new readers for the queries

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

diff --git a/server/compbio/statistic/CassandraRequester.java b/server/compbio/statistic/CassandraRequester.java
index e95291a..0d2ffc0 100755 (executable)
--- a/server/compbio/statistic/CassandraRequester.java
+++ b/server/compbio/statistic/CassandraRequester.java
@@ -5,24 +5,25 @@ 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.beans.DateBean;
+import compbio.beans.JobBean;
+import compbio.beans.ProteinBean;
+import compbio.beans.Total;
+import compbio.beans.TotalByCounterBean;
+import compbio.beans.TotalJobsStatisticBean;
+import compbio.beans.UserBean;
 import compbio.cassandra.CassandraNativeConnector;
-import compbio.cassandra.CassandraReader;
+import compbio.cassandra.CassandraReaderOld;
 import compbio.cassandra.DataBase;
 import compbio.cassandra.Pair;
-import compbio.cassandra.JobBean;
-import compbio.cassandra.Total;
-import compbio.cassandra.TotalByCounterBean;
-import compbio.cassandra.TotalJobsStatisticBean;
-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;
@@ -119,9 +120,9 @@ 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