コード例 #1
0
  public void appendPeptides(Appendable out) {
    try {
      List<String> proteins = new ArrayList<String>(proteinToHits.keySet());
      Collections.sort(proteins);
      for (String protein : proteins) {
        Set<IdentifiedPSM> pps = proteinToHits.get(protein);
        List<IdentifiedPSM> peptides = new ArrayList<IdentifiedPSM>(pps);
        Collections.sort(peptides);

        for (IdentifiedPSM psm : peptides) {
          Polypeptide peptide = (Polypeptide) psm.getPeptide(); // .getUnModified();
          out.append(peptide.toString());
          out.append("\t");
          out.append(psm.getId());
          out.append("\t");
          out.append(protein);
          out.append("\t");
          String rt = String.format("%11.3f", peptide.getRetentionTime()).trim();
          out.append(rt);
          out.append("\n");
        }
      }
    } catch (Exception e) {
      throw new RuntimeException(e);
    }
  }
コード例 #2
0
  public void setPeptideId(final String pPeptideId) {
    if (m_Peptide != null || m_PeptideId != null)
      throw new IllegalStateException("Cannot reset peptide"); // ToDo change
    m_PeptideId = pPeptideId;
    IMainData main = getMainData();
    if (main != null) {
      //   RawPeptideScan rawScan = main.getRawScan(getId());
      //    pMeasured = rawScan;

      ITaxonomy taxonomy = main.getTaxonomy();
      if (taxonomy != null) {
        String peptideId = getPeptideId();
        m_Peptide = taxonomy.getPeptideById(peptideId);
        if (m_Peptide == null)
          m_Peptide = Polypeptide.fromString(peptideId); // key may be all we need
      }
    } else {
      m_Peptide = Polypeptide.fromString(getPeptideId());
    }
    if (m_Peptide != null) {
      IPeptideDigester digester = PeptideBondDigester.getDefaultDigester();
      int missedCleavages = digester.probableNumberMissedCleavages(m_Peptide);
      ((Polypeptide) m_Peptide).setMissedCleavages(missedCleavages);
    }
  }
コード例 #3
0
 public static IdentifiedPSM processPeptide(final String line, double retentionTime, String id) {
   String peptide = XMLUtil.extractAttribute(line, "peptide");
   if (peptide == null) throw new IllegalArgumentException("bad line " + line);
   Polypeptide polypeptide = Polypeptide.fromString(peptide);
   polypeptide.setRetentionTime(retentionTime);
   return new IdentifiedPSM(id, polypeptide);
 }
コード例 #4
0
  /** finish handling and set up the enclosed object Usually called when the end tag is seen */
  @Override
  public void finishProcessing() {
    IMeasuredSpectrum pMeasured = null;

    final double pScore = getScore();
    final double pHyperScore = getHyperScore();
    final double rawScore = getRawScore();
    IonTypeScorer scorer = getIonScore();

    IProteinPosition[] containedInProteins = m_Positions.toArray(IProteinPosition.EMPTY_ARRAY);
    ((Polypeptide) m_Peptide).setContainedInProteins(containedInProteins);
    SpectralMatch scan =
        new SpectralMatch(m_Peptide, pMeasured, pScore, pHyperScore, rawScore, scorer, null);

    if (m_Usage != null) scan.getUsage().addTo(m_Usage);

    setElementObject(scan);
  }