コード例 #1
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 #2
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);
  }