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;
}
