X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=server%2Fcompbio%2Fcontrollers%2FSequenceController.java;h=df4c98720e03b1936a2a2653aa919a50ccb354e1;hb=025c55d49c191f24d0e06c5cbb69a9894c50af22;hp=62ec81e8f2b9fcc10444b662923e1765a38b6068;hpb=c7b32cc1f17ec534d5b98ed27cc2f3a4b52daad6;p=proteocache.git

diff --git a/server/compbio/controllers/SequenceController.java b/server/compbio/controllers/SequenceController.java
index 62ec81e..df4c987 100644
--- a/server/compbio/controllers/SequenceController.java
+++ b/server/compbio/controllers/SequenceController.java
@@ -10,13 +10,12 @@ import org.springframework.web.bind.annotation.RequestMethod;
 import org.springframework.web.bind.annotation.RequestParam;
 
 import compbio.cassandra.ProteinBean;
-import compbio.cassandra.DataBase;
-import compbio.data.sequence.SequenceUtil;
 import compbio.cassandra.TotalByCounterBean;
 import compbio.statistic.CassandraRequester;
 
 /**
- * Spring controller for sequence search. This version works in the servlet style.
+ * Spring controller for sequence queries. This version works in the servlet
+ * style.
  * 
  * @author Alexander Sherstnev
  * @author Natasha Sherstneva
@@ -25,27 +24,32 @@ import compbio.statistic.CassandraRequester;
  * @version 1.0 December 2013
  */
 @Controller
-public class SequenceController {
-	
+@RequestMapping("/sequence")
+public class SequenceController extends BasicController {
+
 	/**
-	 * pattern for NON-protein alphabet  symbols
+	 * pattern for NON-protein alphabet symbols
 	 */
 	private final Pattern NONPROTEIN = Pattern.compile("[^ARNDCQEGHILKMFPSTWYV]+", Pattern.CASE_INSENSITIVE);
 
-	@RequestMapping(value = "/sequence/query1", method = RequestMethod.GET)
+	@RequestMapping(value = "query", method = RequestMethod.GET)
 	public String formSequenceQuery(Map<String, Object> model) {
+		model.put("username", getPrincipalName());
 		model.put("value", "AAAAA");
-		return "queryProteinSequence";
+		return "query/Sequence";
 	}
 
-	@RequestMapping(value = "/sequence/query2", method = RequestMethod.GET)
+	@RequestMapping(value = "counts/query", method = RequestMethod.GET)
 	public String formCounterQuery(Map<String, Object> model) {
+		model.put("username", getPrincipalName());
 		model.put("value", 5);
-		return "queryProteinSequenceCounter";
+		return "query/SequenceCounts";
 	}
-	
-	@RequestMapping(value = "/sequence/querysequence", method = RequestMethod.GET)
-	public String findSequence(@RequestParam("sequence") String sequence, @RequestParam("protein") String flag, Map<String, Object> model) {
+
+	@RequestMapping(value = "sequence/results", method = RequestMethod.GET)
+	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
@@ -53,25 +57,25 @@ public class SequenceController {
 		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"))
-					model.put("njobs",r.get(0).getJobid().size());
+				if (searchtype.equals("whole"))
+					model.put("njobs", r.get(0).getJobid().size());
 				else
 					model.put("njobs", r.size());
 			}
@@ -81,14 +85,15 @@ public class SequenceController {
 		return "reportProteinSequences";
 	}
 
-	@RequestMapping(value = "/sequence/querycounter", method = RequestMethod.GET)
+	@RequestMapping(value = "counts/results", method = RequestMethod.GET)
 	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;
@@ -97,13 +102,13 @@ public class SequenceController {
 		} 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();