/**
* Process the M/Z data and set the peaks histogram and the intensity histogram
*
* @param mzData the m/z chartData
*/
private void processSpectrumMzData(PeakList mzData, PeakList intensity) {
String spectrumID = mzData.getSpectrumID().toString();
SpectrumData spectrum = getOrCreateSpectrum(spectrumID);
Map<Integer, PrideHistogram> mzHist;
if (spectrum.isIdentified()) {
mzHist = mzIdentifiedHist;
} else {
mzHist = mzUnidentifiedHist;
}
try {
int charge = (int) Math.ceil(spectrum.getPrecursorCharge());
PrideHistogram histogram;
if (mzHist.containsKey(charge)) {
histogram = mzHist.get(charge);
} else {
histogram = new PrideHistogram();
mzHist.put(charge, histogram);
}
for (int pos = 0; pos < mzData.getDoubleArray().length; pos++) {
// for (double value : mzData.getDoubleArray()) {
double value = mzData.getDoubleArray()[pos];
int bin = (int) Math.round(value / MZHistogramChartSpectra.BIN_SIZE);
double intensityValue = intensity.getDoubleArray()[pos];
if (histogram.containsKey(bin)) {
histogram.put(bin, histogram.get(bin) + intensityValue);
} else {
histogram.put(bin, intensityValue);
}
}
} catch (SpectrumDataException e) {
// Do NOT take into account this spectrum because it has not precursor charge
}
}
protected void processSpectrum(SpectrumData spectrum, IDiscoveryDataHolder hd) {
double score;
if (USE_EXPECTED) score = spectrum.getExpectedValue();
else
//noinspection ConstantConditions
score = spectrum.getHyperScoreValue();
if (spectrum.isTrueHit()) {
hd.addTrueDiscovery(score);
// if (spectrum.isModified())
// m_ModifiedHandler.addTrueDiscovery(score);
// else
// m_UnModifiedHandler.addTrueDiscovery(score);
} else {
hd.addFalseDiscovery(score);
if (spectrum.isModified()) throw new UnsupportedOperationException("Fix This"); // ToDo
// m_ModifiedHandler.addFalseDiscovery(score);
// else
// m_UnModifiedHandler.addFalseDiscovery(score);
}
}
/**
* Process the intensity data and set the peaks histogram and the intensity histogram
*
* @param intensity the intensity peaks data
*/
private void processSpectrumIntensityData(PeakList intensity) {
double[] intensityArray = intensity.getDoubleArray();
int bin = intensityArray.length;
if (peaksHist.containsKey(bin)) peaksHist.put(bin, peaksHist.get(bin) + 1);
else peaksHist.put(bin, 1);
SpectrumData spectrum = getOrCreateSpectrum(intensity.getSpectrumID().toString());
Map<Integer, Integer> intensityHist;
if (spectrum.isIdentified()) {
intensityHist = intensityIdentifiedHist;
} else {
intensityHist = intensityUnidentifiedHist;
}
for (double value : intensityArray) {
bin = (int) Math.round(value / 5.0);
if (intensityHist.containsKey(bin)) {
intensityHist.put(bin, intensityHist.get(bin) + 1);
} else {
intensityHist.put(bin, 1);
}
}
}
/**
* Set the precursor mass of the spectrum ID associated to the given precursor charge chartData
*
* @param precursorCharge the precursor charge chartData
*/
private void setSpectrumPrecursorCharge(PrecursorData precursorCharge) {
String spectrumID = precursorCharge.getSpectrumID();
SpectrumData spectrum = getOrCreateSpectrum(spectrumID);
spectrum.setPrecursorCharge(precursorCharge.getValue());
}
/**
* Set the spectrum references
*
* @param spectrumID the spectrum identifier
* @param identified True if the spectrum is identified
*/
private void setSpectrumReferences(String spectrumID, boolean identified) {
SpectrumData spectrum = getOrCreateSpectrum(spectrumID);
spectrum.setIdentified(identified);
}
