Package com.compomics.util.experiment.massspectrometry

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


                return peptideAssumption.getIsotopeNumber(precursor.getMz()) + "";
            case mz:
                precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
                return precursor.getMz() + "";
            case total_spectrum_intensity:
                Spectrum spectrum = SpectrumFactory.getInstance().getSpectrum(spectrumKey);
                return spectrum.getTotalIntensity() + "";
            case max_intensity:
                spectrum = SpectrumFactory.getInstance().getSpectrum(spectrumKey);
                return spectrum.getMaxIntensity() + "";
            case intensity_coverage:
                spectrum = SpectrumFactory.getInstance().getSpectrum(spectrumKey);
                double coveredIntensity = 0;
                Peptide peptide = peptideAssumption.getPeptide();
                ArrayList<IonMatch> matches = peptideSpectrumAnnotator.getSpectrumAnnotation(
                        annotationPreferences.getIonTypes(), annotationPreferences.getNeutralLosses(), annotationPreferences.getValidatedCharges(),
                        peptideAssumption.getIdentificationCharge().value,
                        (MSnSpectrum) spectrum, peptide, 0, searchParameters.getFragmentIonAccuracy(), false, true);
                for (IonMatch ionMatch : matches) {
                    coveredIntensity += ionMatch.peak.intensity;
                }
                double coverage = 100 * coveredIntensity / spectrum.getTotalIntensity();
                return coverage + "";
            case mz_error:
                precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
                return peptideAssumption.getDeltaMass(precursor.getMz(), true) + "";
            case rt:
View Full Code Here


                return tagAssumption.getIsotopeNumber(precursor.getMz()) + "";
            case mz:
                precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
                return precursor.getMz() + "";
            case total_spectrum_intensity:
                Spectrum spectrum = SpectrumFactory.getInstance().getSpectrum(spectrumKey);
                return spectrum.getTotalIntensity() + "";
            case max_intensity:
                spectrum = SpectrumFactory.getInstance().getSpectrum(spectrumKey);
                return spectrum.getMaxIntensity() + "";
            case mz_error:
                precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
                return tagAssumption.getDeltaMass(precursor.getMz(), true) + "";
            case rt:
                precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
View Full Code Here

TOP

Related Classes of com.compomics.util.experiment.massspectrometry.Spectrum

Copyright © 2018 www.massapicom. All rights reserved.
All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.