+ * 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) {
+ 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 List<Pair<String, Integer>> ReadProteinDataByCounter(int counter) {
+ final long startTime = System.currentTimeMillis();
+ String com = "SELECT DISTINCT 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());
+ List<Pair<String, Integer>> res = new ArrayList<Pair<String, Integer>>();
+ int c = 0;
+ for (Row r : rows) {
+ String prot = r.getString("Protein");
+
+ }
+ final long endTime = System.currentTimeMillis();
+ System.out.println (c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
+ return res;
+ }
+
+ /*