Merge branch 'servlets' of https://source.jalview.org/git/proteocache into servlets

[proteocache.git] / server / compbio / controllers / SequenceController.java

diff --git a/server/compbio/controllers/SequenceController.java b/server/compbio/controllers/SequenceController.java
index c57ed1f..a5b1757 100644 (file)
--- a/server/compbio/controllers/SequenceController.java
+++ b/server/compbio/controllers/SequenceController.java
@@ -2,6 +2,7 @@ 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;
@@ -9,16 +10,28 @@ import org.springframework.web.bind.annotation.RequestMethod;
 import org.springframework.web.bind.annotation.RequestParam;
 
 import compbio.cassandra.ProteinBean;
+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.
+ * 
  * @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) {
                model.put("value", "AAAAA");
@@ -30,12 +43,24 @@ public class SequenceController {
                model.put("value", 5);
                return "queryProteinSequenceCounter";
        }
-       
+
        @RequestMapping(value = "/sequence/querysequence", method = RequestMethod.GET)
        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);
@@ -46,7 +71,7 @@ public class SequenceController {
                        model.put("results", r);
                        if (null != r) {
                                if (flag.equals("whole"))
-                                       model.put("njobs",r.get(0).getJobid().size());
+                                       model.put("njobs", r.get(0).getJobid().size());
                                else
                                        model.put("njobs", r.size());
                        }