From 58c9b97523e2273a316a947d977ca7ddd8b1356a Mon Sep 17 00:00:00 2001
From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Wed, 29 Jan 2014 08:03:26 +0000
Subject: [PATCH] Fi bug for wrong job selection

---
 datadb/compbio/cassandra/CassandraReaderOld.java |   21 +++++++++------------
 server/compbio/statistic/CassandraRequester.java |   16 ++++++++--------
 2 files changed, 17 insertions(+), 20 deletions(-)

diff --git a/datadb/compbio/cassandra/CassandraReaderOld.java b/datadb/compbio/cassandra/CassandraReaderOld.java
index 6055e60..ccd13ed 100644
--- a/datadb/compbio/cassandra/CassandraReaderOld.java
+++ b/datadb/compbio/cassandra/CassandraReaderOld.java
@@ -207,27 +207,24 @@ public class CassandraReaderOld {
 	 * getting protein sequence from the db ProteinRow
 	 */
 	public Map<String, String> ReadProtein() {
-		final long startTime = System.currentTimeMillis();
+		//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();
+		//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;
+		Map<String, String> output = new HashMap<String, String>();
 		for (Row r : rows) {
-			String prot = r.getString("Protein");
+			String protein = r.getString("Protein");
 			String prediction = findJnetpred(r.getMap("Predictions", String.class, String.class));
-			if (prot != null || prediction != null)
-				res.put(prot, prediction);
+			if (protein != null && prediction != null) {
+				output.put(protein, prediction);
+			}
 		}
-		final long endTime = System.currentTimeMillis();
-		System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
-		return res;
+		//final long endTime = System.currentTimeMillis();
+		return output;
 	}
 
 	private String findJnetpred(Map<String, String> pred) {
diff --git a/server/compbio/statistic/CassandraRequester.java b/server/compbio/statistic/CassandraRequester.java
index 1791c0f..1e2d00b 100755
--- a/server/compbio/statistic/CassandraRequester.java
+++ b/server/compbio/statistic/CassandraRequester.java
@@ -201,17 +201,17 @@ public class CassandraRequester {
 	/*
 	 * query: protein feature
 	 */
+
 	public Map<String, String> readProteinsPrediction(String feature, int percent) {
-		Map<String, String> result = db.ReadProtein();
-		;
-		if (result == null)
+		Map<String, String> results = db.ReadProtein();
+		if (results == null)
 			return null;
 		Map<String, String> query = new HashMap<String, String>();
-		for (Map.Entry<String, String> entry : result.entrySet()) {
-			String pred = entry.getValue();
-			if (pred.replaceAll("[^" + feature + "]", "").length() > pred.length() * percent / 100 && (!entry.getKey().equals(""))) {
-				// if (!entry.getKey().equals(""))
-				query.put(entry.getKey(), pred);
+		for (Map.Entry<String, String> entry : results.entrySet()) {
+			String prediction = entry.getValue();
+			String protein = entry.getKey();
+			if (prediction.replaceAll("[^" + feature + "]", "").length() > prediction.length() * percent / 100 && !protein.equals("")) {
+				query.put(protein, prediction);
 			}
 		}
 		return query;
-- 
1.7.10.2