X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=server%2Fcompbio%2Fcontrollers%2FSequenceController.java;h=0f154d3da92b2e711d5fb6531b493872d74cdf6a;hb=de3f241669f5f2bfd8258e87cbd0b19402950f32;hp=8e5bc293d1b47d20a47c627a20ad0575f53f7f1a;hpb=f67950b14ab016e93cca92d9b918a255728d58fd;p=proteocache.git

diff --git a/server/compbio/controllers/SequenceController.java b/server/compbio/controllers/SequenceController.java
index 8e5bc29..0f154d3 100644
--- a/server/compbio/controllers/SequenceController.java
+++ b/server/compbio/controllers/SequenceController.java
@@ -2,22 +2,34 @@ package compbio.controllers;
 
 import java.util.List;
 import java.util.Map;
+import java.util.regex.Pattern;
 
 import org.springframework.stereotype.Controller;
 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.DataBase;
-
+import compbio.data.sequence.SequenceUtil;
 import compbio.statistic.CassandraRequester;
 
 /**
+ * Spring controller for sequence search. This version works in the servlet style.
+ * 
  * @author Alexander Sherstnev
  * @author Natasha Sherstneva
+ * 
+ * @since 0.5
+ * @version 1.0 December 2013
  */
 @Controller
 public class SequenceController {
+	
+	/**
+	 * pattern for NON-protein alphabet  symbols
+	 */
+	private final Pattern NONPROTEIN = Pattern.compile("[^ARNDCQEGHILKMFPSTWYV]+", Pattern.CASE_INSENSITIVE);
 
 	@RequestMapping(value = "/sequence/query1", method = RequestMethod.GET)
 	public String formSequenceQuery(Map<String, Object> model) {
@@ -35,18 +47,32 @@ public class SequenceController {
 	public String findSequence(@RequestParam("sequence") String sequence, @RequestParam("protein") String flag, Map<String, Object> model) {
 		final long startTime = System.currentTimeMillis();
 
+		// input checks
 		String trimmedsequence = sequence.replaceAll("\\s", "");
+		if (trimmedsequence.equalsIgnoreCase("")) {
+			model.put("error", "The sequence cann't be empty");
+			model.put("value", sequence);
+			return "queryProteinSequence";
+		}
+		if (NONPROTEIN.matcher(trimmedsequence).find()) {
+			model.put("error", "The sequence contains symbols not from the standard protein alphabet");
+			model.put("value", sequence);
+			return "queryProteinSequence";
+		}
+
 		model.put("njobs", 0);
 		model.put("prot", trimmedsequence);
 		model.put("flag", flag);
 
 		if (0 < trimmedsequence.length()) {
 			CassandraRequester cr = new CassandraRequester();
-			List<DataBase> r = cr.readProteins(trimmedsequence, flag);
+			List<ProteinBean> r = cr.readProteins(trimmedsequence, flag);
 			model.put("results", r);
 			if (null != r) {
-				System.out.println("result size = " + r.size());
-				model.put("njobs", r.size());
+				if (flag.equals("whole"))
+					model.put("njobs",r.get(0).getJobid().size());
+				else
+					model.put("njobs", r.size());
 			}
 		}
 		final long endTime = System.currentTimeMillis();