public PeptideCollection getNonIndeterminents() {
PeptideCollection pc = new PeptideCollection();
for (PeptideHit p : peptideHits) {
if (!p.isIndeterminate()) {
pc.addPeptideHit(p);
}
}
return pc;
}
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 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;
}