private String siiToString(SpectrumIdentificationItem sii) {
String siiString = "";
siiString =
"\""
+ sii.getId()
+ "\""
+ sep
+ sii.getRank()
+ sep
+ sii.isPassThreshold()
+ sep
+ sii.getCalculatedMassToCharge()
+ sep
+ sii.getExperimentalMassToCharge()
+ sep
+ sii.getChargeState();
Peptide pep =
peptideIdHashMap.get(sii.getPeptideRef()); // get Peptide via the hash for this object
siiString += sep + "\"" + pep.getPeptideSequence() + "\"";
// Handle Mods
siiString += sep;
String modString = "";
if (pep.getModification() != null) {
int i = 0;
for (Modification mod : pep.getModification()) {
if (i > 0) {
modString += ";"; // Add an extra separator between mods
}
modString += modToString(mod);
i++;
}
}
if (pep.getSubstitutionModification() != null) {
int i = 0;
for (SubstitutionModification subMod : pep.getSubstitutionModification()) {
if (i > 0 || !modString.equals("")) {
modString += ";"; // Add an extra separator between mods
}
modString += subModToString(subMod);
i++;
}
}
siiString += modString;
Map<String, String> mapNameToValue = new HashMap<>();
for (AbstractParam param : sii.getParamGroup()) {
mapNameToValue.put(param.getName(), param.getValue());
// System.out.println("test1" + param.getName() + "-> " + param.getValue());
}
// Handle scores
for (int i = 0; i < columnToScoreMap.size(); i++) {
String score = columnToScoreMap.get(i);
// System.out.println("test2" + score);
if (mapNameToValue.containsKey(score)) {
String scoreValue = mapNameToValue.get(score);
// System.out.println("test3" + scoreValue);
siiString += sep + scoreValue;
} else {
siiString += sep;
}
}
// Handle all protein maps
siiString += sep + "\"";
List<PeptideEvidenceRef> peptideEvidenceRefList = sii.getPeptideEvidenceRef();
Boolean isDecoy = false;
for (int i = 0; i < peptideEvidenceRefList.size(); i++) {
PeptideEvidenceRef peptideEvidenceRef = peptideEvidenceRefList.get(i);
PeptideEvidence peptideEvidence =
peptideEvidenceIdHashMap.get(peptideEvidenceRef.getPeptideEvidenceRef());
DBSequence dbSeq = dbSequenceIdHashMap.get(peptideEvidence.getDBSequenceRef());
if (i > 0) {
siiString += ";"; // Add an extra separator between mods
}
siiString +=
dbSeq.getAccession()
+ "_"
+ peptideEvidence.getStart()
+ "_"
+ peptideEvidence.getEnd()
+ "_"
+ peptideEvidence.getPre()
+ "_"
+ peptideEvidence.getPost();
if (peptideEvidence.isIsDecoy()) {
isDecoy = true;
}
}
siiString += "\"";
siiString += sep + isDecoy;
return siiString;
}
