/**
* Performs the action
*
* @param req The http request object
* @param context The servlet context
* @return True if the action could be performed
*/
public boolean performAction(HttpServletRequest req, ServletContext context)
throws ApplicationException {
Collection phenotypes = null;
try {
MugenCaller caller = (MugenCaller) req.getSession().getAttribute("caller");
Navigator nav = (Navigator) req.getSession().getAttribute("navigator");
Collection funcsigs = new ArrayList();
String type = req.getParameter("_type");
String message = "";
if (exists(type)) {
message =
"<b>NOTE: Sampling unit filter may be incorrectly adjusted since listing originated from Functional Significance Types view which is <u>Sampling unit independent</u>.</b>";
funcsigs =
modelManager.getFunctionalSignificancesForType(
Integer.parseInt(type), caller, nav.getPageManager());
nav.getPageManager()
.setMax(modelManager.getNumberOfSignificancesForType(Integer.parseInt(type), caller));
} else {
funcsigs = modelManager.getFunctionalSignificances(caller, nav.getPageManager());
nav.getPageManager()
.setMax(modelManager.getNumberOfFunctionalSignificances(caller.getSuid(), caller));
}
Collection samplingunits = samplingUnitManager.getSamplingUnits(caller.getPid(), caller);
req.setAttribute("message", message);
req.setAttribute("funcsigs", funcsigs);
req.setAttribute("samplingunits", samplingunits);
return true;
} catch (ApplicationException e) {
throw e;
} catch (Exception e) {
e.printStackTrace();
throw new ApplicationException("Could not retrieve functional significances.");
}
}
/**
* Performs the action
*
* @param request The http request object
* @param context The servlet context
* @throws com.arexis.mugen.exceptions.ApplicationException If the action could not be performed
* @return True if the action could be performed
*/
public boolean performAction(HttpServletRequest request, ServletContext context)
throws ApplicationException {
try {
HttpSession session = request.getSession();
MugenCaller caller = (MugenCaller) session.getAttribute("caller");
Navigator nav = (Navigator) request.getSession().getAttribute("navigator");
FormDataManager formDataManager =
getFormDataManager(
MugenFormDataManagerFactory.U_MARKER_SET_MEMBERSHIP_FILTER,
MugenFormDataManagerFactory.WEB_FORM,
request);
System.out.println(formDataManager.toString());
int suid = caller.getSuid();
int sid = caller.getSid();
Collection umarkersets = genotypeManager.getUMarkerSets(caller, sid);
String tmpUmsid = formDataManager.getValue("umsid");
int umsid = 0;
// If it is the first time we show the page...
// Choose the first unified marker set
if (!exists(tmpUmsid)) {
Iterator i = umarkersets.iterator();
if (i.hasNext()) {
UMarkerSetDTO dto = (UMarkerSetDTO) i.next();
umsid = dto.getUmsid();
}
}
// else, use the requested unified marker set id
else {
umsid = Integer.parseInt(tmpUmsid);
}
Collection available = genotypeManager.getUMarkers(caller);
Collection included =
genotypeManager.getUMarkerSetPositions(umsid, caller, nav.getPageManager());
if (umarkersets.size() == 0) {
available = new ArrayList();
included = new ArrayList();
}
available.removeAll(included);
request.setAttribute("umarkersets", umarkersets);
request.setAttribute("available", available);
request.setAttribute("included", included);
request.setAttribute(
"species", samplingUnitManager.getSpeciesForProject(caller.getPid(), caller));
request.setAttribute("formdata", formDataManager);
return true;
} catch (ApplicationException e) {
throw new ApplicationException(
"Could not get unified marker set membership information: " + e.getMessage());
} catch (Exception e) {
e.printStackTrace();
throw new ApplicationException("Could not get unified marker set membership information.");
}
}
