Fix problems with Natasha's code

[proteocache.git] / datadb / compbio / cassandra / CassandraNativeConnector.java

diff --git a/datadb/compbio/cassandra/CassandraNativeConnector.java b/datadb/compbio/cassandra/CassandraNativeConnector.java
index 8e86624..4ba9377 100644 (file)
--- a/datadb/compbio/cassandra/CassandraNativeConnector.java
+++ b/datadb/compbio/cassandra/CassandraNativeConnector.java
@@ -268,121 +268,6 @@ public class CassandraNativeConnector {
        }
 
        /*
-        * getting data from the db ProteinData
-        */
-       public Integer ReadDateTable(long queryDate) {
-               final long startTime = System.currentTimeMillis();
-               String com = "SELECT jobtime, JobID FROM ProteinKeyspace.ProteinData WHERE jobtime = " + queryDate + ";";
-               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");
-               return rows.size();
-       }
-
-       /*
-        * getting part of protein sequence from the db ProteinRow
-        */
-       public List<StructureProteinPrediction>  ReadPartOfSequence(String queryProtein) {
-               final long startTime = System.currentTimeMillis();
-               String com = "SELECT * FROM ProteinKeyspace.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>();
-               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));         
-                               res.add(structure);
-                               ++c;
-                       }
-               }
-               final long endTime = System.currentTimeMillis();
-               System.out.println (c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
-               return res;
-       }
-
-       /*
-        * getting protein sequences by counter
-        */
-       public Map<String, Integer>  ReadProteinDataByCounter() {
-               final long startTime = System.currentTimeMillis();
-               String com = "SELECT Protein FROM ProteinKeyspace.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());
-               Map<String, Integer> res = new HashMap<String, Integer>();
-               int c = 0;
-               for (Row r : rows) {
-                       String protein = r.getString("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");
-               return res;
-       }
-       
-       /*
-        * getting data from the db ProteinData
-        */
-       public Integer ReadDateTable(long queryDate) {
-               final long startTime = System.currentTimeMillis();
-               String com = "SELECT jobtime, JobID FROM ProteinKeyspace.ProteinData WHERE jobtime = " + queryDate + ";";
-               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");        
-               return rows.size();
-       }
-
-       /*
-        * getting whole protein sequence from the db ProteinRow
-        */
-       public List<StructureProteinPrediction> ReadWholeSequence(String queryProtein) {
-               final long startTime = System.currentTimeMillis();
-               String com = "SELECT JobID, Predictions FROM ProteinKeyspace.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());
-               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));         
-                       res.add(structure);
-                       ++c;
-               }
-               final long endTime = System.currentTimeMillis();
-               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) {
@@ -464,7 +349,7 @@ public class CassandraNativeConnector {
                return res;
        }
 
-
+       /*
         * getting earlest date of jobs from the db
         */
        public long getEarliestDateInDB() {