@Test
  public void testConditioning() {
    XTandemMain main =
        new XTandemMain(
            XTandemUtilities.getResourceStream("smallSample/tandem.params"),
            "smallSample/tandem.params");
    main.loadScoringTest();
    main.loadSpectra();
    Scorer sa = main.getScoreRunner();
    IScoredScan[] conditionedScans = sa.getScans();
    final IScoredScan conditionedScan = conditionedScans[0];

    SpectrumCondition sc = sa.getSpectrumCondition();
    final IScoringAlgorithm alg = sa.getAlgorithm();
    IMeasuredSpectrum scan = alg.conditionSpectrum(conditionedScan, sc);
    Set<Integer> goodMasses = buildMassSet();

    final ISpectrumPeak[] sps = scan.getPeaks();
    for (int i = 0; i < sps.length; i++) {
      ISpectrumPeak sp = sps[i];
      validateMass(sp, peaks[2 * i], goodMasses);
      //     validatePeak(sp,peaks[2 * i],peaks[2 * i + 1]);
    }
    Assert.assertEquals(goodMasses.size(), 0);
    XTandemUtilities.breakHere();
  }
  public ProteinMapper(XTandemMain app) {
    super(app);

    ScoringModifications scoringMods = app.getScoringMods();

    PeptideModification[] modifications = scoringMods.getModifications();
    m_Modifications = modifications;

    setGenerateDecoysForModifiedPeptides(
        app.getBooleanParameter(
            XTandemUtilities.CREATE_DECOY_FOR_MODIFIED_PEPTIDES_PROPERTY, Boolean.FALSE));

    // hard code modifications of cystein
  }