datadb/compbio/cassandra/readers/FeaturesReader.java

   1 package compbio.cassandra.readers;
   2
   3 import java.util.HashMap;
   4 import java.util.List;
   5 import java.util.Map;
   6
   7 import com.datastax.driver.core.ResultSet;
   8 import com.datastax.driver.core.Row;
   9
  10
  11 public class FeaturesReader extends CassandraReader {
  12
  13         public FeaturesReader() {
  14                 super();
  15         }
  16
  17         /**
  18          * query protein feature
  19          *
  20          * @param feature
  21          *                      protein SS feature
  22          *
  23          * @param percent
  24          *                      percent SS feature in protein sequence
  25          *
  26          * @return UserBean to the controller SSFeaturesController
  27          **/
  28
  29          public Map<String, String> readProteinsPrediction(String feature, int percent) {
  30                  ResultSet results = CassandraQuery("SELECT * FROM ProteinRow;");
  31                  if (results.isExhausted())
  32                                 return null;
  33                 List<Row> rows = results.all();
  34                 Map<String, String> query = new HashMap<String, String>();
  35                 for (Row r : rows) {
  36                         String prot = r.getString("Protein");
  37                         String prediction = findJnetpred(r.getMap("Predictions", String.class, String.class));
  38                         if (prot != null && prediction != null && (!prot.equals(""))) {
  39                                 if (prediction.replaceAll("[^" + feature + "]", "").length() > prediction.length() * percent / 100 ) {
  40                                         query.put(prot, prediction);
  41                                 }
  42                         }
  43                 }
  44                 return query;
  45         }
  46
  47
  48         private String findJnetpred(Map<String, String> pred) {
  49                 if (pred != null) {
  50                         if (pred.containsKey("jnetpred"))
  51                                 return pred.get("jnetpred");
  52                 }
  53                 return null;
  54         }
  55
  56
  57 }