@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
}