X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=server%2Fcompbio%2Fstatistic%2FCassandraRequester.java;h=3e5db8a354f46858bdaab803df8c7f51a4942e37;hb=0e1f92db0e4043bfa93417481274b6461cdb09cd;hp=e95291a61f6fef5c0cbae25488b3878e81fee394;hpb=bf5e83e2959a3b88963cb9a8da68fc50ce4329af;p=proteocache.git

diff --git a/server/compbio/statistic/CassandraRequester.java b/server/compbio/statistic/CassandraRequester.java
index e95291a..3e5db8a 100755
--- a/server/compbio/statistic/CassandraRequester.java
+++ b/server/compbio/statistic/CassandraRequester.java
@@ -5,13 +5,14 @@ import java.text.SimpleDateFormat;
 import java.util.ArrayList;
 import java.util.Calendar;
 import java.util.Date;
+import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
 import compbio.cassandra.DateBean;
 import compbio.cassandra.ProteinBean;
 import compbio.cassandra.CassandraNativeConnector;
-import compbio.cassandra.CassandraReader;
+import compbio.cassandra.CassandraReaderOld;
 import compbio.cassandra.DataBase;
 import compbio.cassandra.Pair;
 import compbio.cassandra.JobBean;
@@ -22,7 +23,7 @@ import compbio.cassandra.UserBean;
 import compbio.engine.JobStatus;
 
 public class CassandraRequester {
-	private CassandraReader db = new CassandraReader();
+	private CassandraReaderOld db = new CassandraReaderOld();
 	private ArrayList<DataBase> query;
 	private static long currentDate = 0;
 	private static long earlestDate = 0;
@@ -121,7 +122,7 @@ public class CassandraRequester {
 	 * query: total number of jobs for the period from date1 till date2
 	 */
 	public TotalJobsStatisticBean countJobs(String date1, String date2) {
-		if (null == date1) {
+	/*	if (null == date1) {
 			date1 = "1970/1/1";
 		}
 		if (null == date2) {
@@ -130,17 +131,16 @@ public class CassandraRequester {
 		if (!isThisDateValid(date1, formatYYMMDD) || !isThisDateValid(date2, formatYYMMDD)) {
 			System.out.println("CassandraRequester.countJobs: wrong format for date1 " + date1 + "or date2 " + date2);
 			return null;
-		}
+		}*/
 		SetDateRange();
 		long dateStart = DateParsing(date1, formatYYMMDD);
 		long dateEnd = DateParsing(date2, formatYYMMDD);
-		if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
+/*		if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
 			return null;
 		if (dateStart < earlestDate)
 			dateStart = earlestDate;
 		if (dateEnd > currentDate)
-			dateStart = currentDate;
-
+			dateStart = currentDate;*/
 		Calendar start = Calendar.getInstance();
 		start.setTime(new Date(dateStart));
 		Calendar end = Calendar.getInstance();
@@ -184,22 +184,40 @@ public class CassandraRequester {
 	/*
 	 * query: protein sequence
 	 */
-	public List<ProteinBean> readProteins(String protIn, String flag) {
+	public List<ProteinBean> readProteins(String protIn, String searchtype) {
 		List<ProteinBean> result;
-		if (flag.equals("whole"))
+		if (searchtype.equals("whole"))
 			result = db.ReadWholeSequence(protIn);
 		else
 			result = db.ReadPartOfSequence(protIn);
 		if (result == null)
 			return null;
 
-		if (flag.equals("part")) {
+		if (searchtype.equals("partial")) {
 			for (ProteinBean entry : result) {
 				entry.setSubProt(CreateSubprot(entry.getSequence(), protIn));
 			}
 		}
 		return result;
 	}
+	
+	/*
+	 * query: protein feature
+	 */
+	public Map<String, String> readProteinsPrediction(String feature, int percent) {
+		Map<String, String> result = db.ReadProtein();;
+		if (result == null)
+			return null;
+		Map<String, String> query = new HashMap<String, String>();
+		for (Map.Entry<String, String> entry : result.entrySet()) {
+			String pred = entry.getValue();			
+			if (pred.replaceAll("[^"+feature+"]", "").length() > pred.length() * percent / 100 && (!entry.getKey().equals(""))) {
+			//	if (!entry.getKey().equals(""))
+					query.put(entry.getKey(), pred);
+			}	
+		}
+		return query;
+	}
 
 	/*
 	 * query protein sequences with number of jobs