Example #1
0
 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;
 }
Example #2
0
 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;
 }