private String sirToString(SpectrumIdentificationResult sir) {
String sirString = "";
SpectraData spectraData = spectraDataIdHashMap.get(sir.getSpectraDataRef());
sirString += spectraData.getLocation() + sep + "\"" + sir.getSpectrumID() + "\"";
Double rtInSeconds = -1.0;
String spectrumTitle = "";
// <cvParam accession="MS:1001114" name="retention time(s)" cvRef="PSI-MS" value="3488.676"
// unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
// <cvParam accession="MS:1000796" name="spectrum title" cvRef="PSI-MS"
// value="mam_050108o_CPTAC_study6_6E004.6805.6805.1" />
//
for (CvParam cvParam : sir.getCvParam()) {
// Updated by FG: checking for old CV param 1114 or newer correct CV term 16.
if (cvParam.getAccession().equals("MS:1001114")
|| cvParam.getAccession().equals("MS:1000016")) {
if (cvParam.getUnitAccession().equals("UO:0000010")) {
rtInSeconds = Double.parseDouble(cvParam.getValue());
} else if (cvParam.getUnitAccession().equals("UO:0000031")) {
rtInSeconds = Double.parseDouble(cvParam.getValue()) / 60; // Convert minutes to seconds
} else {
System.out.println("Error parsing RT - unit not recognised");
}
}
if (cvParam.getAccession().equals("MS:1000796")) {
spectrumTitle = cvParam.getValue();
}
}
sirString += sep + "\"" + spectrumTitle + "\"" + sep + rtInSeconds;
return sirString;
}
