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

  public static String peptideToString(Peptide peptide) {
    StringBuffer buf = new StringBuffer();
    Format mzFormat = MZmineCore.getConfiguration().getMZFormat();


    Protein protein = peptide.getProtein();
    ProteinSection section;
    section = protein.getSection(peptide);
    buf.append(protein.getSysname() + ":" + section.getName() + "; "
        + protein.getHits() + " hits");


    buf.append("\n" + peptide.getSequence());
    buf.append("\nPeptideMz ");
    buf.append(mzFormat.format(peptide.getMass()));

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


      // Protein info
      ProteinSection section;
      tokens = proteinInfos[pepIndex].split(":");
      String sysname = tokens[0].replace("\"", "");


      Protein protein = pepDataFile.getProtein(sysname);
      if (protein == null)
        protein = new Protein(sysname);


      int startRegion = Integer.parseInt(tokens[2]);
      int stopRegion = Integer.parseInt(tokens[3]);
      int multiplicity = Integer.parseInt(tokens[4]);
      section = new ProteinSection(startRegion, stopRegion, multiplicity);


      // Link peptide and protein
      peptide.setProtein(protein);
      protein.addPeptide(peptide, section, isTopScore);

Related Classes of net.sf.mzmine.modules.peaklistmethods.identification.mascot.data.ProteinSection

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