X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=datadb%2Fcompbio%2Fcassandra%2FCassandraReader.java;h=6e3587bca084484f3c1b3a45ef96c7a14eddda69;hb=92420f700bca908529b5dc0e0e998dd2a7f98bc2;hp=250c7053448d2b4d329f6e273f98c67fd2eb64c9;hpb=1128ff389aa843f434814b4a67fbc3b683683d12;p=proteocache.git

diff --git a/datadb/compbio/cassandra/CassandraReader.java b/datadb/compbio/cassandra/CassandraReader.java
index 250c705..6e3587b 100644
--- a/datadb/compbio/cassandra/CassandraReader.java
+++ b/datadb/compbio/cassandra/CassandraReader.java
@@ -51,6 +51,30 @@ public class CassandraReader {
 	}
 
 	/*
+	 * getting data from the db
+	 */
+	public List<Pair<String, String>> ReadProteinData(long day) {
+		final long startTime = System.currentTimeMillis();
+		String com = "SELECT JobID, Protein FROM ProteinData WHERE jobtime = " + day + ";";
+		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");
+		List<Pair<String, String>> res = new ArrayList<Pair<String, String>>();
+		int c = 0;
+		for (Row r : rows) {
+			Pair<String, String> pair = new Pair<String, String>(r.getString("JobID"), r.getString("Protein"));
+			res.add(pair);
+			++c;
+		}
+		final long endTime = System.currentTimeMillis();
+		System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
+		return res;
+	}
+	/*
 	 * getting data from the db JobDateInfo
 	 */
 	public List<Long> ReadDateTable(long queryDate) {
@@ -73,7 +97,7 @@ public class CassandraReader {
 	/*
 	 * getting whole protein sequence from the db ProteinRow
 	 */
-	public List<StructureProteinPrediction> ReadWholeSequence(String queryProtein) {
+	public List<AnnotatedProteinSequenceBean> ReadWholeSequence(String queryProtein) {
 		final long startTime = System.currentTimeMillis();
 		String com = "SELECT JobID, Predictions FROM ProteinRow WHERE Protein = '" + queryProtein + "';";
 		System.out.println("Command: " + com);
@@ -84,11 +108,15 @@ public class CassandraReader {
 		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>();
+		List<AnnotatedProteinSequenceBean> res = new ArrayList<AnnotatedProteinSequenceBean>();
 		int c = 0;
 		for (Row r : rows) {
-			StructureProteinPrediction structure = new StructureProteinPrediction(queryProtein, r.getString("JobID"), r.getMap(
+			AnnotatedProteinSequenceBean structure = new AnnotatedProteinSequenceBean(queryProtein, r.getString("JobID"), r.getMap(
 					"Predictions", String.class, String.class));
+			if (structure.getPrediction().containsKey("jnetpred"))
+				structure.setJnetpred(structure.getPrediction().get("jnetpred"));
+			else
+				structure.setJnetpred("");
 			res.add(structure);
 			++c;
 		}
@@ -100,7 +128,7 @@ public class CassandraReader {
 	/*
 	 * getting part of protein sequence from the db ProteinRow
 	 */
-	public List<StructureProteinPrediction> ReadPartOfSequence(String queryProtein) {
+	public List<AnnotatedProteinSequenceBean> ReadPartOfSequence(String queryProtein) {
 		final long startTime = System.currentTimeMillis();
 		String com = "SELECT * FROM ProteinRow;";
 		System.out.println("Command: " + com);
@@ -111,12 +139,12 @@ public class CassandraReader {
 		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>();
+		List<AnnotatedProteinSequenceBean> res = new ArrayList<AnnotatedProteinSequenceBean>();
 		int c = 0;
 		for (Row r : rows) {
 			String prot = r.getString("Protein");
 			if (prot.matches("(.*)" + queryProtein + "(.*)")) {
-				StructureProteinPrediction structure = new StructureProteinPrediction(prot, r.getString("JobID"), r.getMap("Predictions",
+				AnnotatedProteinSequenceBean structure = new AnnotatedProteinSequenceBean(prot, r.getString("JobID"), r.getMap("Predictions",
 						String.class, String.class));
 				res.add(structure);
 				++c;
@@ -157,7 +185,7 @@ public class CassandraReader {
 	}
 
 	/*
-	 * getting protein sequences by counter
+	 * getting log info for jobid
 	 */
 	public StructureJobLog ReadJobLog(String jobid) {
 		final long startTime = System.currentTimeMillis();