Examples of PeptideFragmentation

Examples of net.sf.mzmine.modules.peaklistmethods.identification.mascot.data.PeptideFragmentation

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   * @return
   */
  public static double getIonCoverage(DataPoint[] dataPoints,
      Peptide peptide, SerieIonType ionType, double intensityThreshold) {

    PeptideFragmentation fragmentation = peptide.getFragmentation();
    FragmentIon[] fragmentIons = fragmentation.getFragmentIons(ionType);
    PeptideIdentityDataFile peptideDataFile = peptide.getScan()
        .getPeptideDataFile();
    double fragmentIonMassErrorTol = peptideDataFile
        .getFragmentIonMassErrorTolerance();

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Examples of net.sf.mzmine.modules.peaklistmethods.identification.mascot.data.PeptideFragmentation

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      // Ion serie
      PeptideIonSerie peptideIonSerie = parseIonSeriesSignificance(tokens[8]);
      peptide.setIonSeries(peptideIonSerie);

      // Calculate fragmentation
      PeptideFragmentation fragmentation = new PeptideFragmentation(
          peptide, pepDataFile);
      peptide.setFragmentation(fragmentation);

      // Protein info
      ProteinSection section;
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