1 package compbio.controllers;
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;
11 import compbio.cassandra.ProteinBean;
12 import compbio.cassandra.DataBase;
13 import compbio.cassandra.TotalByCounterBean;
14 import compbio.statistic.CassandraRequester;
17 * @author Alexander Sherstnev
18 * @author Natasha Sherstneva
21 public class SequenceController {
23 @RequestMapping(value = "/sequence/query1", method = RequestMethod.GET)
24 public String formSequenceQuery(Map<String, Object> model) {
25 model.put("value", "AAAAA");
26 return "queryProteinSequence";
29 @RequestMapping(value = "/sequence/query2", method = RequestMethod.GET)
30 public String formCounterQuery(Map<String, Object> model) {
31 model.put("value", 5);
32 return "queryProteinSequenceCounter";
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();
39 String trimmedsequence = sequence.replaceAll("\\s", "");
40 model.put("njobs", 0);
41 model.put("prot", trimmedsequence);
42 model.put("flag", flag);
44 if (0 < trimmedsequence.length()) {
45 CassandraRequester cr = new CassandraRequester();
46 List<ProteinBean> r = cr.readProteins(trimmedsequence, flag);
47 model.put("results", r);
49 if (flag.equals("whole"))
50 model.put("njobs",r.get(0).getJobid().size());
52 model.put("njobs", r.size());
55 final long endTime = System.currentTimeMillis();
56 model.put("timeExecution", (endTime - startTime));
57 return "reportProteinSequences";
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();
64 if (counter.equals("")) {
65 model.put("error", "The value must not be empty");
66 model.put("value", counter);
67 return "queryIPStatistics";
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";
79 if (realcounter < 1) {
80 model.put("error", "The value must be greater than 0");
81 model.put("value", counter);
82 return "queryIPStatistics";
85 CassandraRequester cr = new CassandraRequester();
86 List<TotalByCounterBean> r = cr.readProteinByCounter(realcounter);
87 model.put("results", r);
88 model.put("njobs", 0);
90 model.put("njobs", r.size());
92 final long endTime = System.currentTimeMillis();
93 model.put("timeExecution", (endTime - startTime));
94 model.put("counter", realcounter);
95 return "reportProteinSequencesCounter";