private static void validateMass(ISpectrumPeak pSp, double pPeak, Set<Integer> goodMasses) {
final double mass = pSp.getMassChargeRatio();
final int imass = asInt(mass);
if (!goodMasses.contains(imass)) {
// try one off
if (goodMasses.contains(imass - 1)) {
goodMasses.remove(imass - 1);
return;
}
if (goodMasses.contains(imass + 1)) {
goodMasses.remove(imass + 1);
return;
}
}
if (!goodMasses.contains(imass)) System.out.println("Missing mass " + imass);
goodMasses.remove(imass);
}
@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();
}
/**
* these are the masses XTandem has
*
* @return
*/
public static Set<Integer> buildMassSet() {
Set<Integer> holder = new HashSet<Integer>();
for (int i = 0; i < peaks.length; i += 2) {
holder.add(asInt(peaks[i]));
}
return holder;
}