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 ActionForward execute(
ActionMapping mapping,
ActionForm form,
HttpServletRequest request,
HttpServletResponse response)
throws Exception {
log.info("Got request for GO Slim analysis for ProtenProphet protein inference");
// form for filtering and display options
ProteinProphetFilterForm filterForm = (ProteinProphetFilterForm) form;
// get the protein inference id
int pinferId = filterForm.getPinferId();
long s = System.currentTimeMillis();
// Get the peptide definition; We don't get peptide definition from ProteinProphet params so
// just
// use a dummy one.
PeptideDefinition peptideDef = new PeptideDefinition();
peptideDef.setUseCharge(true);
peptideDef.setUseMods(true);
// filtering criteria from the request
ProteinProphetFilterCriteria filterCriteria_request = filterForm.getFilterCriteria(peptideDef);
// protein Ids
List<Integer> proteinIds = null;
ProteinInferSessionManager sessionManager = ProteinInferSessionManager.getInstance();
// Check if we already have information in the session
ProteinProphetFilterCriteria filterCriteria_session =
sessionManager.getFilterCriteriaForProteinProphet(request, pinferId);
proteinIds = sessionManager.getStoredProteinIds(request, pinferId);
// If we don't have a filtering criteria in the session return an error
if (filterCriteria_session == null || proteinIds == null) {
log.info("NO information in session for: " + pinferId);
// redirect to the /viewProteinInferenceResult action if this different from the
// protein inference ID stored in the session
log.error("Stale ProteinProphet ID: " + pinferId);
response.setContentType("text/html");
response.getWriter().write("STALE_ID");
return null;
} else {
log.info("Found information in session for: " + pinferId);
System.out.println("stored protein ids: " + proteinIds.size());
// we will use the sorting column and sorting order from the filter criteria in the session.
filterCriteria_request.setSortBy(filterCriteria_session.getSortBy());
filterCriteria_request.setSortOrder(filterCriteria_session.getSortOrder());
boolean match = matchFilterCriteria(filterCriteria_session, filterCriteria_request);
// if the filtering criteria has changed we need to filter the results again
if (!match) {
log.info("Filtering criteria has changed");
proteinIds = ProteinProphetResultsLoader.getProteinIds(pinferId, filterCriteria_request);
}
}
long e = System.currentTimeMillis();
log.info(
"Got filtered nrseq protein ids for GO Slim analysis in: "
+ TimeUtils.timeElapsedMinutes(s, e)
+ " minutes");
request.setAttribute("pinferId", pinferId);
request.setAttribute("goAspect", filterForm.getGoAspect());
request.setAttribute("goSlimTermId", filterForm.getGoSlimTermId());
if (filterForm.isGetGoSlimTree()) {
// We have the protein inference protein IDs; Get the corresponding nrseq protein IDs
List<Integer> nrseqIds = new ArrayList<Integer>(proteinIds.size());
ProteinferDAOFactory factory = ProteinferDAOFactory.instance();
ProteinferProteinDAO protDao = factory.getProteinferProteinDao();
for (int proteinId : proteinIds) {
ProteinferProtein protein = protDao.loadProtein(proteinId);
nrseqIds.add(protein.getNrseqProteinId());
}
request.setAttribute("nrseqProteinIds", nrseqIds);
return mapping.findForward("GoTree");
} else {
// We have the protein inference protein IDs; Get the corresponding nrseq protein IDs and
// protein group IDs
List<GOAnalysisProtein> goAnalysisProteins =
new ArrayList<GOAnalysisProtein>(proteinIds.size());
ProteinferDAOFactory factory = ProteinferDAOFactory.instance();
ProteinProphetProteinDAO protDao = factory.getProteinProphetProteinDao();
for (int proteinId : proteinIds) {
ProteinProphetProtein protein = protDao.loadProtein(proteinId);
goAnalysisProteins.add(
new GOAnalysisProtein(protein.getNrseqProteinId(), protein.getGroupId()));
}
request.setAttribute("goSlimProteins", goAnalysisProteins);
request.setAttribute(
"doGroupAnalysis", true); // default is to get GO information at the group level
return mapping.findForward("Success");
}
}
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();
}