X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=server%2Fcompbio%2Fcontrollers%2FSequenceController.java;fp=server%2Fcompbio%2Fcontrollers%2FSequenceController.java;h=105ef2ffc9d35abf19a939046e9c707c85bdb7cb;hb=e8b88c0c8e432f8bc1aefdbd81df81e9ef706242;hp=df4c98720e03b1936a2a2653aa919a50ccb354e1;hpb=429ba39df7f7dbf7c7f940bafd5126cfab9fca61;p=proteocache.git

diff --git a/server/compbio/controllers/SequenceController.java b/server/compbio/controllers/SequenceController.java
index df4c987..105ef2f 100644
--- a/server/compbio/controllers/SequenceController.java
+++ b/server/compbio/controllers/SequenceController.java
@@ -9,8 +9,10 @@ import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestMethod;
 import org.springframework.web.bind.annotation.RequestParam;
 
-import compbio.cassandra.ProteinBean;
-import compbio.cassandra.TotalByCounterBean;
+import compbio.beans.ProteinBean;
+import compbio.beans.TotalByCounterBean;
+import compbio.cassandra.readers.ReaderByCounter;
+import compbio.cassandra.readers.SequenceReader;
 import compbio.statistic.CassandraRequester;
 
 /**
@@ -32,6 +34,14 @@ public class SequenceController extends BasicController {
 	 */
 	private final Pattern NONPROTEIN = Pattern.compile("[^ARNDCQEGHILKMFPSTWYV]+", Pattern.CASE_INSENSITIVE);
 
+	/**
+	 * form a query page for search protein sequence. The servlet should be
+	 * available for users and admins only. 
+	 * 
+	 * @param model
+	 *            MVC model
+	 * @return link to the JSP query page
+	 */
 	@RequestMapping(value = "query", method = RequestMethod.GET)
 	public String formSequenceQuery(Map<String, Object> model) {
 		model.put("username", getPrincipalName());
@@ -39,6 +49,14 @@ public class SequenceController extends BasicController {
 		return "query/Sequence";
 	}
 
+	/**
+	 * form a query page for statistics: Protein by job count. The servlet should be
+	 * available for users and admins only. 
+	 * 
+	 * @param model
+	 *            MVC model
+	 * @return link to the JSP query page
+	 */
 	@RequestMapping(value = "counts/query", method = RequestMethod.GET)
 	public String formCounterQuery(Map<String, Object> model) {
 		model.put("username", getPrincipalName());
@@ -46,6 +64,17 @@ public class SequenceController extends BasicController {
 		return "query/SequenceCounts";
 	}
 
+	/**
+	 * form a report page for search protein sequence.
+	 * 
+	 * @param model
+	 *            MVC model object
+	 * @param sequence
+	 *            protein sequence or part of sequence
+	 * @param searchtype
+	 *            defined whether the whole sequence or part of sequence would be searched
+	 * @return link to the report JSP page
+	 */
 	@RequestMapping(value = "sequence/results", method = RequestMethod.GET)
 	public String findSequence(@RequestParam("sequence") String sequence, @RequestParam("searchtype") String searchtype,
 			Map<String, Object> model) {
@@ -70,14 +99,14 @@ public class SequenceController extends BasicController {
 		model.put("searchtype", searchtype);
 
 		if (0 < trimmedsequence.length()) {
-			CassandraRequester cr = new CassandraRequester();
-			List<ProteinBean> r = cr.readProteins(trimmedsequence, searchtype);
-			model.put("results", r);
-			if (null != r) {
+			SequenceReader reader = new SequenceReader();
+			List<ProteinBean> result = reader.readProteins(trimmedsequence, searchtype);
+			model.put("results", result);
+			if (null != result) {
 				if (searchtype.equals("whole"))
-					model.put("njobs", r.get(0).getJobid().size());
+					model.put("njobs", result.get(0).getJobid().size());
 				else
-					model.put("njobs", r.size());
+					model.put("njobs", result.size());
 			}
 		}
 		final long endTime = System.currentTimeMillis();
@@ -85,6 +114,15 @@ public class SequenceController extends BasicController {
 		return "reportProteinSequences";
 	}
 
+	/**
+	 * form a report page for statistics: Protein by job count.
+	 * 
+	 * @param model
+	 *            MVC model object
+	 * @param counter
+	 *           
+	 * @return link to the report JSP page
+	 */
 	@RequestMapping(value = "counts/results", method = RequestMethod.GET)
 	public String countSequences(@RequestParam("counterJob") String counter, Map<String, Object> model) {
 		model.put("username", getPrincipalName());
@@ -111,8 +149,9 @@ public class SequenceController extends BasicController {
 			return "query/SequenceCounts";
 		}
 
-		CassandraRequester cr = new CassandraRequester();
-		List<TotalByCounterBean> r = cr.readProteinByCounter(realcounter);
+		ReaderByCounter reader = new ReaderByCounter();
+
+		List<TotalByCounterBean> r = reader.readProteinByCounter(realcounter);
 		model.put("results", r);
 		model.put("njobs", 0);
 		if (null != r) {