public PeptideTerminalAAResult calculateForRunSearchAnalysisIds(
int analysisId, List<Integer> runSearchAnalysisIds) {
long s = System.currentTimeMillis();
PeptideTerminalAAResult result = new PeptideTerminalAAResult();
result.setAnalysisId(analysisId);
result.setScoreCutoff(this.scoreCutoff);
result.setScoreType("PERC_PSM_QVAL");
result.setEnzyme(this.enzyme);
for (Integer rsaId : runSearchAnalysisIds) {
PeptideTerminalAAResult rsaResult = calculateForRunSearchAnalysis(analysisId, rsaId);
result.combineWith(rsaResult);
}
long e = System.currentTimeMillis();
log.info("Total time to get results " + TimeUtils.timeElapsedSeconds(s, e) + " seconds");
log.info("Total filtered results: " + result.getTotalResultCount());
result.setEnzyme(enzyme);
return result;
}
public PeptideTerminalAAResult calculateForRunSearchAnalysis(
int analysisId, int runSearchAnalysisId) {
if (lookAtUniqPeptides) {
if (this.peptides == null) {
peptides = new HashSet<String>();
}
}
PercolatorResultDAO percDao = DAOFactory.instance().getPercolatorResultDAO();
PercolatorResultFilterCriteria filterCriteria = new PercolatorResultFilterCriteria();
filterCriteria.setMaxQValue(scoreCutoff);
long s = System.currentTimeMillis();
PeptideTerminalAAResultBuilder builder = new PeptideTerminalAAResultBuilder(analysisId, enzyme);
builder.setScoreCutoff(this.scoreCutoff);
builder.setScoreType("PERC_PSM_QVAL");
int totalResults = 0;
List<Integer> percResultIds =
percDao.loadIdsForRunSearchAnalysis(runSearchAnalysisId, filterCriteria, null);
log.info(
"Found "
+ percResultIds.size()
+ " Percolator results at qvalue <= "
+ scoreCutoff
+ " for runSearchAnalysisID "
+ runSearchAnalysisId);
for (Integer percResultId : percResultIds) {
PercolatorResult pres = percDao.loadForPercolatorResultId(percResultId);
MsSearchResultPeptide peptide = pres.getResultPeptide();
String seq = peptide.getPeptideSequence();
if (this.lookAtUniqPeptides) {
String fullseq = peptide.getPreResidue() + "." + seq + "." + peptide.getPostResidue();
if (peptides.contains(fullseq)) continue;
else peptides.add(fullseq);
}
totalResults++;
char ntermMinusOne = peptide.getPreResidue(); // nterm - 1 residue
builder.addNtermMinusOneCount(ntermMinusOne);
char nterm = seq.charAt(0); // nterm residue
builder.addNtermCount(nterm);
char cterm = seq.charAt(seq.length() - 1); // cterm residue
builder.addCtermCount(cterm);
char ctermPlusOne = peptide.getPostResidue(); // cterm + 1 residue
builder.addCtermPlusOneCount(ctermPlusOne);
int numEnzTerm = 0;
if (this.rule != null)
numEnzTerm = rule.getNumEnzymaticTermini(seq, ntermMinusOne, ctermPlusOne);
builder.addEnzymaticTerminiCount(numEnzTerm);
}
long e = System.currentTimeMillis();
log.info(
"Time to get results for runSearchAnalysisId "
+ runSearchAnalysisId
+ " "
+ TimeUtils.timeElapsedSeconds(s, e)
+ " seconds");
log.info("# filtered results: " + totalResults);
builder.setTotalResultCount(totalResults);
return builder.getResult();
}