Make all necessary changes for combining old and new servlets

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

diff --git a/server/compbio/statistic/CassandraRequester.java b/server/compbio/statistic/CassandraRequester.java
index afba67b..72ec074 100755 (executable)
--- a/server/compbio/statistic/CassandraRequester.java
+++ b/server/compbio/statistic/CassandraRequester.java
@@ -9,12 +9,12 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 
+import compbio.cassandra.AnnotatedProteinSequenceBean;
 import compbio.cassandra.CassandraNativeConnector;
 import compbio.cassandra.CassandraReader;
 import compbio.cassandra.DataBase;
 import compbio.cassandra.Pair;
 import compbio.cassandra.StructureJobLog;
-import compbio.cassandra.StructureProteinPrediction;
 
 public class CassandraRequester {
        private CassandraReader db = new CassandraReader();
@@ -158,7 +158,7 @@ public class CassandraRequester {
                System.out.println("StatisticsProt.readLength: total number of dates = " + query.size());
                return query;
        }
-       
+
        /*
         * query: jobs and sequence at date
         */
@@ -190,34 +190,34 @@ public class CassandraRequester {
                System.out.println("StatisticsProt.readLength: total number of dates = " + query.size());
                return query;
        }
+
+
        /* 
         * query: protein sequence
         * */
        public List<DataBase> readProteins(String protIn, String flag) {
-               if (protIn == null)
-                       return null;
-               System.out.println(protIn.length());
                query = new ArrayList<DataBase>();
-               List<StructureProteinPrediction> res;
+               List<AnnotatedProteinSequenceBean> res;
                if (flag.equals("whole")) 
                        res = db.ReadWholeSequence(protIn);
                 else 
-                        res = (protIn.length() > 0) ? db.ReadPartOfSequence(protIn) : null;
+                       res = db.ReadPartOfSequence(protIn);
                if (res == null)
                        return null;
-               for (StructureProteinPrediction entry : res) {
-                               DataBase bean = new DataBase();
-                               bean.setProt(entry.getSequence());
-                               bean.setId(entry.getJobid());
-                               bean.setJpred(entry.getJnetpred());
-                               if (flag.equals("part"))
-                                       bean.setSubProt(CreateSubprot (entry.getSequence(), protIn));                           
-                               query.add(bean);
-                       
+               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));
+                       }
+                       query.add(db);
                }
                return query;
        }
        
+
        /* 
         * query protein sequences with number of jobs
         */