X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=datadb%2Fcompbio%2Fcassandra%2FCassandraReader.java;fp=datadb%2Fcompbio%2Fcassandra%2FCassandraReader.java;h=1720c48a397eaf2ff6b327edbc19862c9b96b434;hb=c15dbff6d660ba14d41407bebeceda4414f45068;hp=00a9f27f265667b3eaea9de2331f345111cea3f2;hpb=c1ae48e93c766434005e5d5201af8ad23bc0a59b;p=proteocache.git

diff --git a/datadb/compbio/cassandra/CassandraReader.java b/datadb/compbio/cassandra/CassandraReader.java
index 00a9f27..1720c48 100644
--- a/datadb/compbio/cassandra/CassandraReader.java
+++ b/datadb/compbio/cassandra/CassandraReader.java
@@ -11,6 +11,7 @@ import org.apache.log4j.Logger;
 import com.datastax.driver.core.Row;
 import com.datastax.driver.core.Session;
 import com.datastax.driver.core.ResultSet;
+
 import compbio.engine.JobStatus;
 
 public class CassandraReader {
@@ -198,6 +199,40 @@ public class CassandraReader {
 	}
 
 	/*
+	 * getting protein sequence from the db ProteinRow
+	 */
+	public Map<String, String> ReadProtein() {
+		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());
+		Map<String, String> res = new HashMap<String, String>();
+		int c = 0;
+		for (Row r : rows) {
+			String prot = r.getString("Protein");
+			String prediction = findJnetpred(r.getMap("Predictions", String.class, String.class));
+			if (prot != null || prediction != null)	
+				res.put(prot, prediction);
+		}
+		final long endTime = System.currentTimeMillis();
+		System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
+		return res;
+	}
+
+	private String findJnetpred (Map<String,String> pred) {
+		if (pred != null) {
+			if (pred.containsKey("jnetpred")) 
+				return pred.get("jnetpred");
+		}
+		return null;
+	}
+	/*
 	 * getting protein sequences by counter
 	 */
 	public Map<String, Integer> ReadProteinSequenceByCounter() {