/**
* Method used to load the spectra chartData structure with the required chartData
*
* @param accessionNumber the experiment accession number
* @throws SpectralDataPerExperimentException throws a SpectralDataPerExperimentException
*/
private void initialize(String accessionNumber) throws SpectralDataPerExperimentException {
spectra = new HashMap<String, SpectrumData>();
// this.accessionNumber = accessionNumber;
printMessage("Start");
long start = System.currentTimeMillis();
printMessage("Loading identified spectrum ", false);
Map<String, Boolean> spectrumReferences = dbac.precursorSpectrumIdentified(accessionNumber);
int cont = 0;
int total = 0;
for (String key : spectrumReferences.keySet()) {
setSpectrumReferences(key, spectrumReferences.get(key));
if (spectrumReferences.get(key)) cont++;
total++;
}
printMessage("(found: " + cont + " identified of " + total + ")", false);
long step1 = System.currentTimeMillis();
printMessage("............ OK [" + (step1 - start) + " ms]");
printMessage("Loading precursor mass chartData ", false);
List<PrecursorData> precursorMass = dbac.precursorMassData(accessionNumber);
for (PrecursorData pm : precursorMass) {
setSpectrumPrecursorMass(pm);
}
// The precursor charge has been loaded from the database
if (precursorMass.size() > 0) state.setPrecursorMassesLoaded(true);
long step2 = System.currentTimeMillis();
printMessage("............ OK [" + (step2 - step1) + " ms]");
printMessage("Loading precursor charge chartData ", false);
List<PrecursorData> precursorCharge = dbac.precursorChargeData(accessionNumber);
for (PrecursorData pc : precursorCharge) {
setSpectrumPrecursorCharge(pc);
}
// The precursor charge has been loaded from the database
if (precursorCharge.size() > 0) state.setPrecursorChargesLoaded(true);
long step3 = System.currentTimeMillis();
printMessage("............ OK [" + (step3 - step2) + " ms]");
// ToDo: What to do when precursorMass size is not the same than precursorCharge size
printMessage("Loading MZ and Intensity values ", false);
PeakListBasicInfo mzListBasicInfo = dbac.peakListMzInfo(accessionNumber);
PeakListBasicInfo intensityListBasicInfo = dbac.peakListIntensityInfo(accessionNumber);
if (mzListBasicInfo != null && intensityListBasicInfo != null) {
PeakListManager mzData = new PeakListManager(dbac, mzListBasicInfo);
PeakListManager intensityData = new PeakListManager(dbac, intensityListBasicInfo);
Iterator<PeakList> mzIterator = mzData.iterator();
Iterator<PeakList> intensityIterator = intensityData.iterator();
while (mzIterator.hasNext() && intensityIterator.hasNext()) {
PeakList mz = mzIterator.next();
PeakList intensity = intensityIterator.next();
processSpectrumMzData(mz, intensity);
processSpectrumIntensityData(intensity);
}
}
long step4 = System.currentTimeMillis();
printMessage("............ OK [" + (step4 - step4) + " ms]");
printMessage("Loading proteins identifications by peptides ", false);
setProteinsPeptides(dbac.getProteinsIdentification(accessionNumber));
long step5 = System.currentTimeMillis();
printMessage("............ OK [" + (step5 - step4) + " ms]");
printMessage("Spectra Loaded [" + (step5 - start) / 1000 + " seconds]");
dataControl();
}
public int getExperimentID() {
if (experimentID == -1) experimentID = dbac.getExperimentID(accessionNumber);
return experimentID;
}