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