of recalibrateSpectrum()

eu.isas.peptideshaker.recalibration.SpectrumRecalibrator.recalibrateSpectrum()
Recalibrates a spectrum. @param fileName the name of the file where to find the spectrum @param spectrumTitle the title of the spectrum @param recalibratePrecursor boolean indicating whether precursors shallbe recalibrated @param recalibrateFragmentIons boolean indicating whether fragment ionsshall be recalibrated @return a recalibrated spectrum @throws IOException @throws MzMLUnmarshallerException

Examples of eu.isas.peptideshaker.recalibration.SpectrumRecalibrator.recalibrateSpectrum()


                    String spectrumKey = Spectrum.getSpectrumKey(fileName, spectrumTitle);


                    MSnSpectrum spectrum = null;
                    if (recalibrate) {
                        spectrum = spectrumRecalibrator.recalibrateSpectrum(fileName, spectrumTitle, true, true);
                        spectrum.writeMgf(writerRecalibration);
                    }
                    if (identification.matchExists(spectrumKey)) {
                        psParameter = (PSParameter) identification.getSpectrumMatchParameter(spectrumKey, psParameter);
                        Integer charge = new Integer(psParameter.getSpecificMapKey());

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Examples of eu.isas.peptideshaker.recalibration.SpectrumRecalibrator.recalibrateSpectrum()


                if (debug) {
                    //System.out.println(new Date() + " recalibrating " + spectrumTitle + "\n");
                }


                MSnSpectrum recalibratedSpectrum = spectrumRecalibrator.recalibrateSpectrum(fileName, spectrumTitle, recalibratePrecursors, recalibrateFragmentIons);
                recalibratedSpectrum.writeMgf(writer);
                writer.flush();


                if (waitingHandler != null) {
                    if (waitingHandler.isRunCanceled()) {

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