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