+ * getting data from the db ProteinData
+ */
+ public Integer ReadDateTable(long queryDate) {
+ final long startTime = System.currentTimeMillis();
+ 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();
+ System.out.println("Query time is " + (queryTime - startTime) + " msec");
+ if (results.isExhausted())
+ return 0;
+ List<Row> rows = results.all();
+ final long endTime = System.currentTimeMillis();
+ System.out.println("Processing time is " + (endTime - queryTime) + " 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 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) {
+ final long startTime = System.currentTimeMillis();
+ 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>();
+ 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 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;
+ }
+
+ /*