X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=server%2Fcompbio%2Fstatistic%2FStatisticsProt.java;h=05375c094c7640ce53f343110b900c1d3de4fc84;hb=1835d87d090291da1db317c27c7463191bfb54c4;hp=c0150b734847637d4733cf60a5465b1095152130;hpb=91a82ea55a1ed4aa913fb9a0d6fdbfe897bb50ad;p=proteocache.git

diff --git a/server/compbio/statistic/StatisticsProt.java b/server/compbio/statistic/StatisticsProt.java
index c0150b7..05375c0 100755
--- 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);
 	}