Add new still not-working code for native binary protocol version

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

diff --git a/server/compbio/statistic/StatisticsProt.java b/server/compbio/statistic/StatisticsProt.java
index c0150b7..05375c0 100755 (executable)
--- a/server/compbio/statistic/StatisticsProt.java
+++ b/server/compbio/statistic/StatisticsProt.java
@@ -9,21 +9,11 @@ import java.util.Date;
 import java.util.Iterator;
 import java.util.List;
 
-import me.prettyprint.cassandra.serializers.LongSerializer;
-import me.prettyprint.cassandra.serializers.StringSerializer;
-import me.prettyprint.hector.api.beans.ColumnSlice;
-import me.prettyprint.hector.api.beans.HColumn;
-import me.prettyprint.hector.api.beans.OrderedRows;
-import me.prettyprint.hector.api.beans.Row;
-import me.prettyprint.hector.api.factory.HFactory;
-import me.prettyprint.hector.api.query.QueryResult;
-import me.prettyprint.hector.api.query.RangeSlicesQuery;
-import me.prettyprint.hector.api.query.SliceQuery;
-import compbio.cassandra.CassandraCreate;
+import compbio.cassandra.CassandraNativeConnector;
 import compbio.cassandra.DataBase;
 
 public class StatisticsProt {
-       private CassandraCreate cc = new CassandraCreate();
+       private CassandraNativeConnector cc = new CassandraNativeConnector();
        private ArrayList<DataBase> query;
        private static long currentDate = 0;
        private static long earlestDate = 0;
@@ -55,6 +45,7 @@ public class StatisticsProt {
                end.setTime(new Date(dateEnd));
                query = new ArrayList<DataBase>();
                int day = 0;
+               /*
                for (Date date = start.getTime(); !start.after(end); start.add(Calendar.DATE, 1), date = start.getTime()) {
                        SliceQuery<Long, String, String> result = HFactory.createSliceQuery(cc.GetKeyspace(), LongSerializer.get(),
                                        StringSerializer.get(), StringSerializer.get());
@@ -72,6 +63,7 @@ public class StatisticsProt {
                                System.out.println("no data");
                        }
                }
+               */
                System.out.println("StatisticsProt.readLength: total number of dates = " + query.size());
                return query;
        }
@@ -105,6 +97,7 @@ public class StatisticsProt {
                List<Integer> totalTime = new ArrayList<Integer>();
                for (int i = 0; i < nbins; i++)
                        totalTime.add(i, 0);
+               /*
                for (Date date = start.getTime(); !start.after(end); start.add(Calendar.DATE, 1), date = start.getTime()) {
                        List<Integer> timeResult = new ArrayList<Integer>();
                        SliceQuery<Long, String, String> result = HFactory.createSliceQuery(cc.GetKeyspace(), LongSerializer.get(),
@@ -142,6 +135,7 @@ public class StatisticsProt {
                                query.add(db);
                        }
                }
+               */
                DataBase db = new DataBase();
                db.setTimeTotalExec(totalTime);
                query.add(db);
@@ -154,6 +148,7 @@ public class StatisticsProt {
         * */
        public List<DataBase> readProteins(String protIn) {
                query = new ArrayList<DataBase>();
+               /*
                SliceQuery<String, String, String> result = HFactory.createSliceQuery(cc.GetKeyspace(), StringSerializer.get(),
                                StringSerializer.get(), StringSerializer.get());
                result.setColumnFamily("ProteinRow");
@@ -172,6 +167,7 @@ public class StatisticsProt {
                                query.add(db);
                        }
                }
+               */
                return query;
        }
 
@@ -180,11 +176,12 @@ public class StatisticsProt {
         * */
        public List<DataBase> readProtID(int counter) {
                query = new ArrayList<DataBase>();
-               int row_count = 100000000;
+               int row_count = 100;
+               /*
                RangeSlicesQuery<String, String, String> result = HFactory.createRangeSlicesQuery(cc.GetKeyspace(), StringSerializer.get(),
                                StringSerializer.get(), StringSerializer.get());
                result.setColumnFamily("ProteinRow");
-               result.setRange(null, null, false, Integer.MAX_VALUE);
+               result.setRange(null, null, false, 100);
                result.setRowCount(row_count);
                String last_key = null;
                while (true) {
@@ -196,13 +193,14 @@ public class StatisticsProt {
                                Row<String, String, String> row = rowsIterator.next();
                                last_key = row.getKey();
                                List<HColumn<String, String>> clms = row.getColumnSlice().getColumns();
-                               int npred = 0;
-                               for (HColumn<String, String> cln : clms) {
-                                       String name = cln.getName();
-                                       if (name.matches("(.*)jnetpred")) {
-                                               ++npred;
-                                       }
-                               }
+                               //int npred = 0;
+                               //for (HColumn<String, String> cln : clms) {
+                               //      String name = cln.getName();
+                               //      if (name.matches("(.*)jnetpred")) {
+                               //              ++npred;
+                               //      }
+                               //}
+                               int npred = clms.size();
                                if (npred > counter) {
                                        DataBase db = new DataBase();
                                        db.setProt(last_key);
@@ -212,7 +210,7 @@ public class StatisticsProt {
                        }
                        if (rows.getCount() < row_count)
                                break;
-               }
+               }*/
                return query;
        }
 
@@ -222,6 +220,7 @@ public class StatisticsProt {
        public List<DataBase> readPart(String protIn) {
                int row_count = 10000;
                query = new ArrayList<DataBase>();
+               /*
                RangeSlicesQuery<String, String, String> result = HFactory.createRangeSlicesQuery(cc.GetKeyspace(), StringSerializer.get(),
                                StringSerializer.get(), StringSerializer.get());
                result.setColumnFamily("ProteinRow");
@@ -266,6 +265,7 @@ public class StatisticsProt {
                        if (rows.getCount() < row_count)
                                break;
                }
+               */
                return query;
        }
 
@@ -323,6 +323,7 @@ public class StatisticsProt {
         * ???
         */
        public long CountID(String id) {
+               /*
                SliceQuery<String, String, String> sliceQuery = HFactory.createSliceQuery(cc.GetKeyspace(), StringSerializer.get(),
                                StringSerializer.get(), StringSerializer.get());
                sliceQuery.setColumnFamily("ProteinLog").setKey(id).setRange("", "", false, 100);
@@ -333,6 +334,8 @@ public class StatisticsProt {
                long datBeginLong = TimeConvert(datBegin);
                long datEndLong = TimeConvert(datEnd);
                return (datEndLong - datBeginLong) / 1000;
+               */
+               return 0;
        }
 
        /*
@@ -373,6 +376,7 @@ public class StatisticsProt {
        public long earliestDate() {
                ArrayList<Long> dateSort = new ArrayList<Long>();
                int row_count = 10000;
+               /*
                RangeSlicesQuery<Long, String, String> result = HFactory.createRangeSlicesQuery(cc.GetKeyspace(), LongSerializer.get(),
                                StringSerializer.get(), StringSerializer.get());
                result.setColumnFamily("ProteinData");
@@ -391,7 +395,7 @@ public class StatisticsProt {
                        }
                        if (rows.getCount() < row_count)
                                break;
-               }
+               }*/
                Collections.sort(dateSort);
                return dateSort.get(0);
        }