X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=server%2Fcompbio%2Fcontrollers%2FSSFeaturesController.java;h=3c663615839fd1615d2b4fe8c0c05f776e3624e4;hb=a4e4432c6f5812208d72d9f6bea7aff1aa850817;hp=ba81cab0acfa20752390867900915855845cd4eb;hpb=8256bed38c0abeefe003adf6d9f126113f9cc5b3;p=proteocache.git

diff --git a/server/compbio/controllers/SSFeaturesController.java b/server/compbio/controllers/SSFeaturesController.java
index ba81cab..3c66361 100644
--- a/server/compbio/controllers/SSFeaturesController.java
+++ b/server/compbio/controllers/SSFeaturesController.java
@@ -10,8 +10,8 @@ import org.springframework.web.bind.annotation.RequestParam;
 import compbio.statistic.CassandraRequester;
 
 /**
- * Spring controller for sequence queries. This version works in the servlet
- * style.
+ * Spring controller for protein secondary structure features. This version
+ * works in the servlet style.
  * 
  * @author Alexander Sherstnev
  * @author Natasha Sherstneva
@@ -23,6 +23,15 @@ import compbio.statistic.CassandraRequester;
 @RequestMapping("/features")
 public class SSFeaturesController extends BasicController {
 
+	/**
+	 * form a query page for protein secondary structure feaatures: Proteins
+	 * with given fraction of H/E (helix/beta sheets)
+	 * 
+	 * @param model
+	 *            MVC model object
+	 * 
+	 * @return link to the report JSP page
+	 */
 	@RequestMapping(value = "query", method = RequestMethod.GET)
 	public String formCounterQuery(Map<String, Object> model) {
 		model.put("username", getPrincipalName());
@@ -31,6 +40,21 @@ public class SSFeaturesController extends BasicController {
 		return "query/SSFeatures";
 	}
 
+	/**
+	 * form a results page for protein secondary structure features: Proteins
+	 * with given fraction of H/E (helix/beta sheets) All proteins with E/H
+	 * higher than a given percent of the length are returned
+	 * 
+	 * @param model
+	 *            MVC model object
+	 * @param typeFeature
+	 *            type of SS: H/E (helix/beta sheets)
+	 * @param percent
+	 *            fraction of the protein length predicted as H/E (helix/beta
+	 *            sheets)
+	 * 
+	 * @return link to the report JSP page
+	 */
 	@RequestMapping(value = "results", method = RequestMethod.GET)
 	public String countSequences(@RequestParam("TypeFeatures") String typeFeature, @RequestParam("Percent") String percent,
 			Map<String, Object> model) {
@@ -69,25 +93,25 @@ public class SSFeaturesController extends BasicController {
 		Map<String, String> r = cr.readProteinsPrediction(typeFeature, realpercent);
 		model.put("results", r);
 		model.put("njobs", 0);
-		String csvline = "";
+		StringBuilder csvline = new StringBuilder("");
 		if (null != r) {
 			model.put("njobs", r.size());
-			csvline = "\'Prediction%20number\',\'Protein%20Sequence\', \'Secondary%20Structure%20Prediction\'%0A";
-		}
+			csvline.append("\'Prediction%20number\',\'Protein%20Sequence\', \'Secondary%20Structure%20Prediction\'%0A");
 
-		// form line for CSV file
-		int counter = 1;
-		for (Map.Entry<String, String> entry : r.entrySet()) {
-			csvline += "\'" + counter + "\',\'" + entry.getKey() + "\',\'" + entry.getValue() + "\'%0A";
-			++counter;
+			// form line for CSV file
+			int counter = 1;
+			for (Map.Entry<String, String> entry : r.entrySet()) {
+				csvline.append("\'" + counter + "\',\'" + entry.getKey() + "\',\'" + entry.getValue() + "\'%0A");
+				++counter;
+			}
 		}
-		model.put("csvfile", csvline);
+		model.put("csvfile", csvline.toString());
 
 		final long endTime = System.currentTimeMillis();
 		model.put("timeExecution", (endTime - startTime));
 		model.put("feature", typeFeature);
 		model.put("percent", realpercent);
-		return "reportSSFeatures";
+		return "reports/SSFeatures";
 	}
 
 }