X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=datadb%2Fcompbio%2Fcassandra%2FCassandraReader.java;h=6e3587bca084484f3c1b3a45ef96c7a14eddda69;hb=92420f700bca908529b5dc0e0e998dd2a7f98bc2;hp=b5277388275e95d670b0ddbb2b03cba723519dc8;hpb=8a0caa40d0fa288a0ad23f6af2aab1b0de0d50cd;p=proteocache.git

diff --git a/datadb/compbio/cassandra/CassandraReader.java b/datadb/compbio/cassandra/CassandraReader.java
index b527738..6e3587b 100644
--- a/datadb/compbio/cassandra/CassandraReader.java
+++ b/datadb/compbio/cassandra/CassandraReader.java
@@ -97,7 +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);
@@ -108,10 +108,10 @@ 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));
 			if (structure.getPrediction().containsKey("jnetpred"))
 				structure.setJnetpred(structure.getPrediction().get("jnetpred"));
@@ -128,7 +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);
@@ -139,12 +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;