package compbio.controllers;
-import java.security.Principal;
import java.util.List;
import java.util.Map;
import java.util.regex.Pattern;
*/
@Controller
@RequestMapping("/sequence")
-public class SequenceController {
+public class SequenceController extends BasicController {
/**
* pattern for NON-protein alphabet symbols
private final Pattern NONPROTEIN = Pattern.compile("[^ARNDCQEGHILKMFPSTWYV]+", Pattern.CASE_INSENSITIVE);
@RequestMapping(value = "query", method = RequestMethod.GET)
- public String formSequenceQuery(Map<String, Object> model, Principal principal) {
- model.put("username", principal.getName());
+ public String formSequenceQuery(Map<String, Object> model) {
+ model.put("username", getPrincipalName());
model.put("value", "AAAAA");
- return "queryProteinSequence";
+ return "query/Sequence";
}
@RequestMapping(value = "counts/query", method = RequestMethod.GET)
- public String formCounterQuery(Map<String, Object> model, Principal principal) {
- model.put("username", principal.getName());
+ public String formCounterQuery(Map<String, Object> model) {
+ model.put("username", getPrincipalName());
model.put("value", 5);
- return "queryProteinSequenceCounter";
+ return "query/SequenceCounts";
}
@RequestMapping(value = "sequence/results", method = RequestMethod.GET)
- public String findSequence(@RequestParam("sequence") String sequence, @RequestParam("protein") String flag, Map<String, Object> model,
- Principal principal) {
- model.put("username", principal.getName());
+ public String findSequence(@RequestParam("sequence") String sequence, @RequestParam("searchtype") String searchtype,
+ Map<String, Object> model) {
+ model.put("username", getPrincipalName());
final long startTime = System.currentTimeMillis();
// input checks
if (trimmedsequence.equalsIgnoreCase("")) {
model.put("error", "The sequence cann't be empty");
model.put("value", sequence);
- return "queryProteinSequence";
+ return "query/Sequence";
}
if (NONPROTEIN.matcher(trimmedsequence).find()) {
model.put("error", "The sequence contains symbols not from the standard protein alphabet");
model.put("value", sequence);
- return "queryProteinSequence";
+ return "query/Sequence";
}
model.put("njobs", 0);
model.put("prot", trimmedsequence);
- model.put("flag", flag);
+ model.put("searchtype", searchtype);
if (0 < trimmedsequence.length()) {
CassandraRequester cr = new CassandraRequester();
- List<ProteinBean> r = cr.readProteins(trimmedsequence, flag);
+ List<ProteinBean> r = cr.readProteins(trimmedsequence, searchtype);
model.put("results", r);
if (null != r) {
- if (flag.equals("whole"))
+ if (searchtype.equals("whole"))
model.put("njobs", r.get(0).getJobid().size());
else
model.put("njobs", r.size());
}
@RequestMapping(value = "counts/results", method = RequestMethod.GET)
- public String countSequences(@RequestParam("counterJob") String counter, Map<String, Object> model, Principal principal) {
- model.put("username", principal.getName());
+ public String countSequences(@RequestParam("counterJob") String counter, Map<String, Object> model) {
+ model.put("username", getPrincipalName());
final long startTime = System.currentTimeMillis();
if (counter.equals("")) {
model.put("error", "The value must not be empty");
model.put("value", counter);
- return "queryIPStatistics";
+ return "query/SequenceCounts";
}
int realcounter;
} catch (NumberFormatException e) {
model.put("error", "The value must be an integer number");
model.put("value", counter);
- return "queryIPStatistics";
+ return "query/SequenceCounts";
}
if (realcounter < 1) {
model.put("error", "The value must be greater than 0");
model.put("value", counter);
- return "queryIPStatistics";
+ return "query/SequenceCounts";
}
CassandraRequester cr = new CassandraRequester();