From: Daniel Barton <daluke.barton@gmail.com>
Date: Thu, 22 Aug 2013 13:00:35 +0000 (+0100)
Subject: Import RNAalifold removed from RNAStructReader. @XmlSeeAlso line added
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8116c0444fe98e8eb21bcdd8ded06e1429085823;p=jabaws.git

Import RNAalifold removed from RNAStructReader. @XmlSeeAlso line added
to ScoreManager.
---

diff --git a/datamodel/compbio/data/sequence/RNAStructReader.java b/datamodel/compbio/data/sequence/RNAStructReader.java
index 7ebba4c..5eec46f 100644
--- a/datamodel/compbio/data/sequence/RNAStructReader.java
+++ b/datamodel/compbio/data/sequence/RNAStructReader.java
@@ -13,8 +13,6 @@ import java.util.regex.Pattern;
 
 import org.apache.log4j.Logger;
 
-import compbio.runner.structure.RNAalifold;
-
 // Utility class for reading alifold output
 
 public class RNAStructReader {
@@ -157,7 +155,7 @@ public class RNAStructReader {
 		return new RNAStructScoreManager(structs, data);
 	}
 	
-	// Just for the purpose of creating nee TreeSet<Score> objects of length one
+	// Just for the purpose of creating new TreeSet<Score> objects of length one
 	// for adding to a 'data' list to make a ScoreManager
 	private static TreeSet<Score> newSetScore(Enum<?> res, List<Float> scores) {
 		// first convert List<Float> to float[]
diff --git a/datamodel/compbio/data/sequence/RNAStructScoreManager.java b/datamodel/compbio/data/sequence/RNAStructScoreManager.java
index e792969..d2da2e1 100644
--- a/datamodel/compbio/data/sequence/RNAStructScoreManager.java
+++ b/datamodel/compbio/data/sequence/RNAStructScoreManager.java
@@ -28,6 +28,7 @@ public class RNAStructScoreManager extends ScoreManager {
 	
 
 	public RNAStructScoreManager(List<String> structs, List<TreeSet<Score>> data) {
+		
 		assert(structs.size() == data.size());
 		
 		List<ScoreHolder> seqScores = new ArrayList<ScoreHolder>();
@@ -57,6 +58,7 @@ public class RNAStructScoreManager extends ScoreManager {
 			data.add(sch.scores);
 		}
 		return data;
+		
 	}
 
 	// Send this data Structure back to something approximating the stdoutFile
diff --git a/datamodel/compbio/data/sequence/ScoreManager.java b/datamodel/compbio/data/sequence/ScoreManager.java
index 9b1803d..3c1bc21 100644
--- a/datamodel/compbio/data/sequence/ScoreManager.java
+++ b/datamodel/compbio/data/sequence/ScoreManager.java
@@ -28,8 +28,10 @@ import java.util.TreeSet;
 
 import javax.xml.bind.annotation.XmlAccessType;
 import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlSeeAlso;
 import javax.xml.bind.annotation.XmlTransient;
 
+@XmlSeeAlso({RNAStructScoreManager.class})
 @XmlAccessorType(XmlAccessType.FIELD)
 public class ScoreManager {
 
@@ -49,6 +51,9 @@ public class ScoreManager {
 	}
 
 	private ScoreManager(Map<String, Set<Score>> data) {
+		System.out.println("A ScoreManager was created!!");
+
+		
 		List<ScoreHolder> seqScores = new ArrayList<ScoreHolder>();
 		for (Map.Entry<String, Set<Score>> singleSeqScores : data.entrySet()) {
 			seqScores.add(new ScoreHolder(singleSeqScores.getKey(),
@@ -58,11 +63,18 @@ public class ScoreManager {
 	}
 
 	public static ScoreManager newInstance(Map<String, Set<Score>> data) {
+		System.out.println("A ScoreManager was created!!");
+
+		
 		return new ScoreManager(data);
 	}
 
 	public static ScoreManager newInstanceSingleScore(
 			Map<String, Score> seqScoresMap) {
+		
+		System.out.println("A ScoreManager was created!!");
+
+		
 		Map<String, Set<Score>> multipleScoresMap = new TreeMap<String, Set<Score>>();
 		for (Map.Entry<String, Score> seqScore : seqScoresMap.entrySet()) {
 			Set<Score> scores = new TreeSet<Score>();
@@ -73,6 +85,9 @@ public class ScoreManager {
 	}
 
 	public static ScoreManager newInstanceSingleSequence(Set<Score> data) {
+		System.out.println("A ScoreManager was created!!");
+
+		
 		return new ScoreManager(ScoreManager.SINGLE_ENTRY_KEY,
 				new TreeSet(data));
 	}
diff --git a/testsrc/compbio/ws/client/TestRNAalifoldWS.java b/testsrc/compbio/ws/client/TestRNAalifoldWS.java
index fd8fb9b..5452c4e 100644
--- a/testsrc/compbio/ws/client/TestRNAalifoldWS.java
+++ b/testsrc/compbio/ws/client/TestRNAalifoldWS.java
@@ -27,6 +27,7 @@ import compbio.data.sequence.Alignment;
 import compbio.data.sequence.ClustalAlignmentUtil;
 import compbio.data.sequence.ConservationMethod;
 import compbio.data.sequence.FastaSequence;
+import compbio.data.sequence.RNAStructScoreManager;
 import compbio.data.sequence.ScoreManager;
 import compbio.data.sequence.SequenceUtil;
 import compbio.data.sequence.UnknownFileFormatException;
@@ -40,6 +41,7 @@ import compbio.metadata.RunnerConfig;
 import compbio.metadata.UnsupportedRuntimeException;
 import compbio.metadata.WrongParameterException;
 import compbio.runner.conservation.AACon;
+import compbio.runner.structure.RNAalifold;
 import compbio.util.SysPrefs;
 import compbio.ws.server.RNAalifoldWS;
 
@@ -47,6 +49,7 @@ import compbio.ws.server.RNAalifoldWS;
 public class TestRNAalifoldWS {
 	
 	SequenceAnnotation<RNAalifoldWS> foldws;
+//	RNAalifoldWS foldws;
 	
 	@BeforeTest(groups = {AllTestSuit.test_group_webservices})
 	void initConnection() {
@@ -54,6 +57,7 @@ public class TestRNAalifoldWS {
 		try {
 			JABAService client = Jws2Client.connect(
 					"http://localhost:8080/jabaws", Services.RNAalifoldWS);
+//			foldws = (RNAalifoldWS) client;
 			foldws = (SequenceAnnotation<RNAalifoldWS>) client;
 		} catch (ConnectException e) {
 			e.printStackTrace();
@@ -69,6 +73,7 @@ public class TestRNAalifoldWS {
 	public void testFold() throws FileNotFoundException, IOException,
 			UnknownFileFormatException {
 		
+		
 //		String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
 //				+ File.separator;
 		
@@ -87,7 +92,10 @@ public class TestRNAalifoldWS {
 			
 			String jobId = foldws.customAnalize(fsl, options);
 			System.out.println("J: " + jobId);
-			ScoreManager result = foldws.getAnnotation(jobId);
+			RNAStructScoreManager result = (RNAStructScoreManager)foldws.getAnnotation(jobId);
+
+			
+			// standard and RNAStruct specific ways of formatting scoremanager
 			System.out.println("fold results: \n" + result.toString());
 			
 			Writer writer = new OutputStreamWriter(System.out);
diff --git a/webservices/compbio/data/msa/jaxws/CancelJob.java b/webservices/compbio/data/msa/jaxws/CancelJob.java
index 32660d9..9b1f062 100644
--- a/webservices/compbio/data/msa/jaxws/CancelJob.java
+++ b/webservices/compbio/data/msa/jaxws/CancelJob.java
@@ -7,9 +7,9 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
-@XmlRootElement(name = "cancelJob", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlRootElement(name = "cancelJob", namespace = "http://msa.data.compbio/01/12/2010/")
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "cancelJob", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlType(name = "cancelJob", namespace = "http://msa.data.compbio/01/12/2010/")
 public class CancelJob {
 
     @XmlElement(name = "jobId", namespace = "")
diff --git a/webservices/compbio/data/msa/jaxws/CancelJobResponse.java b/webservices/compbio/data/msa/jaxws/CancelJobResponse.java
index 7ccc190..00a92e2 100644
--- a/webservices/compbio/data/msa/jaxws/CancelJobResponse.java
+++ b/webservices/compbio/data/msa/jaxws/CancelJobResponse.java
@@ -7,9 +7,9 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
-@XmlRootElement(name = "cancelJobResponse", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlRootElement(name = "cancelJobResponse", namespace = "http://msa.data.compbio/01/12/2010/")
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "cancelJobResponse", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlType(name = "cancelJobResponse", namespace = "http://msa.data.compbio/01/12/2010/")
 public class CancelJobResponse {
 
     @XmlElement(name = "return", namespace = "")
diff --git a/webservices/compbio/data/msa/jaxws/GetJobStatus.java b/webservices/compbio/data/msa/jaxws/GetJobStatus.java
index 5fd70f5..438b3a0 100644
--- a/webservices/compbio/data/msa/jaxws/GetJobStatus.java
+++ b/webservices/compbio/data/msa/jaxws/GetJobStatus.java
@@ -7,9 +7,9 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
-@XmlRootElement(name = "getJobStatus", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlRootElement(name = "getJobStatus", namespace = "http://msa.data.compbio/01/12/2010/")
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "getJobStatus", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlType(name = "getJobStatus", namespace = "http://msa.data.compbio/01/12/2010/")
 public class GetJobStatus {
 
     @XmlElement(name = "jobId", namespace = "")
diff --git a/webservices/compbio/data/msa/jaxws/GetJobStatusResponse.java b/webservices/compbio/data/msa/jaxws/GetJobStatusResponse.java
index 0f8ba68..0f81c39 100644
--- a/webservices/compbio/data/msa/jaxws/GetJobStatusResponse.java
+++ b/webservices/compbio/data/msa/jaxws/GetJobStatusResponse.java
@@ -7,9 +7,9 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
-@XmlRootElement(name = "getJobStatusResponse", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlRootElement(name = "getJobStatusResponse", namespace = "http://msa.data.compbio/01/12/2010/")
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "getJobStatusResponse", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlType(name = "getJobStatusResponse", namespace = "http://msa.data.compbio/01/12/2010/")
 public class GetJobStatusResponse {
 
     @XmlElement(name = "return", namespace = "")
diff --git a/webservices/compbio/data/msa/jaxws/GetLimit.java b/webservices/compbio/data/msa/jaxws/GetLimit.java
index 6b04bc0..64514ba 100644
--- a/webservices/compbio/data/msa/jaxws/GetLimit.java
+++ b/webservices/compbio/data/msa/jaxws/GetLimit.java
@@ -7,9 +7,9 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
-@XmlRootElement(name = "getLimit", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlRootElement(name = "getLimit", namespace = "http://msa.data.compbio/01/12/2010/")
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "getLimit", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlType(name = "getLimit", namespace = "http://msa.data.compbio/01/12/2010/")
 public class GetLimit {
 
     @XmlElement(name = "presetName", namespace = "")
diff --git a/webservices/compbio/data/msa/jaxws/GetLimitResponse.java b/webservices/compbio/data/msa/jaxws/GetLimitResponse.java
index 249e7e4..8147fa6 100644
--- a/webservices/compbio/data/msa/jaxws/GetLimitResponse.java
+++ b/webservices/compbio/data/msa/jaxws/GetLimitResponse.java
@@ -7,9 +7,9 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
-@XmlRootElement(name = "getLimitResponse", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlRootElement(name = "getLimitResponse", namespace = "http://msa.data.compbio/01/12/2010/")
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "getLimitResponse", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlType(name = "getLimitResponse", namespace = "http://msa.data.compbio/01/12/2010/")
 public class GetLimitResponse {
 
     @XmlElement(name = "return", namespace = "")
diff --git a/webservices/compbio/data/msa/jaxws/GetLimits.java b/webservices/compbio/data/msa/jaxws/GetLimits.java
index b8668d9..152f72e 100644
--- a/webservices/compbio/data/msa/jaxws/GetLimits.java
+++ b/webservices/compbio/data/msa/jaxws/GetLimits.java
@@ -6,9 +6,9 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
-@XmlRootElement(name = "getLimits", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlRootElement(name = "getLimits", namespace = "http://msa.data.compbio/01/12/2010/")
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "getLimits", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlType(name = "getLimits", namespace = "http://msa.data.compbio/01/12/2010/")
 public class GetLimits {
 
 
diff --git a/webservices/compbio/data/msa/jaxws/GetLimitsResponse.java b/webservices/compbio/data/msa/jaxws/GetLimitsResponse.java
index f503c23..8bb6cc9 100644
--- a/webservices/compbio/data/msa/jaxws/GetLimitsResponse.java
+++ b/webservices/compbio/data/msa/jaxws/GetLimitsResponse.java
@@ -7,9 +7,9 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
-@XmlRootElement(name = "getLimitsResponse", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlRootElement(name = "getLimitsResponse", namespace = "http://msa.data.compbio/01/12/2010/")
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "getLimitsResponse", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlType(name = "getLimitsResponse", namespace = "http://msa.data.compbio/01/12/2010/")
 public class GetLimitsResponse {
 
     @XmlElement(name = "return", namespace = "")
diff --git a/webservices/compbio/data/msa/jaxws/GetPresets.java b/webservices/compbio/data/msa/jaxws/GetPresets.java
index 2e57fb8..04d5d12 100644
--- a/webservices/compbio/data/msa/jaxws/GetPresets.java
+++ b/webservices/compbio/data/msa/jaxws/GetPresets.java
@@ -6,9 +6,9 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
-@XmlRootElement(name = "getPresets", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlRootElement(name = "getPresets", namespace = "http://msa.data.compbio/01/12/2010/")
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "getPresets", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlType(name = "getPresets", namespace = "http://msa.data.compbio/01/12/2010/")
 public class GetPresets {
 
 
diff --git a/webservices/compbio/data/msa/jaxws/GetPresetsResponse.java b/webservices/compbio/data/msa/jaxws/GetPresetsResponse.java
index ad2942b..7755793 100644
--- a/webservices/compbio/data/msa/jaxws/GetPresetsResponse.java
+++ b/webservices/compbio/data/msa/jaxws/GetPresetsResponse.java
@@ -7,9 +7,9 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
-@XmlRootElement(name = "getPresetsResponse", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlRootElement(name = "getPresetsResponse", namespace = "http://msa.data.compbio/01/12/2010/")
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "getPresetsResponse", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlType(name = "getPresetsResponse", namespace = "http://msa.data.compbio/01/12/2010/")
 public class GetPresetsResponse {
 
     @XmlElement(name = "return", namespace = "")
diff --git a/webservices/compbio/data/msa/jaxws/GetResultResponse.java b/webservices/compbio/data/msa/jaxws/GetResultResponse.java
index bbf4468..d8596b0 100644
--- a/webservices/compbio/data/msa/jaxws/GetResultResponse.java
+++ b/webservices/compbio/data/msa/jaxws/GetResultResponse.java
@@ -13,14 +13,14 @@ import javax.xml.bind.annotation.XmlType;
 public class GetResultResponse {
 
     @XmlElement(name = "return", namespace = "")
-    private compbio.data.sequence.RNAstruct _return;
+    private compbio.data.sequence.Alignment _return;
 
     /**
      * 
      * @return
-     *     returns RNAstruct
+     *     returns Alignment
      */
-    public compbio.data.sequence.RNAstruct getReturn() {
+    public compbio.data.sequence.Alignment getReturn() {
         return this._return;
     }
 
@@ -29,7 +29,7 @@ public class GetResultResponse {
      * @param _return
      *     the value for the _return property
      */
-    public void setReturn(compbio.data.sequence.RNAstruct _return) {
+    public void setReturn(compbio.data.sequence.Alignment _return) {
         this._return = _return;
     }
 
diff --git a/webservices/compbio/data/msa/jaxws/GetRunnerOptions.java b/webservices/compbio/data/msa/jaxws/GetRunnerOptions.java
index 9128b3f..9d59cd3 100644
--- a/webservices/compbio/data/msa/jaxws/GetRunnerOptions.java
+++ b/webservices/compbio/data/msa/jaxws/GetRunnerOptions.java
@@ -6,9 +6,9 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
-@XmlRootElement(name = "getRunnerOptions", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlRootElement(name = "getRunnerOptions", namespace = "http://msa.data.compbio/01/12/2010/")
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "getRunnerOptions", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlType(name = "getRunnerOptions", namespace = "http://msa.data.compbio/01/12/2010/")
 public class GetRunnerOptions {
 
 
diff --git a/webservices/compbio/data/msa/jaxws/GetRunnerOptionsResponse.java b/webservices/compbio/data/msa/jaxws/GetRunnerOptionsResponse.java
index fb467ca..2278aa2 100644
--- a/webservices/compbio/data/msa/jaxws/GetRunnerOptionsResponse.java
+++ b/webservices/compbio/data/msa/jaxws/GetRunnerOptionsResponse.java
@@ -7,9 +7,9 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
-@XmlRootElement(name = "getRunnerOptionsResponse", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlRootElement(name = "getRunnerOptionsResponse", namespace = "http://msa.data.compbio/01/12/2010/")
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "getRunnerOptionsResponse", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlType(name = "getRunnerOptionsResponse", namespace = "http://msa.data.compbio/01/12/2010/")
 public class GetRunnerOptionsResponse {
 
     @XmlElement(name = "return", namespace = "")
diff --git a/webservices/compbio/data/msa/jaxws/JobSubmissionExceptionBean.java b/webservices/compbio/data/msa/jaxws/JobSubmissionExceptionBean.java
index a916bce..869aea5 100644
--- a/webservices/compbio/data/msa/jaxws/JobSubmissionExceptionBean.java
+++ b/webservices/compbio/data/msa/jaxws/JobSubmissionExceptionBean.java
@@ -13,9 +13,9 @@ import javax.xml.bind.annotation.XmlType;
  * Generated source version: 2.2.3
  * 
  */
-@XmlRootElement(name = "JobSubmissionException", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlRootElement(name = "JobSubmissionException", namespace = "http://msa.data.compbio/01/12/2010/")
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "JobSubmissionException", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlType(name = "JobSubmissionException", namespace = "http://msa.data.compbio/01/12/2010/")
 public class JobSubmissionExceptionBean {
 
     private String message;
diff --git a/webservices/compbio/data/msa/jaxws/LimitExceededExceptionBean.java b/webservices/compbio/data/msa/jaxws/LimitExceededExceptionBean.java
index 0ddadef..9e63199 100644
--- a/webservices/compbio/data/msa/jaxws/LimitExceededExceptionBean.java
+++ b/webservices/compbio/data/msa/jaxws/LimitExceededExceptionBean.java
@@ -13,9 +13,9 @@ import javax.xml.bind.annotation.XmlType;
  * Generated source version: 2.2.3
  * 
  */
-@XmlRootElement(name = "LimitExceededException", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlRootElement(name = "LimitExceededException", namespace = "http://msa.data.compbio/01/12/2010/")
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "LimitExceededException", namespace = "http://msa.data.compbio/01/01/2010/", propOrder = {
+@XmlType(name = "LimitExceededException", namespace = "http://msa.data.compbio/01/12/2010/", propOrder = {
     "actualNumberofSequences",
     "message",
     "numberOfSequencesAllowed",
diff --git a/webservices/compbio/data/msa/jaxws/PullExecStatistics.java b/webservices/compbio/data/msa/jaxws/PullExecStatistics.java
index db1be6e..7ab918b 100644
--- a/webservices/compbio/data/msa/jaxws/PullExecStatistics.java
+++ b/webservices/compbio/data/msa/jaxws/PullExecStatistics.java
@@ -7,9 +7,9 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
-@XmlRootElement(name = "pullExecStatistics", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlRootElement(name = "pullExecStatistics", namespace = "http://msa.data.compbio/01/12/2010/")
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "pullExecStatistics", namespace = "http://msa.data.compbio/01/01/2010/", propOrder = {
+@XmlType(name = "pullExecStatistics", namespace = "http://msa.data.compbio/01/12/2010/", propOrder = {
     "jobId",
     "position"
 })
diff --git a/webservices/compbio/data/msa/jaxws/PullExecStatisticsResponse.java b/webservices/compbio/data/msa/jaxws/PullExecStatisticsResponse.java
index 068b404..ef36b8d 100644
--- a/webservices/compbio/data/msa/jaxws/PullExecStatisticsResponse.java
+++ b/webservices/compbio/data/msa/jaxws/PullExecStatisticsResponse.java
@@ -7,9 +7,9 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
-@XmlRootElement(name = "pullExecStatisticsResponse", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlRootElement(name = "pullExecStatisticsResponse", namespace = "http://msa.data.compbio/01/12/2010/")
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "pullExecStatisticsResponse", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlType(name = "pullExecStatisticsResponse", namespace = "http://msa.data.compbio/01/12/2010/")
 public class PullExecStatisticsResponse {
 
     @XmlElement(name = "return", namespace = "")
diff --git a/webservices/compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.java b/webservices/compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.java
index 4561f5f..79f413a 100644
--- a/webservices/compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.java
+++ b/webservices/compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.java
@@ -13,9 +13,9 @@ import javax.xml.bind.annotation.XmlType;
  * Generated source version: 2.2.3
  * 
  */
-@XmlRootElement(name = "ResultNotAvailableException", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlRootElement(name = "ResultNotAvailableException", namespace = "http://msa.data.compbio/01/12/2010/")
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "ResultNotAvailableException", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlType(name = "ResultNotAvailableException", namespace = "http://msa.data.compbio/01/12/2010/")
 public class ResultNotAvailableExceptionBean {
 
     private String message;
diff --git a/webservices/compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.java b/webservices/compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.java
index 6927cf6..b349081 100644
--- a/webservices/compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.java
+++ b/webservices/compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.java
@@ -13,9 +13,9 @@ import javax.xml.bind.annotation.XmlType;
  * Generated source version: 2.2.3
  * 
  */
-@XmlRootElement(name = "UnsupportedRuntimeException", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlRootElement(name = "UnsupportedRuntimeException", namespace = "http://msa.data.compbio/01/12/2010/")
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "UnsupportedRuntimeException", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlType(name = "UnsupportedRuntimeException", namespace = "http://msa.data.compbio/01/12/2010/")
 public class UnsupportedRuntimeExceptionBean {
 
     private String message;
diff --git a/webservices/compbio/data/msa/jaxws/WrongParameterExceptionBean.java b/webservices/compbio/data/msa/jaxws/WrongParameterExceptionBean.java
index beb4d07..630d8a5 100644
--- a/webservices/compbio/data/msa/jaxws/WrongParameterExceptionBean.java
+++ b/webservices/compbio/data/msa/jaxws/WrongParameterExceptionBean.java
@@ -13,9 +13,9 @@ import javax.xml.bind.annotation.XmlType;
  * Generated source version: 2.2.3
  * 
  */
-@XmlRootElement(name = "WrongParameterException", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlRootElement(name = "WrongParameterException", namespace = "http://msa.data.compbio/01/12/2010/")
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "WrongParameterException", namespace = "http://msa.data.compbio/01/01/2010/")
+@XmlType(name = "WrongParameterException", namespace = "http://msa.data.compbio/01/12/2010/")
 public class WrongParameterExceptionBean {
 
     private String message;
diff --git a/webservices/compbio/ws/server/RNAalifoldWS.java b/webservices/compbio/ws/server/RNAalifoldWS.java
index d640e27..b07882a 100644
--- a/webservices/compbio/ws/server/RNAalifoldWS.java
+++ b/webservices/compbio/ws/server/RNAalifoldWS.java
@@ -31,17 +31,8 @@ public class RNAalifoldWS extends SequenceAnnotationService<RNAalifold>
 	public RNAalifoldWS() {
 		super (new RNAalifold(), log);
 	}
-
-	
-//	// for testing
-//	@Override
-//	public RNAStructScoreManager getAnnotation(String jobId) 
-//			throws ResultNotAvailableException {
-//		return WSUtil.getAnnotation(jobId, log);
-//	}
-	
 	
-	// Only purpose of Overrides is to replace "analize" with "fold" method 
+	// Only purpose is to replace "analize" with "fold" method 
 	// so that a clustal input file and not fasta will be generated
 	@Override
 	public String analize(List<FastaSequence> sequences)
@@ -53,7 +44,7 @@ public class RNAalifoldWS extends SequenceAnnotationService<RNAalifold>
 				getLimit(""));
 	}
 
-	// Only purpose of Overrides is to replace "analize" with "fold" method 
+	// Only purpose is to replace "analize" with "fold" method 
 		// so that a clustal input file and not fasta will be generated
 	@Override
 	public String customAnalize(List<FastaSequence> sequences,
diff --git a/webservices/compbio/ws/server/WSUtil.java b/webservices/compbio/ws/server/WSUtil.java
index e80b1e5..d230cde 100644
--- a/webservices/compbio/ws/server/WSUtil.java
+++ b/webservices/compbio/ws/server/WSUtil.java
@@ -27,6 +27,7 @@ import org.apache.log4j.Logger;
 
 import compbio.data.sequence.Alignment;
 import compbio.data.sequence.FastaSequence;
+import compbio.data.sequence.RNAStructScoreManager;
 import compbio.data.sequence.ScoreManager;
 import compbio.engine.AsyncExecutor;
 import compbio.engine.Configurator;
@@ -215,12 +216,12 @@ public final class WSUtil {
 		ConfiguredExecutable<T> aacon = (ConfiguredExecutable<T>) asyncEngine
 				.getResults(jobId);
 		
-		
 		ScoreManager mas = aacon.getResults();
 		
 		log.trace(jobId + " getConservation : " + mas);
 		return mas;
 	}
+	
 
 	/*
 	 * UNUSED