server/compbio/controllers/SequenceController.java

   1 package compbio.controllers;
   2
   3 import java.util.List;
   4 import java.util.Map;
   5
   6 import org.springframework.stereotype.Controller;
   7 import org.springframework.web.bind.annotation.RequestMapping;
   8 import org.springframework.web.bind.annotation.RequestMethod;
   9 import org.springframework.web.bind.annotation.RequestParam;
  10
  11 import compbio.cassandra.ProteinBean;
  12 import compbio.cassandra.DataBase;
  13 import compbio.cassandra.TotalByCounterBean;
  14 import compbio.statistic.CassandraRequester;
  15
  16 /**
  17  * @author Alexander Sherstnev
  18  * @author Natasha Sherstneva
  19  */
  20 @Controller
  21 public class SequenceController {
  22
  23         @RequestMapping(value = "/sequence/query1", method = RequestMethod.GET)
  24         public String formSequenceQuery(Map<String, Object> model) {
  25                 model.put("value", "AAAAA");
  26                 return "queryProteinSequence";
  27         }
  28
  29         @RequestMapping(value = "/sequence/query2", method = RequestMethod.GET)
  30         public String formCounterQuery(Map<String, Object> model) {
  31                 model.put("value", 5);
  32                 return "queryProteinSequenceCounter";
  33         }
  34
  35         @RequestMapping(value = "/sequence/querysequence", method = RequestMethod.GET)
  36         public String findSequence(@RequestParam("sequence") String sequence, @RequestParam("protein") String flag, Map<String, Object> model) {
  37                 final long startTime = System.currentTimeMillis();
  38
  39                 String trimmedsequence = sequence.replaceAll("\\s", "");
  40                 model.put("njobs", 0);
  41                 model.put("prot", trimmedsequence);
  42                 model.put("flag", flag);
  43
  44                 if (0 < trimmedsequence.length()) {
  45                         CassandraRequester cr = new CassandraRequester();
  46                         List<ProteinBean> r = cr.readProteins(trimmedsequence, flag);
  47                         model.put("results", r);
  48                         if (null != r) {
  49                                 if (flag.equals("whole"))
  50                                         model.put("njobs",r.get(0).getJobid().size());
  51                                 else
  52                                         model.put("njobs", r.size());
  53                         }
  54                 }
  55                 final long endTime = System.currentTimeMillis();
  56                 model.put("timeExecution", (endTime - startTime));
  57                 return "reportProteinSequences";
  58         }
  59
  60         @RequestMapping(value = "/sequence/querycounter", method = RequestMethod.GET)
  61         public String countSequences(@RequestParam("counterJob") String counter, Map<String, Object> model) {
  62                 final long startTime = System.currentTimeMillis();
  63
  64                 if (counter.equals("")) {
  65                         model.put("error", "The value must not be empty");
  66                         model.put("value", counter);
  67                         return "queryIPStatistics";
  68                 }
  69
  70                 int realcounter;
  71                 try {
  72                         realcounter = Integer.parseInt(counter.trim());
  73                 } catch (NumberFormatException e) {
  74                         model.put("error", "The value must be an integer number");
  75                         model.put("value", counter);
  76                         return "queryIPStatistics";
  77                 }
  78
  79                 if (realcounter < 1) {
  80                         model.put("error", "The value must be greater than 0");
  81                         model.put("value", counter);
  82                         return "queryIPStatistics";
  83                 }
  84
  85                 CassandraRequester cr = new CassandraRequester();
  86                 List<TotalByCounterBean> r = cr.readProteinByCounter(realcounter);
  87                 model.put("results", r);
  88                 model.put("njobs", 0);
  89                 if (null != r) {
  90                         model.put("njobs", r.size());
  91                 }
  92                 final long endTime = System.currentTimeMillis();
  93                 model.put("timeExecution", (endTime - startTime));
  94                 model.put("counter", realcounter);
  95                 return "reportProteinSequencesCounter";
  96         }
  97
  98 }