/** Calculate the frequency of every one of the keys of the X axis */
@Override
protected void processData(ExperimentSummaryData summaryData) {
Map<Integer, Integer> valuesIdentified = new HashMap<Integer, Integer>();
Map<Integer, Integer> valuesUnidentified = new HashMap<Integer, Integer>();
List<Double> chargeIdentified = summaryData.getPrecChargeVecExp(true);
int maxChargeFound = 0;
for (double key : chargeIdentified) {
int auxKey = (int) key;
int value = valuesIdentified.containsKey(auxKey) ? valuesIdentified.get(auxKey) + 1 : 1;
valuesIdentified.put(auxKey, value);
if (auxKey > maxChargeFound) maxChargeFound = auxKey;
}
List<Double> chargeUnidentified = summaryData.getPrecChargeVecExp(false);
for (double key : chargeUnidentified) {
int auxKey = (int) key;
int value = valuesUnidentified.containsKey(auxKey) ? valuesUnidentified.get(auxKey) + 1 : 1;
valuesUnidentified.put(auxKey, value);
if (auxKey > maxChargeFound) maxChargeFound = auxKey;
}
if (maxChargeFound == 0) {
recordError("No correct charges has been found");
return;
}
List<SeriesPair<Integer, Integer>> identified = new ArrayList<SeriesPair<Integer, Integer>>();
// List<SeriesPair<Integer,Integer>> unidentified = new
// ArrayList<SeriesPair<Integer,Integer>>();
// With the 'for' loop we ensure that the SeriesPair are added in an ordered way
for (int key = 1; key <= maxChargeFound; key++) {
// Only the charges found are stored int the intermediate identified
if (valuesIdentified.containsKey(key))
identified.add(new SeriesPair<Integer, Integer>(key, valuesIdentified.get(key)));
// if(valuesUnidentified.containsKey(key))
// unidentified.add(new SeriesPair<Integer, Integer>(key,valuesUnidentified.get(key)));
}
if (identified.isEmpty()) {
recordError("The experiment does not contain identified spectra");
return;
}
intermediateData = new IntermediateData();
// In this case the type and the name of the series are the same
intermediateData.addPrideChartSerie(
new DataSeries<Integer, Integer>(
DataSeriesType.IDENTIFIED_SPECTRA, "Identified Spectra", identified));
// intermediateData.addPrideChartSerie(new
// DataSeries<Integer,Integer>(DataSeriesType.UNIDENTIFIED_SPECTRA, "Unidentified Spectra",
// unidentified));
try {
intermediateData.setVariable("experimentSize", summaryData.size());
} catch (JSONException e) {
e.printStackTrace();
}
}
@Override
protected boolean isDataConsistent(ExperimentSummaryData summaryData) {
if (!summaryData.getState().isPrecursorChargesLoaded())
recordError("The experiment does not contain precursor charges");
if (!summaryData.getState().isPrecursorMassesLoaded())
recordError("The experiment does not contain precursor masses");
if (summaryData.getProteinsPeptides().size() == 0)
recordError("The experiment does not contain identifications data");
return isValid();
}
@Override
protected boolean isDataConsistent(ExperimentSummaryData summaryData) {
if (!summaryData.getState().isPrecursorChargesLoaded())
recordError("The experiment does not contain precursor charge values");
return isValid();
}
@Override
protected void processData(ExperimentSummaryData summaryData) {
List<Double> data = new ArrayList<Double>();
for (ProteinPeptide pp : summaryData.getProteinsPeptides()) {
SpectrumData sData;
try {
Comparable spectrumID = pp.getSpectrumID();
sData = summaryData.getSpectrum(String.valueOf(spectrumID));
} catch (ProteinPeptideException e) {
// If there is not spectrumID, the precursor mass and charge could not be found
continue;
}
double mz;
int charge;
try {
mz = sData.getPrecursorMass();
charge = (int) sData.getPrecursorCharge();
} catch (Exception e) {
System.err.println(e.getMessage());
continue;
}
// the sum of the PTM masses is stored in the ProteinPeptide object, but for calling
// the calculateDeltaMz method, we need a list of PTM (the Water loss mono mass value
// will be added by the method)
List<Double> ptmMasses = new ArrayList<Double>();
ptmMasses.add(pp.getPtmMass());
Double deltaMass =
MoleculeUtilities.calculateDeltaMz(pp.getSequence(), mz, charge, ptmMasses);
if (deltaMass != null) data.add(deltaMass);
}
if (data.size() == 0) {
recordError("Peptide sequences could not be associated to a MS 1 precursor");
return;
}
Map<Double, Integer> histogram = new HashMap<Double, Integer>();
double min = Collections.min(data);
double max = Collections.max(data);
double binWidth = Math.abs((max - min) / (double) BINS);
binWidth = binWidth < MIN_BIN_WIDTH ? MIN_BIN_WIDTH : binWidth;
for (double value : data) {
int bin = (int) Math.round(value / binWidth);
double pos = bin * binWidth;
if (histogram.keySet().contains(pos)) {
histogram.put(pos, histogram.get(pos) + 1);
} else {
histogram.put(pos, 1);
}
}
List<SeriesPair<Double, Double>> deltaMasses = new ArrayList<SeriesPair<Double, Double>>();
if (histogram.keySet().size() == 1) {
for (Double key : histogram.keySet()) {
if (key > 0.0) { // To center the chart on 0
deltaMasses.add(new SeriesPair<Double, Double>(-key - MIN_BIN_WIDTH, 0.0));
}
deltaMasses.add(new SeriesPair<Double, Double>(key - MIN_BIN_WIDTH, 0.0));
deltaMasses.add(new SeriesPair<Double, Double>(key, 1.0));
deltaMasses.add(new SeriesPair<Double, Double>(key + MIN_BIN_WIDTH, 0.0));
if (key < 0.0) { // To center the chart on 0
deltaMasses.add(new SeriesPair<Double, Double>(-key + MIN_BIN_WIDTH, 0.0));
}
}
} else {
int maxFreq = Collections.max(histogram.values());
for (int pos = -BINS; pos < BINS; pos++) {
double key = pos * binWidth;
double value = histogram.containsKey(key) ? histogram.get(key) / (double) maxFreq : 0.0;
deltaMasses.add(new SeriesPair<Double, Double>(key, value));
}
}
DataSeries series = new DataSeries<Double, Double>(null, "deltaMasses", deltaMasses);
intermediateData = new IntermediateData(series);
try {
intermediateData.setVariable("sequenceNumber", data.size());
} catch (JSONException e) {
e.printStackTrace();
}
}