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");
}
}
private boolean matchFilterCriteria(
ProteinProphetFilterCriteria filterCritSession, ProteinProphetFilterCriteria filterCriteria) {
return filterCritSession.equals(filterCriteria);
}