X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=server%2Fcompbio%2Fcontrollers%2FSequenceController.java;h=4eb5844692b62a622168334bdee5459a0c55fed2;hb=a4e4432c6f5812208d72d9f6bea7aff1aa850817;hp=9e92273ba352fdeaeaa8cc5fae345f7fe56ef413;hpb=04ad9aafdb2d827c8282edf84ab130d5bc0d923e;p=proteocache.git

diff --git a/server/compbio/controllers/SequenceController.java b/server/compbio/controllers/SequenceController.java
index 9e92273..4eb5844 100644
--- 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
@@ -98,32 +98,33 @@ 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
+				}
+				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()) {
+						jobline.append("\'\',\'" + pr.getKey() + "\',\'" + pr.getValue() + "\'%0A");
+					}
 					for (String job : jobs) {
-						csvline += "\'" + job + "\',\'Sequence\',\'" + protein + "\',\'%0A";
-						for (Map.Entry<String, String> pr : predictions.entrySet()) {
-							csvline += "\'\',\'" + pr.getKey() + "\',\'" + pr.getValue() + "\'%0A";
-						}
+						csvline.append("\'" + job + "\',\'Sequence\',\'" + protein + "\',\'%0A" + jobline.toString());
 					}
 				}
 			}
 		}
-		model.put("csvfile", csvline);
+		model.put("csvfile", csvline.toString());
 
 		final long endTime = System.currentTimeMillis();
 		model.put("timeExecution", (endTime - startTime));
@@ -169,24 +170,23 @@ 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();