Remove keyspace name from queries

diff --git a/datadb/compbio/cassandra/CassandraNativeConnector.java b/datadb/compbio/cassandra/CassandraNativeConnector.java
index 4ba9377..6e6992d 100644 (file)
--- a/datadb/compbio/cassandra/CassandraNativeConnector.java
+++ b/datadb/compbio/cassandra/CassandraNativeConnector.java
@@ -204,7 +204,7 @@ public class CassandraNativeConnector {
         */
        public List<Pair<String, String>> ReadProteinDataTable() {
                final long startTime = System.currentTimeMillis();
-               String com = "SELECT DataBegin,DataEnd FROM ProteinKeyspace.ProteinLog;";
+               String com = "SELECT DataBegin,DataEnd FROM ProteinLog;";
                System.out.println("Command: " + com);
                ResultSet results = session.execute(com);
                final long queryTime = System.currentTimeMillis();
@@ -228,7 +228,7 @@ public class CassandraNativeConnector {
         */
        public Integer ReadDateTable(long queryDate) {
                final long startTime = System.currentTimeMillis();
-               String com = "SELECT jobtime, JobID FROM ProteinKeyspace.ProteinData WHERE jobtime = " + queryDate + ";";
+               String com = "SELECT jobtime, JobID FROM ProteinData WHERE jobtime = " + queryDate + ";";
                System.out.println("Command: " + com);
                ResultSet results = session.execute(com);
                final long queryTime = System.currentTimeMillis();
@@ -237,7 +237,7 @@ public class CassandraNativeConnector {
                        return 0;
                List<Row> rows = results.all();
                final long endTime = System.currentTimeMillis();
-               System.out.println ("Processing time is " + (endTime - queryTime) + " msec");
+               System.out.println("Processing time is " + (endTime - queryTime) + " msec");
                return rows.size();
        }
 
@@ -246,81 +246,83 @@ public class CassandraNativeConnector {
         */
        public List<StructureProteinPrediction> ReadWholeSequence(String queryProtein) {
                final long startTime = System.currentTimeMillis();
-               String com = "SELECT JobID, Predictions FROM ProteinKeyspace.ProteinRow WHERE Protein = '" + queryProtein + "';";
+               String com = "SELECT JobID, Predictions FROM ProteinRow WHERE Protein = '" + queryProtein + "';";
                System.out.println("Command: " + com);
                ResultSet results = session.execute(com);
                if (results.isExhausted())
                        return null;
                final long queryTime = System.currentTimeMillis();
                List<Row> rows = results.all();
-               System.out.println ("Query time is " + (queryTime - startTime) + " msec");
-               System.out.println (" rows analysed,  " + rows.size());
+               System.out.println("Query time is " + (queryTime - startTime) + " msec");
+               System.out.println(" rows analysed,  " + rows.size());
                List<StructureProteinPrediction> res = new ArrayList<StructureProteinPrediction>();
                int c = 0;
                for (Row r : rows) {
-                       StructureProteinPrediction structure = new StructureProteinPrediction(queryProtein, r.getString("JobID"), r.getMap("Predictions", String.class, String.class));         
+                       StructureProteinPrediction structure = new StructureProteinPrediction(queryProtein, r.getString("JobID"), r.getMap(
+                                       "Predictions", String.class, String.class));
                        res.add(structure);
                        ++c;
                }
                final long endTime = System.currentTimeMillis();
-               System.out.println (c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
+               System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
                return res;
        }
 
        /*
         * getting part of protein sequence from the db ProteinRow
         */
-       public List<StructureProteinPrediction>  ReadPartOfSequence(String queryProtein) {
+       public List<StructureProteinPrediction> ReadPartOfSequence(String queryProtein) {
                final long startTime = System.currentTimeMillis();
-               String com = "SELECT * FROM ProteinKeyspace.ProteinRow;";
+               String com = "SELECT * FROM ProteinRow;";
                System.out.println("Command: " + com);
                ResultSet results = session.execute(com);
                if (results.isExhausted())
                        return null;
                final long queryTime = System.currentTimeMillis();
                List<Row> rows = results.all();
-               System.out.println ("Query time is " + (queryTime - startTime) + " msec");   
-               System.out.println (" rows analysed,  " + rows.size());
-               List<StructureProteinPrediction>  res = new ArrayList<StructureProteinPrediction>();
+               System.out.println("Query time is " + (queryTime - startTime) + " msec");
+               System.out.println(" rows analysed,  " + rows.size());
+               List<StructureProteinPrediction> res = new ArrayList<StructureProteinPrediction>();
                int c = 0;
                for (Row r : rows) {
                        String prot = r.getString("Protein");
                        if (prot.matches("(.*)" + queryProtein + "(.*)")) {
-                               StructureProteinPrediction structure = new StructureProteinPrediction(prot, r.getString("JobID"), r.getMap("Predictions", String.class, String.class));         
+                               StructureProteinPrediction structure = new StructureProteinPrediction(prot, r.getString("JobID"), r.getMap("Predictions",
+                                               String.class, String.class));
                                res.add(structure);
                                ++c;
                        }
                }
                final long endTime = System.currentTimeMillis();
-               System.out.println (c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
+               System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
                return res;
        }
-       
+
        /*
         * getting protein sequences by counter
         */
-       public Map<String, Integer>  ReadProteinDataByCounter() {
+       public Map<String, Integer> ReadProteinDataByCounter() {
                final long startTime = System.currentTimeMillis();
-               String com = "SELECT Protein FROM ProteinKeyspace.ProteinRow;";
+               String com = "SELECT Protein FROM ProteinRow;";
                System.out.println("Command: " + com);
                ResultSet results = session.execute(com);
                if (results.isExhausted())
                        return null;
                final long queryTime = System.currentTimeMillis();
                List<Row> rows = results.all();
-               System.out.println ("Query time is " + (queryTime - startTime) + " msec");   
-               System.out.println (" rows analysed,  " + rows.size());
+               System.out.println("Query time is " + (queryTime - startTime) + " msec");
+               System.out.println(" rows analysed,  " + rows.size());
                Map<String, Integer> res = new HashMap<String, Integer>();
                int c = 0;
                for (Row r : rows) {
                        String protein = r.getString("Protein");
-                       if (res.containsKey(protein)) 
+                       if (res.containsKey(protein))
                                res.put(protein, res.get(protein) + 1);
                        else
                                res.put(protein, 1);
                }
                final long endTime = System.currentTimeMillis();
-               System.out.println (c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
+               System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
                return res;
        }
 
@@ -342,10 +344,11 @@ public class CassandraNativeConnector {
                if (results1.isExhausted())
                        return null;
                Row row1 = results1.one();
-               StructureJobLog res = new StructureJobLog(row.getString("Protein"), row.getString("JobID"), row.getString("DataBegin"), row.getString("DataEnd"), row.getString("ip"), row1.getMap("Predictions", String.class, String.class));
-               System.out.println ("Query time is " + (queryTime - startTime) + " msec");   
+               StructureJobLog res = new StructureJobLog(row.getString("Protein"), row.getString("JobID"), row.getString("DataBegin"),
+                               row.getString("DataEnd"), row.getString("ip"), row1.getMap("Predictions", String.class, String.class));
+               System.out.println("Query time is " + (queryTime - startTime) + " msec");
                final long endTime = System.currentTimeMillis();
-               System.out.println (" rows analysed, execution time is " + (endTime - startTime) + " msec");
+               System.out.println(" rows analysed, execution time is " + (endTime - startTime) + " msec");
                return res;
        }
 
@@ -354,11 +357,11 @@ public class CassandraNativeConnector {
         */
        public long getEarliestDateInDB() {
                final long startTime = System.currentTimeMillis();
-               String com = "SELECT jobtime,JobID FROM ProteinKeyspace.ProteinData;";
+               String com = "SELECT jobtime,JobID FROM ProteinData;";
                System.out.println("Command: " + com);
                ResultSet results = session.execute(com);
                final long queryTime = System.currentTimeMillis();
-               System.out.println ("Query time is  " + (queryTime - startTime) + " msec");
+               System.out.println("Query time is  " + (queryTime - startTime) + " msec");
 
                Calendar cal = Calendar.getInstance();
                long res = cal.getTimeInMillis();
@@ -372,7 +375,7 @@ public class CassandraNativeConnector {
                        ++c;
                }
                final long endTime = System.currentTimeMillis();
-               System.out.println (c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
+               System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
                return res;
        }