Examples of MSnSpectrum

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

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        }

        if (assumptionFilter.getSequenceCoverage() != null) {

            SpectrumFactory spectrumFactory = SpectrumFactory.getInstance();
            MSnSpectrum spectrum = (MSnSpectrum) spectrumFactory.getSpectrum(spectrumKey);
            Peptide peptide = peptideAssumption.getPeptide();
            if (peptideSpectrumAnnotator == null) {
                peptideSpectrumAnnotator = new PeptideSpectrumAnnotator();
            }
            HashMap<Integer, ArrayList<IonMatch>> ionMatches = peptideSpectrumAnnotator.getCoveredAminoAcids(annotationPreferences.getIonTypes(),
                    annotationPreferences.getNeutralLosses(), annotationPreferences.getValidatedCharges(),
                    peptideAssumption.getIdentificationCharge().value, spectrum, peptide, spectrum.getIntensityLimit(annotationPreferences.getAnnotationIntensityLimit()),
                    searchParameters.getFragmentIonAccuracy(), false, annotationPreferences.isHighResolutionAnnotation());

            double nCovered = 0;
            int nAA = peptide.getSequence().length();
            for (int i = 0; i <= nAA; i++) {
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Examples of com.compomics.util.experiment.massspectrometry.MSnSpectrum

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                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()) {
                        break;
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Examples of com.compomics.util.experiment.massspectrometry.MSnSpectrum

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        RunMzDeviation runError = runMzDeviationMap.get(fileName);
        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());
        }

        return new MSnSpectrum(2, newPrecursor, spectrumTitle, peakList, fileName);
    }
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Examples of com.compomics.util.experiment.massspectrometry.MSnSpectrum

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        PtmtableContent tempContent, tableContent = new PtmtableContent();
        SpectrumFactory spectrumFactory = SpectrumFactory.getInstance();

        for (String spectrumKey : spectrumKeys) {
            try {
                MSnSpectrum spectrum = (MSnSpectrum) spectrumFactory.getSpectrum(spectrumKey);
                SpectrumMatch spectrumMatch = peptideShakerGUI.getIdentification().getSpectrumMatch(spectrumKey);
                tempContent = PtmtableContent.getPTMTableContent(peptide, ptm, nPTM, spectrum, annotationPreferences.getIonTypes(),
                        annotationPreferences.getNeutralLosses(), annotationPreferences.getValidatedCharges(),
                        spectrumMatch.getBestPeptideAssumption().getIdentificationCharge().value,
                        annotationPreferences.getFragmentIonAccuracy(), spectrum.getIntensityLimit(annotationPreferences.getAnnotationIntensityLimit()));
                tempContent.normalize();
                tableContent.addAll(tempContent);
            } catch (Exception e) {
                peptideShakerGUI.catchException(e);
            }
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Examples of com.compomics.util.experiment.massspectrometry.MSnSpectrum

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     */
    private void insertBarCharts() {

        AnnotationPreferences annotationPreferences = peptideShakerGUI.getAnnotationPreferences();
        PtmtableContent tempContent, tableContent = new PtmtableContent();
        MSnSpectrum spectrum;
        SpectrumMatch spectrumMatch;
        SpectrumFactory spectrumFactory = SpectrumFactory.getInstance();
        PTMFactory ptmFactory = PTMFactory.getInstance();
        String ptmName = ptm.getName(), shortName = ptmFactory.getShortName(ptmName);

        for (String spectrumKey : spectrumKeys) {
            try {
                spectrum = (MSnSpectrum) spectrumFactory.getSpectrum(spectrumKey);
                spectrumMatch = peptideShakerGUI.getIdentification().getSpectrumMatch(spectrumKey);
                tempContent = PtmtableContent.getPTMTableContent(peptide, ptm, nPTM, spectrum, annotationPreferences.getIonTypes(),
                        annotationPreferences.getNeutralLosses(), annotationPreferences.getValidatedCharges(),
                        spectrumMatch.getBestPeptideAssumption().getIdentificationCharge().value,
                        annotationPreferences.getFragmentIonAccuracy(), spectrum.getIntensityLimit(annotationPreferences.getAnnotationIntensityLimit()));
                tempContent.normalize();
                tableContent.addAll(tempContent);
            } catch (Exception e) {
                peptideShakerGUI.catchException(e);
            }
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