@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();
}
/**
* return true if a mass such as that of a throretical peak is within the range to scpre
*
* @param mass positive testMass
* @return as above
*/
@Override
public boolean isMassWithinRange(double mass, int charge, IScoringAlgorithm alg) {
if (m_PrecursorCharge == 0) {
// try charge 2
double test1 =
(getMassChargeRatio() - XTandemUtilities.getProtonMass()) * 2
+ XTandemUtilities.getProtonMass();
if (alg.isWithinLimits(test1, mass, 0)) return true;
// try charge 3
double test2 =
(getMassChargeRatio() - XTandemUtilities.getProtonMass()) * 3
+ XTandemUtilities.getProtonMass();
if (alg.isWithinLimits(test2, mass, 0)) return true;
// try charge 1 -NOTE THIS IS NEW
double test3 = getMassChargeRatio();
if (alg.isWithinLimits(test3, mass, 0)) return true;
return false; // give up
} else {
double test = getPrecursorMass();
boolean withinLimits = alg.isWithinLimits(test, mass, m_PrecursorCharge);
if (withinLimits) return true;
return false; // give up
}
}
