OrthologsController.java

package org.genedb.web.mvc.controller;

//import org.genedb.db.dao.SequenceDao;
//import org.genedb.querying.core.QueryException;
//import org.genedb.querying.tmpquery.GeneSummary;
import org.genedb.web.mvc.controller.download.BaseCachingController;
//
//import org.apache.log4j.Logger;
//import org.gmod.schema.feature.Polypeptide;
//import org.gmod.schema.feature.ProteinMatch;
//import org.gmod.schema.mapped.Feature;
//import org.gmod.schema.mapped.FeatureRelationship;
//import org.springframework.stereotype.Controller;
//import org.springframework.ui.Model;
//import org.springframework.web.bind.annotation.PathVariable;
//import org.springframework.web.bind.annotation.RequestMapping;
//import org.springframework.web.bind.annotation.RequestMethod;
//import org.springframework.web.bind.annotation.RequestParam;
//
//import java.util.Collection;
//import java.util.List;
//
//import javax.servlet.ServletRequest;
//import javax.servlet.http.HttpSession;
//
//import com.google.common.collect.Lists;

/**
 * Returns all features (orthologs) that belong to a particular cluster
 *
 * @author Chinmay Patel (cp2)
 */
//@Controller
//@RequestMapping("/Orthologs")
public class OrthologsController extends BaseCachingController {

//    private static final Logger logger = Logger.getLogger(OrthologsController.class);
//
//    private static final String NO_VALUE_SUPPLIED = "_NO_VALUE_SUPPLIED";
//
//    private SequenceDao sequenceDao;
//    private String listResultsView;
//    private String genePage;
//
//    public void setGenePage(String genePage) {
//        this.genePage = genePage;
//    }
//
//    public void setListResultsView(String listResultsView) {
//        this.listResultsView = listResultsView;
//    }
//
//    public void setSequenceDao(SequenceDao sequenceDao) {
//        this.sequenceDao = sequenceDao;
//    }
//
//    @RequestMapping(method = RequestMethod.GET , value="/{cluster}")
//    public String processForm(
//            @PathVariable(value="cluster") String clusterName,
//            @RequestParam(value="suppress", required=false) String suppress,
//            ServletRequest request,
//            HttpSession session,
//            Model model) throws QueryException {
//
//        String viewName = listResultsView;
//
//        List<String> orthologs = Lists.newArrayList();
//
//        Feature cluster = sequenceDao.getFeatureByUniqueName(clusterName, ProteinMatch.class);
//        if (cluster == null) {
//            logger.error(String.format("Unable to find cluster '%s' of type ProteinMatch", clusterName));
//        } else {
//
//            Collection<FeatureRelationship> relations = cluster.getFeatureRelationshipsForObjectId();
//            for (FeatureRelationship featureRel : relations) {
//                Feature f = featureRel.getSubjectFeature();
//
//                if (! (f instanceof Polypeptide)) {
//                    logger.error(String.format("Didn't get a polypeptide when I expected one - got '%s'", f.getClass().toString()));
//                    continue;
//                }
//
//                Polypeptide protein = (Polypeptide) f;
//                orthologs.add(protein.getTranscript().getUniqueName());
//            }
//        }
//
//
//        switch (orthologs.size()) {
//        case 0:
//            // TODO return a proper error message
//            viewName = "redirect:/Homepage";
//            break;
//        case 1:
//            String gene = orthologs.get(0);
//            model.addAttribute("name", gene);
//            viewName = genePage;
//            break;
//        default:
//            List<GeneSummary> gs = possiblyConvertList(orthologs);
//            //String resultsKey = cacheResults(gs, null, null, session.getId());
//
////            model.addAttribute("key", resultsKey);
////            model.addAttribute("taxonNodeName", taxonName);
//            logger.debug("Found results for query (Size: '"+gs.size()+"' key: '"+resultsKey+"')- redirecting to Results controller");
//            model.addAttribute("resultsSize", gs.size());
//            //viewName = "list/results2";
//            return "redirect:/Results/"+resultsKey;
//        }
//        return viewName;
//    }

}