private void initial() {
NormalDistribution nd = new NormalDistribution();
String[] seqList = this.sequence.split(";");
for (String seq : seqList) {
BaseIsotopomer bIso = new BaseIsotopomer(seq, this.isotopomerWidth);
TIntDoubleMap chargeScaleMap = new TIntDoubleHashMap();
int centralCharge = bIso.getCentralChargeState();
int totalChargeState = (bIso.getMaxChargeState() - centralCharge) * 2;
double step = 6.0 / totalChargeState;
// calculate right side of the central charge state (inclusive) to 10+ charge
double x = 0.0;
for (int i = centralCharge; i > 8; i--) {
double factor = nd.density(x);
x += step;
chargeScaleMap.put(i, factor);
}
// calculate left side of the central charge state (exclusive) to max charge
x = step;
for (int i = centralCharge + 1; i <= bIso.getMaxChargeState(); i++) {
double factor = nd.density(x);
x += step;
chargeScaleMap.put(i, factor);
}
// build list of Isotopomer
for (int charge : chargeScaleMap.keys()) {
ChargedIsotopomer cIso = new ChargedIsotopomer(bIso, charge);
isotopomerList.add(cIso);
TDoubleDoubleMap tempPeakMap = cIso.getScaledPeakMap(chargeScaleMap.get(charge));
for (double mz : tempPeakMap.keys()) {
double intensity = peakMap.get(mz);
if (intensity == peakMap.getNoEntryValue()) {
peakMap.put(mz, tempPeakMap.get(mz));
} else {
peakMap.put(mz, intensity + tempPeakMap.get(mz));
}
}
}
}
}
/**
* Create prefix residue mass spectrum (PRM spectrum) with subset of peak list from Ms2Query
* peaklist based on their intensity values (higher intensity first). The output spectrum contains
* double of number plus 2 peaks after inserting reverse peaks, start peak and whole mass.
*
* @param query Ms2Query from MgfReader
* @param number number of peaks with large intensity values from original peak list
*/
public PRMSpectrum(Ms2Query query, int number) {
this.prmSpectrum = new ArrayList<>();
int z = query.getPrecursorCharge();
proteinMass = (query.getPrecursorMZ() * z) - (z * Constants.PROTON_MASS); // Neutral mass
// String title = query.getTitle();
TDoubleDoubleMap massToIntensity2dp =
new TDoubleDoubleHashMap(); // This is for checking if we have duplication - use the mass at
// 4dp with higher intensity, add intensity
PeakList peakList =
new PeakList(query.getPeakList()); // Convert Map<Double, Double> to TDoubleDoubleMap
// Work on the top number
TDoubleDoubleMap topNPeakList = peakList.getIntensePeaks(number);
prmSpectrum.add(
new PRMPeak(Double.parseDouble(df.format(0.0)), 50.0, 0)); // origin 0.0, forward
prmSpectrum.add(
new PRMPeak(
Double.parseDouble(df.format(Constants.CTERM + Constants.HYDROGEN_MASS)),
50.0,
1)); // origin C term group needed for finding y ion series, reverse
prmSpectrum.add(
new PRMPeak(
Double.parseDouble(df.format(proteinMass)), 50.0, 1)); // last y ion mass, reverse
// Todo: check the following to FOR statements. What if pepMass=2500, mz=1250, then the
// intensity at 1250 will be double counted?
// Todo: It seems that the intensity will not be used in the output result.
// first test for duplicate peaks, and include higher intensity ones
// the mass in the peaklist is de-charged mass
// Create forward PRM peak list
for (double mz : topNPeakList.keys()) {
// Todo: check if mz is +1 charged or other possible charged
// Calculate mz (from mgf) and take the decimal formate set in df
double decimalFormatMass = Double.parseDouble(df.format(mz - Constants.PROTON_MASS));
// Get intensity value of mz
double intensity = Double.parseDouble(df.format(topNPeakList.get(mz)));
PRMPeak tempPeak = new PRMPeak(decimalFormatMass);
// index of the first occurrence of the tempPeak in prmSpectrum, -1 if prmSpectrum doesn't
// contain the element.
int ind = prmSpectrum.indexOf(tempPeak);
double newIntensity = 50.0;
if (ind != -1) {
// get the specific PRM peak by removing it from prmSpectrum
PRMPeak rmPeak = prmSpectrum.remove(ind);
double oldIntensity = rmPeak.getIntensity();
newIntensity = oldIntensity + intensity;
}
prmSpectrum.add(
new PRMPeak(
decimalFormatMass, newIntensity, 0)); // Direction should be always 0 at this stage
}
// Now get the inverse mzs and check we are not duplicating
// Create reverse PRM peak list
for (double mz : topNPeakList.keys()) {
// Calculate mz (from mgf) and take the decimal formate set in df
double inverseFormatMass =
Double.parseDouble(df.format(proteinMass - (mz - Constants.PROTON_MASS)));
// Get intensity value of mz
double intensity = Double.parseDouble(df.format(topNPeakList.get(mz)));
if (massToIntensity2dp.containsKey(inverseFormatMass)) {
intensity += massToIntensity2dp.get(inverseFormatMass);
}
PRMPeak tempPeak = new PRMPeak(inverseFormatMass);
// index of the first occurrence of the tempPeak in prmSpectrum, -1 if prmSpectrum doesn't
// contain the element.
int ind = prmSpectrum.indexOf(tempPeak);
double newIntensity = 50.0;
if (ind != -1) {
PRMPeak oldPeak = prmSpectrum.remove(ind);
if (oldPeak.getDirection()
!= 1) { // if the direction of oldPeak is not reverse (it could be either 2 or 0), then
// new direction will be both (value 2).
tempPeak.setDirection(2);
} else {
tempPeak.setDirection(1); // unneccessary?
}
double oldIntensity = oldPeak.getIntensity();
newIntensity = oldIntensity + intensity;
}
prmSpectrum.add(new PRMPeak(inverseFormatMass, newIntensity, tempPeak.getDirection()));
}
Collections.sort(prmSpectrum, MASS_DESCENDING);
}