-
- /*
- * 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 + "(.*)")) {
- // System.out.println(prot);
- 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 protein sequences by counter
- */
- public StructureJobLog ReadJobLog(String jobid) {
- final long startTime = System.currentTimeMillis();
- String com = "SELECT * FROM ProteinKeyspace.ProteinLog WHERE JobID = '" + jobid + "';";
- System.out.println("Command: " + com);
- ResultSet results = session.execute(com);
- if (results.isExhausted())
- return null;
- final long queryTime = System.currentTimeMillis();
- Row row = results.one();
- String com1 = "SELECT * FROM ProteinKeyspace.ProteinRow WHERE JobID = '" + jobid + "' ALLOW FILTERING;";
- System.out.println("Command: " + com1);
- ResultSet results1 = session.execute(com1);
- 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");
- final long endTime = System.currentTimeMillis();
- System.out.println (" rows analysed, execution time is " + (endTime - startTime) + " msec");
- return res;
- }
-
- /*
- * getting earlest date of jobs from the db
- */
- public long getEarliestDateInDB() {
- final long startTime = System.currentTimeMillis();
- String com = "SELECT jobtime,JobID FROM ProteinKeyspace.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");