server/compbio/controllers/SSFeaturesController.java

   1 package compbio.controllers;
   2
   3 import java.util.Map;
   4
   5 import org.springframework.stereotype.Controller;
   6 import org.springframework.web.bind.annotation.RequestMapping;
   7 import org.springframework.web.bind.annotation.RequestMethod;
   8 import org.springframework.web.bind.annotation.RequestParam;
   9
  10 import compbio.statistic.CassandraRequester;
  11
  12 /**
  13  * Spring controller for protein secondary structure features. This version
  14  * works in the servlet style.
  15  *
  16  * @author Alexander Sherstnev
  17  * @author Natasha Sherstneva
  18  *
  19  * @since 0.5
  20  * @version 1.0 December 2013
  21  */
  22 @Controller
  23 @RequestMapping("/features")
  24 public class SSFeaturesController extends BasicController {
  25
  26         /**
  27          * form a query page for protein secondary structure feaatures: Proteins
  28          * with given fraction of H/E (helix/beta sheets)
  29          *
  30          * @param model
  31          *            MVC model object
  32          *
  33          * @return link to the report JSP page
  34          */
  35         @RequestMapping(value = "query", method = RequestMethod.GET)
  36         public String formCounterQuery(Map<String, Object> model) {
  37                 model.put("username", getPrincipalName());
  38                 model.put("type", 'E');
  39                 model.put("value", 50);
  40                 return "query/SSFeatures";
  41         }
  42
  43         /**
  44          * form a results page for protein secondary structure features: Proteins
  45          * with given fraction of H/E (helix/beta sheets) All proteins with E/H
  46          * higher than a given percent of the length are returned
  47          *
  48          * @param model
  49          *            MVC model object
  50          * @param typeFeature
  51          *            type of SS: H/E (helix/beta sheets)
  52          * @param percent
  53          *            fraction of the protein length predicted as H/E (helix/beta
  54          *            sheets)
  55          *
  56          * @return link to the report JSP page
  57          */
  58         @RequestMapping(value = "results", method = RequestMethod.GET)
  59         public String countSequences(@RequestParam("TypeFeatures") String typeFeature, @RequestParam("Percent") String percent,
  60                         Map<String, Object> model) {
  61                 model.put("username", getPrincipalName());
  62                 final long startTime = System.currentTimeMillis();
  63
  64                 if (percent.equals("")) {
  65                         model.put("error", "The value must not be empty");
  66                         model.put("type", typeFeature);
  67                         model.put("value", percent);
  68                         return "query/SSFeatures";
  69                 }
  70
  71                 int realpercent;
  72                 try {
  73                         realpercent = Integer.parseInt(percent.trim());
  74                 } catch (NumberFormatException e) {
  75                         model.put("error", "The value must be an integer number");
  76                         model.put("value", percent);
  77                         return "query/SSFeatures";
  78                 }
  79
  80                 if (realpercent < 1) {
  81                         model.put("error", "The value must be greater than 0");
  82                         model.put("value", percent);
  83                         return "query/SSFeatures";
  84                 }
  85
  86                 if (realpercent > 100) {
  87                         model.put("error", "The value must be less than 100");
  88                         model.put("value", percent);
  89                         return "query/SSFeatures";
  90                 }
  91
  92                 CassandraRequester cr = new CassandraRequester();
  93                 Map<String, String> r = cr.readProteinsPrediction(typeFeature, realpercent);
  94                 model.put("results", r);
  95                 model.put("njobs", 0);
  96                 StringBuilder csvline = new StringBuilder("");
  97                 if (null != r) {
  98                         model.put("njobs", r.size());
  99                         csvline.append("\'Prediction%20number\',\'Protein%20Sequence\', \'Secondary%20Structure%20Prediction\'%0A");
 100
 101                         // form line for CSV file
 102                         int counter = 1;
 103                         for (Map.Entry<String, String> entry : r.entrySet()) {
 104                                 csvline.append("\'" + counter + "\',\'" + entry.getKey() + "\',\'" + entry.getValue() + "\'%0A");
 105                                 ++counter;
 106                         }
 107                 }
 108                 model.put("csvfile", csvline.toString());
 109
 110                 final long endTime = System.currentTimeMillis();
 111                 model.put("timeExecution", (endTime - startTime));
 112                 model.put("feature", typeFeature);
 113                 model.put("percent", realpercent);
 114                 return "reports/SSFeatures";
 115         }
 116
 117 }