private int extractPrecursorCharge(Spectrum spectrum) {
PrecursorList precursorListElement = spectrum.getPrecursorList();
if ((precursorListElement == null) || (precursorListElement.getCount().equals(0))) return 0;
List<Precursor> precursorList = precursorListElement.getPrecursor();
for (Precursor parent : precursorList) {
SelectedIonList selectedIonListElement = parent.getSelectedIonList();
if ((selectedIonListElement == null) || (selectedIonListElement.getCount().equals(0)))
return 0;
List<ParamGroup> selectedIonParams = selectedIonListElement.getSelectedIon();
if (selectedIonParams == null) continue;
for (ParamGroup pg : selectedIonParams) {
List<CVParam> pgCvParams = pg.getCvParam();
for (CVParam param : pgCvParams) {
String accession = param.getAccession();
String value = param.getValue();
if ((accession == null) || (value == null)) continue;
if (accession.equals("MS:1000041")) {
int precursorCharge = Integer.parseInt(value);
return precursorCharge;
}
}
}
}
return 0;
}
private double extractPrecursorMz(Spectrum spectrum) {
PrecursorList precursorListElement = spectrum.getPrecursorList();
if ((precursorListElement == null) || (precursorListElement.getCount().equals(0))) return 0;
List<Precursor> precursorList = precursorListElement.getPrecursor();
for (Precursor parent : precursorList) {
SelectedIonList selectedIonListElement = parent.getSelectedIonList();
if ((selectedIonListElement == null) || (selectedIonListElement.getCount().equals(0)))
return 0;
List<ParamGroup> selectedIonParams = selectedIonListElement.getSelectedIon();
if (selectedIonParams == null) continue;
for (ParamGroup pg : selectedIonParams) {
List<CVParam> pgCvParams = pg.getCvParam();
for (CVParam param : pgCvParams) {
String accession = param.getAccession();
String value = param.getValue();
if ((accession == null) || (value == null)) continue;
// MS:1000040 is used in mzML 1.0,
// MS:1000744 is used in mzML 1.1.0
if (accession.equals("MS:1000040") || accession.equals("MS:1000744")) {
double precursorMz = Double.parseDouble(value);
return precursorMz;
}
}
}
}
return 0;
}