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

Package net.sf.mzmine.modules.peaklistmethods.identification.mascot.data

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

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

   * @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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      // 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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Related Classes of net.sf.mzmine.modules.peaklistmethods.identification.mascot.data.PeptideFragmentation

net.sf.mzmine.util.MascotParserUtils

net.sf.mzmine.util.PeptideUtils

java.util.Iterator

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