server/compbio/controllers/SequenceController.java

   1 package compbio.controllers;
   2
   3 import java.util.List;
   4 import java.util.Map;
   5 import java.util.regex.Pattern;
   6
   7 import org.springframework.stereotype.Controller;
   8 import org.springframework.web.bind.annotation.RequestMapping;
   9 import org.springframework.web.bind.annotation.RequestMethod;
  10 import org.springframework.web.bind.annotation.RequestParam;
  11
  12 import compbio.cassandra.ProteinBean;
  13 import compbio.cassandra.DataBase;
  14 import compbio.data.sequence.SequenceUtil;
  15 import compbio.cassandra.TotalByCounterBean;
  16 import compbio.statistic.CassandraRequester;
  17
  18 /**
  19  * Spring controller for sequence search. This version works in the servlet style.
  20  *
  21  * @author Alexander Sherstnev
  22  * @author Natasha Sherstneva
  23  *
  24  * @since 0.5
  25  * @version 1.0 December 2013
  26  */
  27 @Controller
  28 public class SequenceController {
  29
  30         /**
  31          * pattern for NON-protein alphabet  symbols
  32          */
  33         private final Pattern NONPROTEIN = Pattern.compile("[^ARNDCQEGHILKMFPSTWYV]+", Pattern.CASE_INSENSITIVE);
  34
  35         @RequestMapping(value = "/sequence/query1", method = RequestMethod.GET)
  36         public String formSequenceQuery(Map<String, Object> model) {
  37                 model.put("value", "AAAAA");
  38                 return "queryProteinSequence";
  39         }
  40
  41         @RequestMapping(value = "/sequence/query2", method = RequestMethod.GET)
  42         public String formCounterQuery(Map<String, Object> model) {
  43                 model.put("value", 5);
  44                 return "queryProteinSequenceCounter";
  45         }
  46
  47         @RequestMapping(value = "/sequence/querysequence", method = RequestMethod.GET)
  48         public String findSequence(@RequestParam("sequence") String sequence, @RequestParam("protein") String flag, Map<String, Object> model) {
  49                 final long startTime = System.currentTimeMillis();
  50
  51                 // input checks
  52                 String trimmedsequence = sequence.replaceAll("\\s", "");
  53                 if (trimmedsequence.equalsIgnoreCase("")) {
  54                         model.put("error", "The sequence cann't be empty");
  55                         model.put("value", sequence);
  56                         return "queryProteinSequence";
  57                 }
  58                 if (NONPROTEIN.matcher(trimmedsequence).find()) {
  59                         model.put("error", "The sequence contains symbols not from the standard protein alphabet");
  60                         model.put("value", sequence);
  61                         return "queryProteinSequence";
  62                 }
  63
  64                 model.put("njobs", 0);
  65                 model.put("prot", trimmedsequence);
  66                 model.put("flag", flag);
  67
  68                 if (0 < trimmedsequence.length()) {
  69                         CassandraRequester cr = new CassandraRequester();
  70                         List<ProteinBean> r = cr.readProteins(trimmedsequence, flag);
  71                         model.put("results", r);
  72                         if (null != r) {
  73                                 if (flag.equals("whole"))
  74                                         model.put("njobs",r.get(0).getJobid().size());
  75                                 else
  76                                         model.put("njobs", r.size());
  77                         }
  78                 }
  79                 final long endTime = System.currentTimeMillis();
  80                 model.put("timeExecution", (endTime - startTime));
  81                 return "reportProteinSequences";
  82         }
  83
  84         @RequestMapping(value = "/sequence/querycounter", method = RequestMethod.GET)
  85         public String countSequences(@RequestParam("counterJob") String counter, Map<String, Object> model) {
  86                 final long startTime = System.currentTimeMillis();
  87
  88                 if (counter.equals("")) {
  89                         model.put("error", "The value must not be empty");
  90                         model.put("value", counter);
  91                         return "queryIPStatistics";
  92                 }
  93
  94                 int realcounter;
  95                 try {
  96                         realcounter = Integer.parseInt(counter.trim());
  97                 } catch (NumberFormatException e) {
  98                         model.put("error", "The value must be an integer number");
  99                         model.put("value", counter);
 100                         return "queryIPStatistics";
 101                 }
 102
 103                 if (realcounter < 1) {
 104                         model.put("error", "The value must be greater than 0");
 105                         model.put("value", counter);
 106                         return "queryIPStatistics";
 107                 }
 108
 109                 CassandraRequester cr = new CassandraRequester();
 110                 List<TotalByCounterBean> r = cr.readProteinByCounter(realcounter);
 111                 model.put("results", r);
 112                 model.put("njobs", 0);
 113                 if (null != r) {
 114                         model.put("njobs", r.size());
 115                 }
 116                 final long endTime = System.currentTimeMillis();
 117                 model.put("timeExecution", (endTime - startTime));
 118                 model.put("counter", realcounter);
 119                 return "reportProteinSequencesCounter";
 120         }
 121
 122 }