create ProteinBean

[proteocache.git] / server / compbio / statistic / CassandraRequester.java

diff --git a/server/compbio/statistic/CassandraRequester.java b/server/compbio/statistic/CassandraRequester.java
index f4c4c18..c92b9bf 100755 (executable)
--- a/server/compbio/statistic/CassandraRequester.java
+++ b/server/compbio/statistic/CassandraRequester.java
@@ -9,7 +9,7 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 
-import compbio.cassandra.AnnotatedProteinSequenceBean;
+import compbio.cassandra.ProteinBean;
 import compbio.cassandra.CassandraNativeConnector;
 import compbio.cassandra.CassandraReader;
 import compbio.cassandra.DataBase;
@@ -195,26 +195,21 @@ public class CassandraRequester {
        /* 
         * query: protein sequence
         * */
-       public List<DataBase> readProteins(String protIn, String flag) {
-               query = new ArrayList<DataBase>();
-               List<AnnotatedProteinSequenceBean> res;
+       public List<ProteinBean> readProteins(String protIn, String flag) {
+               List<ProteinBean> result;
                if (flag.equals("whole")) 
-                       res = db.ReadWholeSequence(protIn);
+                       result = db.ReadWholeSequence(protIn);
                 else 
-                       res = db.ReadPartOfSequence(protIn);
-               if (res == null)
+                        result = db.ReadPartOfSequence(protIn);
+               if (result == null)
                        return null;
-               for (AnnotatedProteinSequenceBean entry : res) {
-                       DataBase db = new DataBase();
-                       db.setProt(entry.getSequence());
-                       db.setPredictions(entry);
-                       db.setId(entry.getJobid());
-                       if (flag.equals("part")) {
-                               db.setSubProt(CreateSubprot (entry.getSequence(), protIn));
+               
+               if (flag.equals("part")) {
+                       for (ProteinBean entry : result) {
+                               entry.setSubProt(CreateSubprot(entry.getSequence(), protIn));
                        }
-                       query.add(db);
-               }
-               return query;
+               }                                       
+               return result;
        }