X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=datadb%2Fcompbio%2Fcassandra%2FCassandraReader.java;h=28641dbfd86d2cf0cb1aa6fe6490b73adb7b9073;hb=1835d87d090291da1db317c27c7463191bfb54c4;hp=250c7053448d2b4d329f6e273f98c67fd2eb64c9;hpb=34b63209df068b7671e40e5b298eb184785c83ac;p=proteocache.git

diff --git a/datadb/compbio/cassandra/CassandraReader.java b/datadb/compbio/cassandra/CassandraReader.java
index 250c705..28641db 100644
--- a/datadb/compbio/cassandra/CassandraReader.java
+++ b/datadb/compbio/cassandra/CassandraReader.java
@@ -73,7 +73,7 @@ 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);
@@ -84,10 +84,10 @@ 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));
 			res.add(structure);
 			++c;
@@ -100,7 +100,7 @@ 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 +111,12 @@ 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;