public void computeIndeterminates() {
HashMap<String, HashSet<PeptideHit>> scan2pep = new HashMap<String, HashSet<PeptideHit>>();
HashSet<PeptideHit> pepList;
for (PeptideHit p : peptideHits) {
String scan = p.getScanTuple();
if (scan2pep.containsKey(scan)) {
pepList = scan2pep.get(scan);
} else {
pepList = new HashSet<PeptideHit>();
scan2pep.put(scan, pepList);
}
pepList.add(p);
}
for (HashSet<PeptideHit> pepSet : scan2pep.values()) {
boolean indeterm = false;
if (pepSet.size() > 1) {
HashSet<String> pepSeqs = new HashSet<String>();
for (PeptideHit p : pepSet) {
pepSeqs.add(p.getSequence());
}
if (pepSeqs.size() > 1) indeterm = true;
}
for (PeptideHit p : pepSet) {
p.setIndeterminate(indeterm);
}
}
}
public void addPeptideHit(PeptideHit p) {
if (p == null) {
return;
}
peptideHits.add(p);
experimentSet.add(p.getExperiment());
String key = p.getSequence();
if (minPeptides.containsKey(key)) {
Peptide pg = minPeptides.get(key);
pg.addPeptideHit(p);
} else {
Peptide pg = new Peptide(p);
minPeptides.put(key, pg);
}
}
