List<SAMEntry> samEntries = new ArrayList<SAMEntry>();
PeptideSequenceGenerator sequenceGenerator = new PeptideSequenceGeneratorImpl(
genome, proteinToOLNMap, chromosomeDir);
Set<String> foundProteins = new HashSet<String>();
PeptideSearchResultFilter peptideFilter = null;
if (confidenceScore != null) {
peptideFilter = new ConfidenceScoreFilter(confidenceScore);
}
for (PeptideSearchResult result : peptideSearchResults) {
if (peptideFilter != null && !peptideFilter.accepts(result)) {
continue;
}
PeptideSequence peptide = sequenceGenerator.getPeptideSequence(result);
if (peptide == null) {