Merge branch 'DAO'

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

diff --git a/server/compbio/controllers/SequenceController.java b/server/compbio/controllers/SequenceController.java
index 6db97ef..76b5e20 100644 (file)
--- a/server/compbio/controllers/SequenceController.java
+++ b/server/compbio/controllers/SequenceController.java
@@ -16,8 +16,8 @@ import compbio.cassandra.readers.ReaderByCounter;
 import compbio.cassandra.readers.SequenceReader;
 
 /**
- * Spring controller for sequence queries. This version works in the servlet
- * style.
+ * Spring controller for supporting sequence queries. This version works in the
+ * servlet style.
  * 
  * @author Alexander Sherstnev
  * @author Natasha Sherstneva
@@ -76,7 +76,7 @@ public class SequenceController extends BasicController {
         *            be searched
         * @return link to the report JSP page
         */
-       @RequestMapping(value = "sequence/results", method = RequestMethod.GET)
+       @RequestMapping(value = "results", method = RequestMethod.GET)
        public String findSequence(@RequestParam("sequence") String sequence, @RequestParam("searchtype") String searchtype,
                        Map<String, Object> model) {
                model.put("username", getPrincipalName());
@@ -98,32 +98,37 @@ public class SequenceController extends BasicController {
                model.put("njobs", 0);
                model.put("prot", trimmedsequence);
                model.put("searchtype", searchtype);
-               String csvline = "";
+               StringBuilder csvline = new StringBuilder("");
                if (0 < trimmedsequence.length()) {
                        SequenceReader reader = new SequenceReader();
                        List<ProteinBean> result = reader.readProteins(trimmedsequence, searchtype);
                        model.put("results", result);
                        if (null != result) {
-                               if (searchtype.equals("whole"))
+                               if (searchtype.equals("whole")) {
                                        model.put("njobs", result.get(0).getJobid().size());
-                               else
+                               } else {
                                        model.put("njobs", result.size());
-                               csvline = "\'Job\',\'Annotation\',\'Sequence\'%0A";
-                       }
-                       // form CSV file string
-                       for (ProteinBean entry : result) {
-                               List<String> jobs = entry.getJobid();
-                               String protein = entry.getSequence();
-                               LinkedHashMap<String, String> predictions = entry.getPredictions();
-                               for (String job : jobs) {
-                                       csvline += "\'" + job + "\',\'Sequence\',\'" + protein + "\',\'%0A";
+                               }
+                               csvline.append("\'Job\',\'Annotation\',\'Sequence\'%0A");
+                               for (ProteinBean entry : result) {
+                                       List<String> jobs = entry.getJobid();
+                                       String protein = entry.getSequence();
+                                       LinkedHashMap<String, String> predictions = entry.getPredictions();
+                                       StringBuilder jobline = new StringBuilder();
                                        for (Map.Entry<String, String> pr : predictions.entrySet()) {
-                                               csvline += "\'\',\'" + pr.getKey() + "\',\'" + pr.getValue() + "\'%0A";
+                                               jobline.append("\'\',\'" + pr.getKey() + "\',\'" + pr.getValue() + "\'%0A");
+                                       }
+                                       for (String job : jobs) {
+                                               csvline.append("\'" + job + "\',\'Sequence\',\'" + protein + "\',\'%0A" + jobline.toString());
                                        }
                                }
                        }
+               } else {
+                       model.put("error", "The sequence after trimming is empty");
+                       model.put("value", sequence);
+                       return "query/Sequence";
                }
-               model.put("csvfile", csvline);
+               model.put("csvfile", csvline.toString());
 
                final long endTime = System.currentTimeMillis();
                model.put("timeExecution", (endTime - startTime));
@@ -169,24 +174,23 @@ public class SequenceController extends BasicController {
                List<TotalByCounterBean> r = reader.readProteinByCounter(realcounter);
                model.put("results", r);
                model.put("njobs", 0);
-               String csvline = "";
+               StringBuilder csvline = new StringBuilder("");
                if (null != r) {
                        model.put("njobs", r.size());
-                       csvline = "\'Job%20 count\', \'Protein%20Sequence\'%0A";
-               }
-               // form line for CSV file
-
-               for (TotalByCounterBean b : r) {
-                       if (b.getName().equals("")) {
-                               csvline += "\'" + b.getTotaljobs() + "\',\'Alignment%20job\'%0A";
-                               // fix problem with records without protein sequence (alignment
-                               // jobs)
-                               b.setName("Alignment job");
-                       } else {
-                               csvline += "\'" + b.getTotaljobs() + "\',\'" + b.getName() + "\'%0A";
+                       // form line for CSV file
+                       csvline.append("\'Job%20 count\', \'Protein%20Sequence\'%0A");
+                       for (TotalByCounterBean b : r) {
+                               if (b.getName().equals("")) {
+                                       // fix problem with records without protein sequence
+                                       // (alignment jobs)
+                                       csvline.append("\'" + b.getTotaljobs() + "\',\'Alignment%20job\'%0A");
+                                       b.setName("Alignment job");
+                               } else {
+                                       csvline.append("\'" + b.getTotaljobs() + "\',\'" + b.getName() + "\'%0A");
+                               }
                        }
                }
-               model.put("csvfile", csvline);
+               model.put("csvfile", csvline.toString());
 
                model.put("results", r);
                final long endTime = System.currentTimeMillis();