datadb/compbio/cassandra/readers/PredictionReader.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 public class PredictionReader extends CassandraReader {
  11
  12         public PredictionReader() {
  13                 super();
  14         }
  15
  16         /**
  17          * query: protein feature
  18          *
  19          *  @param feature
  20          *      a feature of secondary structure: Helix or Beta Sheet
  21          *
  22          *  @param percent
  23          *      fraction the feature in the protein
  24          *
  25          * @return Map<String, String> to the controller SSFeaturesController
  26          *
  27          **/
  28         public Map<String, String> readProteinsPrediction(String feature, int percent) {
  29                 ResultSet results = CassandraQuery("SELECT * FROM ProteinRow;");
  30                 if (results.isExhausted())
  31                         return null;
  32                 List<Row> rows = results.all();
  33                 Map<String, String> query = new HashMap<String, String>();
  34                 for (Row r : rows) {
  35                         String prot = r.getString("Protein");
  36                         String prediction = findJnetpred(r.getMap("Predictions", String.class, String.class));
  37                         if (prot != null || prediction != null) {
  38                                 if (prediction.replaceAll("[^"+feature+"]", "").length() > prediction.length() * percent / 100) {
  39                                         query.put(prot, prediction);
  40                                 }
  41                         }
  42                 }
  43                 return query;
  44         }
  45
  46         private String findJnetpred (Map<String,String> pred) {
  47                 if (pred != null) {
  48                         if (pred.containsKey("jnetpred"))
  49                                 return pred.get("jnetpred");
  50                 }
  51                 return null;
  52         }
  53 }