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.statistic.CassandraRequester;
18 * Spring controller for sequence search. This version works in the servlet style.
20 * @author Alexander Sherstnev
21 * @author Natasha Sherstneva
24 * @version 1.0 December 2013
27 public class SequenceController {
30 * pattern for NON-protein alphabet symbols
32 private final Pattern NONPROTEIN = Pattern.compile("[^ARNDCQEGHILKMFPSTWYV]+", Pattern.CASE_INSENSITIVE);
34 @RequestMapping(value = "/sequence/query1", method = RequestMethod.GET)
35 public String formSequenceQuery(Map<String, Object> model) {
36 model.put("value", "AAAAA");
37 return "queryProteinSequence";
40 @RequestMapping(value = "/sequence/query2", method = RequestMethod.GET)
41 public String formCounterQuery(Map<String, Object> model) {
42 model.put("value", 5);
43 return "queryProteinSequenceCounter";
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();
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";
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";
63 model.put("njobs", 0);
64 model.put("prot", trimmedsequence);
65 model.put("flag", flag);
67 if (0 < trimmedsequence.length()) {
68 CassandraRequester cr = new CassandraRequester();
69 List<ProteinBean> r = cr.readProteins(trimmedsequence, flag);
70 model.put("results", r);
72 if (flag.equals("whole"))
73 model.put("njobs",r.get(0).getJobid().size());
75 model.put("njobs", r.size());
78 final long endTime = System.currentTimeMillis();
79 model.put("timeExecution", (endTime - startTime));
80 return "reportProteinSequences";
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();
87 if (counter.equals("")) {
88 model.put("error", "The value must not be empty");
89 model.put("value", counter);
90 return "queryIPStatistics";
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";
102 if (realcounter < 1) {
103 model.put("error", "The value must be greater than 0");
104 model.put("value", counter);
105 return "queryIPStatistics";
108 CassandraRequester cr = new CassandraRequester();
109 List<DataBase> r = cr.readProteinByCounter(realcounter);
110 model.put("results", r);
111 model.put("njobs", 0);
113 model.put("njobs", r.size());
115 final long endTime = System.currentTimeMillis();
116 model.put("timeExecution", (endTime - startTime));
117 model.put("counter", realcounter);
118 return "reportProteinSequencesCounter";