1 package compbio.controllers;
5 import java.util.regex.Pattern;
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;
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;
19 * Spring controller for sequence search. This version works in the servlet style.
21 * @author Alexander Sherstnev
22 * @author Natasha Sherstneva
25 * @version 1.0 December 2013
28 public class SequenceController {
31 * pattern for NON-protein alphabet symbols
33 private final Pattern NONPROTEIN = Pattern.compile("[^ARNDCQEGHILKMFPSTWYV]+", Pattern.CASE_INSENSITIVE);
35 @RequestMapping(value = "/sequence/query1", method = RequestMethod.GET)
36 public String formSequenceQuery(Map<String, Object> model) {
37 model.put("value", "AAAAA");
38 return "queryProteinSequence";
41 @RequestMapping(value = "/sequence/query2", method = RequestMethod.GET)
42 public String formCounterQuery(Map<String, Object> model) {
43 model.put("value", 5);
44 return "queryProteinSequenceCounter";
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();
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";
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";
64 model.put("njobs", 0);
65 model.put("prot", trimmedsequence);
66 model.put("flag", flag);
68 if (0 < trimmedsequence.length()) {
69 CassandraRequester cr = new CassandraRequester();
70 List<ProteinBean> r = cr.readProteins(trimmedsequence, flag);
71 model.put("results", r);
73 if (flag.equals("whole"))
74 model.put("njobs",r.get(0).getJobid().size());
76 model.put("njobs", r.size());
79 final long endTime = System.currentTimeMillis();
80 model.put("timeExecution", (endTime - startTime));
81 return "reportProteinSequences";
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();
88 if (counter.equals("")) {
89 model.put("error", "The value must not be empty");
90 model.put("value", counter);
91 return "queryIPStatistics";
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";
103 if (realcounter < 1) {
104 model.put("error", "The value must be greater than 0");
105 model.put("value", counter);
106 return "queryIPStatistics";
109 CassandraRequester cr = new CassandraRequester();
110 List<TotalByCounterBean> r = cr.readProteinByCounter(realcounter);
111 model.put("results", r);
112 model.put("njobs", 0);
114 model.put("njobs", r.size());
116 final long endTime = System.currentTimeMillis();
117 model.put("timeExecution", (endTime - startTime));
118 model.put("counter", realcounter);
119 return "reportProteinSequencesCounter";