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
  20  * style.
  21  *
  22  * @author Alexander Sherstnev
  23  * @author Natasha Sherstneva
  24  *
  25  * @since 0.5
  26  * @version 1.0 December 2013
  27  */
  28 @Controller
  29 public class SequenceController {
  30
  31         /**
  32          * pattern for NON-protein alphabet symbols
  33          */
  34         private final Pattern NONPROTEIN = Pattern.compile("[^ARNDCQEGHILKMFPSTWYV]+", Pattern.CASE_INSENSITIVE);
  35
  36         @RequestMapping(value = "/sequence/query1", method = RequestMethod.GET)
  37         public String formSequenceQuery(Map<String, Object> model) {
  38                 model.put("value", "AAAAA");
  39                 return "queryProteinSequence";
  40         }
  41
  42         @RequestMapping(value = "/sequence/query2", method = RequestMethod.GET)
  43         public String formCounterQuery(Map<String, Object> model) {
  44                 model.put("value", 5);
  45                 return "queryProteinSequenceCounter";
  46         }
  47
  48         @RequestMapping(value = "/sequence/querysequence", method = RequestMethod.GET)
  49         public String findSequence(@RequestParam("sequence") String sequence, @RequestParam("protein") String flag, Map<String, Object> model) {
  50                 final long startTime = System.currentTimeMillis();
  51
  52                 // input checks
  53                 String trimmedsequence = sequence.replaceAll("\\s", "");
  54                 if (trimmedsequence.equalsIgnoreCase("")) {
  55                         model.put("error", "The sequence cann't be empty");
  56                         model.put("value", sequence);
  57                         return "queryProteinSequence";
  58                 }
  59                 if (NONPROTEIN.matcher(trimmedsequence).find()) {
  60                         model.put("error", "The sequence contains symbols not from the standard protein alphabet");
  61                         model.put("value", sequence);
  62                         return "queryProteinSequence";
  63                 }
  64
  65                 model.put("njobs", 0);
  66                 model.put("prot", trimmedsequence);
  67                 model.put("flag", flag);
  68
  69                 if (0 < trimmedsequence.length()) {
  70                         CassandraRequester cr = new CassandraRequester();
  71                         List<ProteinBean> r = cr.readProteins(trimmedsequence, flag);
  72                         model.put("results", r);
  73                         if (null != r) {
  74                                 if (flag.equals("whole"))
  75                                         model.put("njobs", r.get(0).getJobid().size());
  76                                 else
  77                                         model.put("njobs", r.size());
  78                         }
  79                 }
  80                 final long endTime = System.currentTimeMillis();
  81                 model.put("timeExecution", (endTime - startTime));
  82                 return "reportProteinSequences";
  83         }
  84
  85         @RequestMapping(value = "/sequence/querycounter", method = RequestMethod.GET)
  86         public String countSequences(@RequestParam("counterJob") String counter, Map<String, Object> model) {
  87                 final long startTime = System.currentTimeMillis();
  88
  89                 if (counter.equals("")) {
  90                         model.put("error", "The value must not be empty");
  91                         model.put("value", counter);
  92                         return "queryIPStatistics";
  93                 }
  94
  95                 int realcounter;
  96                 try {
  97                         realcounter = Integer.parseInt(counter.trim());
  98                 } catch (NumberFormatException e) {
  99                         model.put("error", "The value must be an integer number");
 100                         model.put("value", counter);
 101                         return "queryIPStatistics";
 102                 }
 103
 104                 if (realcounter < 1) {
 105                         model.put("error", "The value must be greater than 0");
 106                         model.put("value", counter);
 107                         return "queryIPStatistics";
 108                 }
 109
 110                 CassandraRequester cr = new CassandraRequester();
 111                 List<TotalByCounterBean> r = cr.readProteinByCounter(realcounter);
 112                 model.put("results", r);
 113                 model.put("njobs", 0);
 114                 if (null != r) {
 115                         model.put("njobs", r.size());
 116                 }
 117                 final long endTime = System.currentTimeMillis();
 118                 model.put("timeExecution", (endTime - startTime));
 119                 model.put("counter", realcounter);
 120                 return "reportProteinSequencesCounter";
 121         }
 122
 123 }