public PeptideCollection getNonIndeterminents() {
PeptideCollection pc = new PeptideCollection();
for (PeptideHit p : peptideHits) {
if (!p.isIndeterminate()) {
pc.addPeptideHit(p);
}
}
return pc;
}
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);
}
}
public PeptideCollection filterByProteinCoverage(int minCoverage) {
HashSet<String> proDiscard = new HashSet<String>();
for (String pName : minProteins.keySet()) {
Protein p = minProteins.get(pName);
if (p.getCoveragePercent() < minCoverage) {
proDiscard.add(pName);
}
}
PeptideCollection new_pc = new PeptideCollection();
for (PeptideHit ph : peptideHits) {
new_pc.addPeptideHit(ph.maskProtein(proDiscard));
}
new_pc.createProteinList();
return new_pc;
}
public PeptideCollection filterByPeptidePerProtein(int numPeps) {
HashSet<String> proDiscard = new HashSet<String>();
for (String pName : minProteins.keySet()) {
Protein p = minProteins.get(pName);
if (p.getNumUniquePeptides() < numPeps) {
proDiscard.add(pName);
}
}
PeptideCollection new_pc = new PeptideCollection();
for (PeptideHit ph : peptideHits) {
new_pc.addPeptideHit(ph.maskProtein(proDiscard));
}
new_pc.createProteinList();
return new_pc;
}
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 PeptideCollection getCutoffCollection(double omssa, double mascot, double xtandem) {
// return getCutoffCollection(omssa, mascot, xtandem, false);
// }
public PeptideCollection getCutoffCollection(FilterSettings fs) {
PeptideCollection pc = new PeptideCollection();
for (PeptideHit p : peptideHits) {
if (fs.getUsePepProphet() && p.isPepXML()) {
if (p.getPepProphet() >= fs.getPeptideProphetCutoff()) {
pc.addPeptideHit(p);
}
} else {
switch (p.getSourceType()) {
case MASCOT:
if (fs.getUseIonIdent()) {
if (p.getIonScore() >= p.getIdent()) {
pc.addPeptideHit(p);
}
} else if (p.getExpect() <= fs.getMascotCutoff()) {
pc.addPeptideHit(p);
}
break;
case OMSSA:
if (p.getExpect() <= fs.getOmssaCutoff()) {
pc.addPeptideHit(p);
}
break;
case XTANDEM:
if (p.getExpect() <= fs.getXtandemCutoff()) {
pc.addPeptideHit(p);
}
break;
case SEQUEST:
if (p.getExpect() <= fs.getSequestCutoff()) {
pc.addPeptideHit(p);
}
break;
case PEPXML:
if (!p.CanGetPepProphet() || (p.getPepProphet() >= fs.getPeptideProphetCutoff())) {
pc.addPeptideHit(p);
}
break;
}
}
}
return pc;
}
