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

Conflicts:
	datadb/compbio/cassandra/CassandraReaderOld.java
	server/compbio/statistic/CassandraRequester.java

diff --cc datadb/compbio/cassandra/readers/CassandraReader.java
Simple merge

diff --cc server/compbio/controllers/JobController.java
index 732d07d,0a00d9b..f05234e
--- 1/server/compbio/controllers/JobController.java
--- 2/server/compbio/controllers/JobController.java
+++ b/server/compbio/controllers/JobController.java
@@@ -16,15 -14,13 +14,12 @@@ import org.springframework.web.bind.ann
  import org.springframework.web.bind.annotation.RequestMethod;
  import org.springframework.web.bind.annotation.RequestParam;
  
 -import compbio.statistic.CassandraRequester;
  import compbio.beans.DateBean;
  import compbio.beans.ExecutionTimeBean;
- import compbio.beans.Total;
+ import compbio.beans.JobBean;
  import compbio.beans.TotalExecutionTime;
- import compbio.beans.TotalJobsStatisticBean;
- import compbio.cassandra.DataBase;
  import compbio.cassandra.DateFormatter;
  import compbio.cassandra.readers.CassandraReader;
- import compbio.cassandra.readers.DailyStatisticsReader;
  import compbio.cassandra.readers.ExecutionTimeReader;
  import compbio.cassandra.readers.JobReader;
  import compbio.engine.ExecutionInterval;

diff --cc server/compbio/controllers/SSFeaturesController.java
index 6398eef,3c66361..a961efe
--- 1/server/compbio/controllers/SSFeaturesController.java
--- 2/server/compbio/controllers/SSFeaturesController.java
+++ b/server/compbio/controllers/SSFeaturesController.java
@@@ -7,11 -7,11 +7,11 @@@ import org.springframework.web.bind.ann
  import org.springframework.web.bind.annotation.RequestMethod;
  import org.springframework.web.bind.annotation.RequestParam;
  
 -import compbio.statistic.CassandraRequester;
 +import compbio.cassandra.readers.FeaturesReader;
  
  /**
-  * 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
@@@ -65,23 -89,23 +89,23 @@@ public class SSFeaturesController exten
                        return "query/SSFeatures";
                }
  
 -              CassandraRequester cr = new CassandraRequester();
 -              Map<String, String> r = cr.readProteinsPrediction(typeFeature, realpercent);
 +              FeaturesReader reader = new FeaturesReader();
 +              Map<String, String> r = reader.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));