X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fclient%2FJws2Client.java;h=eda6533fc8d2d02ed04fd7a52724f729c66b1b89;hb=3644426ec0e9e9ceb798bd426085d8d9dd8dbb56;hp=ec3cf6575b7e21b14e3fb136fc987f7d8e85dad9;hpb=7e625752237ee07e815bfb28048bb0b1193b45c5;p=jabaws.git

diff --git a/webservices/compbio/ws/client/Jws2Client.java b/webservices/compbio/ws/client/Jws2Client.java
index ec3cf65..eda6533 100644
--- a/webservices/compbio/ws/client/Jws2Client.java
+++ b/webservices/compbio/ws/client/Jws2Client.java
@@ -37,10 +37,7 @@ import java.io.OutputStream;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.Arrays;
-import java.util.HashMap;
-import java.util.HashSet;
 import java.util.List;
-import java.util.Map;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 
@@ -53,7 +50,7 @@ import compbio.data.msa.MsaWS;
 import compbio.data.msa.SequenceAnnotation;
 import compbio.data.sequence.Alignment;
 import compbio.data.sequence.FastaSequence;
-import compbio.data.sequence.Score;
+import compbio.data.sequence.ScoreManager;
 import compbio.data.sequence.SequenceUtil;
 import compbio.data.sequence.UnknownFileFormatException;
 import compbio.metadata.JobSubmissionException;
@@ -162,9 +159,9 @@ public class Jws2Client {
 				outStream = System.out;
 			}
 			if (service.getServiceType() == SequenceAnnotation.class) {
-				Map<String, HashSet<Score>> result = analize(inputFile,
+				ScoreManager result = analize(inputFile,
 						((SequenceAnnotation<T>) msaws), preset, customOptions);
-				assert !result.values().isEmpty() : "No Result reported!";
+
 				IOHelper.writeOut(outStream, result);
 			} else {
 				alignment = align(inputFile, (MsaWS<T>) msaws, preset,
@@ -204,12 +201,11 @@ public class Jws2Client {
 	 * @return Set<Score> the conservation scores
 	 * @throws UnknownFileFormatException
 	 */
-	<T> HashMap<String, HashSet<Score>> analize(File file,
-			SequenceAnnotation<T> wsproxy, Preset<T> preset,
-			List<Option<T>> customOptions) {
+	<T> ScoreManager analize(File file, SequenceAnnotation<T> wsproxy,
+			Preset<T> preset, List<Option<T>> customOptions) {
 
 		List<FastaSequence> fastalist = null;
-		HashMap<String, HashSet<Score>> scores = null;
+		ScoreManager scores = null;
 		try {
 			fastalist = SequenceUtil.openInputStream(file.getAbsolutePath());
 			assert !fastalist.isEmpty() : "Input is empty!";
@@ -230,8 +226,6 @@ public class Jws2Client {
 			Thread.sleep(2000);
 
 			scores = wsproxy.getAnnotation(jobId);
-			assert scores != null && !scores.values().isEmpty() : "Scores are NULL for job: "
-					+ jobId;
 
 		} catch (IOException e) {
 			System.err