1 package compbio.controllers;
3 import java.security.Principal;
6 import java.util.regex.Pattern;
8 import org.springframework.stereotype.Controller;
9 import org.springframework.web.bind.annotation.RequestMapping;
10 import org.springframework.web.bind.annotation.RequestMethod;
11 import org.springframework.web.bind.annotation.RequestParam;
13 import compbio.cassandra.ProteinBean;
14 import compbio.cassandra.TotalByCounterBean;
15 import compbio.statistic.CassandraRequester;
18 * Spring controller for sequence queries. This version works in the servlet
21 * @author Alexander Sherstnev
22 * @author Natasha Sherstneva
25 * @version 1.0 December 2013
28 @RequestMapping("/sequence")
29 public class SequenceController {
32 * pattern for NON-protein alphabet symbols
34 private final Pattern NONPROTEIN = Pattern.compile("[^ARNDCQEGHILKMFPSTWYV]+", Pattern.CASE_INSENSITIVE);
36 @RequestMapping(value = "query", method = RequestMethod.GET)
37 public String formSequenceQuery(Map<String, Object> model, Principal principal) {
38 model.put("username", principal.getName());
39 model.put("value", "AAAAA");
40 return "queryProteinSequence";
43 @RequestMapping(value = "counts/query", method = RequestMethod.GET)
44 public String formCounterQuery(Map<String, Object> model, Principal principal) {
45 model.put("username", principal.getName());
46 model.put("value", 5);
47 return "queryProteinSequenceCounter";
50 @RequestMapping(value = "sequence/results", method = RequestMethod.GET)
51 public String findSequence(@RequestParam("sequence") String sequence, @RequestParam("protein") String flag, Map<String, Object> model,
52 Principal principal) {
53 model.put("username", principal.getName());
54 final long startTime = System.currentTimeMillis();
57 String trimmedsequence = sequence.replaceAll("\\s", "");
58 if (trimmedsequence.equalsIgnoreCase("")) {
59 model.put("error", "The sequence cann't be empty");
60 model.put("value", sequence);
61 return "queryProteinSequence";
63 if (NONPROTEIN.matcher(trimmedsequence).find()) {
64 model.put("error", "The sequence contains symbols not from the standard protein alphabet");
65 model.put("value", sequence);
66 return "queryProteinSequence";
69 model.put("njobs", 0);
70 model.put("prot", trimmedsequence);
71 model.put("flag", flag);
73 if (0 < trimmedsequence.length()) {
74 CassandraRequester cr = new CassandraRequester();
75 List<ProteinBean> r = cr.readProteins(trimmedsequence, flag);
76 model.put("results", r);
78 if (flag.equals("whole"))
79 model.put("njobs", r.get(0).getJobid().size());
81 model.put("njobs", r.size());
84 final long endTime = System.currentTimeMillis();
85 model.put("timeExecution", (endTime - startTime));
86 return "reportProteinSequences";
89 @RequestMapping(value = "counts/results", method = RequestMethod.GET)
90 public String countSequences(@RequestParam("counterJob") String counter, Map<String, Object> model, Principal principal) {
91 model.put("username", principal.getName());
92 final long startTime = System.currentTimeMillis();
94 if (counter.equals("")) {
95 model.put("error", "The value must not be empty");
96 model.put("value", counter);
97 return "queryIPStatistics";
102 realcounter = Integer.parseInt(counter.trim());
103 } catch (NumberFormatException e) {
104 model.put("error", "The value must be an integer number");
105 model.put("value", counter);
106 return "queryIPStatistics";
109 if (realcounter < 1) {
110 model.put("error", "The value must be greater than 0");
111 model.put("value", counter);
112 return "queryIPStatistics";
115 CassandraRequester cr = new CassandraRequester();
116 List<TotalByCounterBean> r = cr.readProteinByCounter(realcounter);
117 model.put("results", r);
118 model.put("njobs", 0);
120 model.put("njobs", r.size());
122 final long endTime = System.currentTimeMillis();
123 model.put("timeExecution", (endTime - startTime));
124 model.put("counter", realcounter);
125 return "reportProteinSequencesCounter";