@SuppressWarnings({"UnusedParameters", "UnusedAssignment"})
protected boolean handleSearchHit(
String[] lines,
double retentionTime,
boolean onlyUniquePeptides,
ISpectrumDataFilter... filters) {
//noinspection UnnecessaryLocalVariable,UnusedDeclaration,UnusedAssignment
Double expectedValue = null;
//noinspection UnnecessaryLocalVariable,UnusedDeclaration,UnusedAssignment
Double hyperScoreValue = null;
int index = 0;
String line = lines[index++]; // handle first line
while (!line.contains("<search_hit")) {
line = lines[index++];
if (index >= lines.length) return false;
}
String id = scan_id;
if ("".equals(id)) throw new UnsupportedOperationException("Fix This"); // ToDo
boolean trueHit = !line.contains("protein=\"DECOY_");
boolean processSpectrum = parseHitValue(line) <= 2;
//noinspection UnnecessaryLocalVariable,UnusedDeclaration,UnusedAssignment
boolean isUnique = true;
//noinspection UnnecessaryLocalVariable,UnusedDeclaration,UnusedAssignment
boolean isModified = false;
if (!line.contains("hit_rank=\"1\"")) return false;
IdentifiedPSM peptide = processPeptide(line, retentionTime, id);
IProtein protein = null;
for (; index < lines.length; index++) {
line = lines[index];
if (line.contains("</search_hit")) break; // we are done
if (line.contains(" modified_peptide="))
peptide = processModifiedPeptide(line, retentionTime, id);
if (line.contains("<alternative_protein")) {
isUnique = false;
if (onlyUniquePeptides) processSpectrum = false; // only process unique hits
}
if (line.contains("<search_score name=\"hyperscore\" value=\"")) {
hyperScoreValue = parseValue(line);
}
if (line.contains("<search_score name=\"expect\" value=\"")) {
expectedValue = parseValue(line);
}
if (line.contains("protein=\"DECOY_")) { // another protein
if (trueHit) processSpectrum = false; // one decoy one not
}
if (line.contains("<alternative_protein")) { // another protein
if (!trueHit && !line.contains("protein=\"DECOY_")) // we start as decoy and fit to a real
processSpectrum = false; // one decoy one not
}
if (line.contains("protein_descr=\"")) {
protein = processProtein(line);
}
}
if (processSpectrum) {
@SuppressWarnings("ConstantConditions")
String idP = protein.getId();
if (id.contains("DECOY")) return false;
Set<IdentifiedPSM> pps = proteinToHits.get(idP);
if (pps == null) {
pps = new HashSet<IdentifiedPSM>();
proteinToHits.put(idP, pps);
}
pps.add(peptide);
return true; // processed
}
return false; // unprocessed
}
