private static int insertPeptideHitsIntoCompiler(
PIACompiler compiler,
List<PeptideHit> peptideHits,
ProteinMap proteinMap,
SearchDatabase searchDatabase,
int charge,
Double precursorMZ,
Double retentionTime,
String sourceId,
String spectrumTitle,
PIAInputFile file,
SpectrumIdentification spectrumID,
boolean isDecoy) {
String sourceIdStr = sourceId;
if (peptideHits == null) {
return 0;
}
int nrPepHits = 0;
Matcher matcher = MzIdentMLTools.patternScanInTitle.matcher(spectrumTitle);
if (matcher.matches()) {
sourceIdStr = "index=" + matcher.group(1);
}
// the peptideHits are the SpectrumPeptideMatches
for (PeptideHit peptideHit : peptideHits) {
PeptideSpectrumMatch psm;
psm =
compiler.createNewPeptideSpectrumMatch(
charge,
precursorMZ,
peptideHit.getDeltaMass(),
retentionTime,
peptideHit.getSequence(),
peptideHit.getMissedCleavages(),
sourceIdStr,
spectrumTitle,
file,
spectrumID);
psm.setIsDecoy(isDecoy);
// get the peptide from the compiler or, if need be, add it
Peptide peptide;
peptide = compiler.getPeptide(peptideHit.getSequence());
if (peptide == null) {
peptide = compiler.insertNewPeptide(peptideHit.getSequence());
}
// add the spectrum to the peptide
peptide.addSpectrum(psm);
// go through the protein hits
@SuppressWarnings("unchecked")
List<ProteinHit> proteins = peptideHit.getProteinHits();
for (ProteinHit proteinHit : proteins) {
FastaHeaderInfos fastaInfo = FastaHeaderInfos.parseHeaderInfos(proteinHit.getAccession());
if (fastaInfo == null) {
fastaInfo =
new FastaHeaderInfos(
null,
proteinHit.getAccession(),
proteinMap.getProteinID(proteinHit.getAccession()).getDescription());
} else {
// if there was a protein description different to the now parsed one, take the original
// from mascot
String proteinDescription =
proteinMap.getProteinID(proteinHit.getAccession()).getDescription();
if ((proteinDescription != null)
&& (proteinDescription.trim().length() > 0)
&& !proteinDescription.equals(fastaInfo.getDescription())) {
fastaInfo = new FastaHeaderInfos(null, fastaInfo.getAccession(), proteinDescription);
}
}
// add the Accession to the compiler (if it is not already there)
Accession acc = compiler.getAccession(fastaInfo.getAccession());
if (acc == null) {
// unfortunately, the sequence is not stored in the dat file
acc = compiler.insertNewAccession(fastaInfo.getAccession(), null);
}
acc.addFile(file.getID());
if ((fastaInfo.getDescription() != null) && (fastaInfo.getDescription().length() > 0)) {
acc.addDescription(file.getID(), fastaInfo.getDescription());
}
acc.addSearchDatabaseRef(searchDatabase.getId());
// add the accession occurrence to the peptide
peptide.addAccessionOccurrence(acc, proteinHit.getStart(), proteinHit.getStop());
// now insert the connection between peptide and accession into the compiler
compiler.addAccessionPeptideConnection(acc, peptide);
}
// add the scores
ScoreModel score;
score = new ScoreModel(peptideHit.getIonsScore(), ScoreModelEnum.MASCOT_SCORE);
psm.addScore(score);
score = new ScoreModel(peptideHit.getExpectancy(), ScoreModelEnum.MASCOT_EXPECT);
psm.addScore(score);
// add the modifications
com.compomics.mascotdatfile.util.interfaces.Modification[] mods =
peptideHit.getModifications();
for (int loc = 0; loc < mods.length; loc++) {
if (mods[loc] != null) {
Modification modification;
Character residue;
if ((loc == 0) || (loc > psm.getSequence().length())) {
residue = '.';
} else {
residue = psm.getSequence().charAt(loc - 1);
}
modification = new Modification(residue, mods[loc].getMass(), mods[loc].getType(), null);
psm.addModification(loc, modification);
}
}
compiler.insertCompletePeptideSpectrumMatch(psm);
nrPepHits++;
}
return nrPepHits;
}
