From d1d2e0d38c08f6ac5ce95cfbf049c4ddcdc49e62 Mon Sep 17 00:00:00 2001
From: pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Date: Thu, 10 Feb 2011 13:50:10 +0000
Subject: [PATCH] Finally, the new web services are working

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3738 e3abac25-378b-4346-85de-24260fe3988d
---
 datamodel/compbio/data/sequence/Range.java         |    6 ++
 datamodel/compbio/data/sequence/Score.java         |   21 +++---
 datamodel/compbio/data/sequence/ScoreManager.java  |   15 ++--
 how_to_add_new_webservice.txt                      |    4 ++
 .../compbio/data/sequence/SequenceUtilTester.java  |    5 +-
 .../data/msa/jaxws/GetAnnotationResponse.java      |   10 ++-
 .../data/msa/jaxws/JobSubmissionExceptionBean.java |    4 +-
 .../data/msa/jaxws/LimitExceededExceptionBean.java |    4 +-
 .../msa/jaxws/ResultNotAvailableExceptionBean.java |    4 +-
 .../msa/jaxws/UnsupportedRuntimeExceptionBean.java |    4 +-
 .../msa/jaxws/WrongParameterExceptionBean.java     |    4 +-
 .../compbio/ws/server/resource/AAConWS.wsdl        |   72 ++++++++++----------
 .../compbio/ws/server/resource/AAConWS_schema1.xsd |   34 ++++++---
 .../ws/server/resource/DisemblWS_schema1.xsd       |   34 ++++++---
 .../ws/server/resource/GlobPlotWS_schema1.xsd      |   34 ++++++---
 .../compbio/ws/server/resource/JronnWS_schema1.xsd |   34 ++++++---
 wsbuild.xml                                        |    6 +-
 17 files changed, 182 insertions(+), 113 deletions(-)

diff --git a/datamodel/compbio/data/sequence/Range.java b/datamodel/compbio/data/sequence/Range.java
index 839ae28..1fabc07 100644
--- a/datamodel/compbio/data/sequence/Range.java
+++ b/datamodel/compbio/data/sequence/Range.java
@@ -5,6 +5,12 @@ public class Range implements Comparable<Range> {
 	public final int from;
 	public final int to;
 
+	private Range() {
+		// JAXB default constructor should not be used
+		from = 0;
+		to = from;
+	}
+
 	public Range(int from, int to) {
 		this.from = from;
 		this.to = to;
diff --git a/datamodel/compbio/data/sequence/Score.java b/datamodel/compbio/data/sequence/Score.java
index b61c74e..f28bd0d 100644
--- a/datamodel/compbio/data/sequence/Score.java
+++ b/datamodel/compbio/data/sequence/Score.java
@@ -12,8 +12,6 @@ import java.util.TreeSet;
 
 import javax.xml.bind.annotation.XmlAccessType;
 import javax.xml.bind.annotation.XmlAccessorType;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlTransient;
 
 import compbio.util.annotation.Immutable;
 
@@ -28,25 +26,22 @@ import compbio.util.annotation.Immutable;
 @Immutable
 public class Score {
 
-	@XmlTransient
 	static final NumberFormat NUMBER_FORMAT = NumberFormat
 			.getNumberInstance(Locale.UK);
 	static {
 		NUMBER_FORMAT.setGroupingUsed(false);
 		NUMBER_FORMAT.setMaximumFractionDigits(3);
 	}
+	// This should be Enum<?> but JAXB cannot serialize it.
+	private final String method;
 
-	private Enum<?> method;
-	// private String method;
-
-	@XmlElement
 	private TreeSet<Range> ranges = new TreeSet<Range>();
 
-	@XmlElement
 	private ArrayList<Float> scores = new ArrayList<Float>(0);
 
 	private Score() {
 		// JaXB default constructor
+		method = null;
 	}
 
 	/**
@@ -60,7 +55,7 @@ public class Score {
 	 *            alignment
 	 */
 	public Score(Enum<?> method, ArrayList<Float> scores) {
-		this.method = method;
+		this.method = method.toString();
 		this.scores = new ArrayList<Float>(scores);
 	}
 
@@ -76,18 +71,18 @@ public class Score {
 	 *            function, usually can be calculated based on scores
 	 */
 	public Score(Enum<?> method, ArrayList<Float> scores, TreeSet<Range> ranges) {
-		this.method = method;
+		this.method = method.toString();
 		this.ranges = ranges;
 		this.scores = scores;
 	}
 
 	public Score(Enum<?> method, TreeSet<Range> ranges) {
-		this.method = method;
+		this.method = method.toString();
 		this.ranges = ranges;
 	}
 
 	public Score(Enum<?> method, float[] scores) {
-		this.method = method;
+		this.method = method.toString();
 		this.scores = toList(scores);
 	}
 
@@ -103,7 +98,7 @@ public class Score {
 	 * 
 	 * @return the ConservationMethod
 	 */
-	public Enum<?> getMethod() {
+	public String getMethod() {
 		return method;
 	}
 
diff --git a/datamodel/compbio/data/sequence/ScoreManager.java b/datamodel/compbio/data/sequence/ScoreManager.java
index f384308..7ddf894 100644
--- a/datamodel/compbio/data/sequence/ScoreManager.java
+++ b/datamodel/compbio/data/sequence/ScoreManager.java
@@ -13,10 +13,12 @@ import java.util.Set;
 
 import javax.xml.bind.annotation.XmlAccessType;
 import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlTransient;
 
 @XmlAccessorType(XmlAccessType.FIELD)
 public class ScoreManager {
 
+	@XmlTransient
 	public static final String SINGLE_ENTRY_KEY = "Alignment";
 
 	private List<ScoreHolder> seqScores;
@@ -104,7 +106,6 @@ public class ScoreManager {
 		}
 		writer.flush();
 	}
-	
 
 	@Override
 	public int hashCode() {
@@ -132,13 +133,11 @@ public class ScoreManager {
 		return true;
 	}
 
-
-
 	@XmlAccessorType(XmlAccessType.FIELD)
 	public static class ScoreHolder {
 
 		public String id;
-		public Set<Score> scores;
+		public HashSet<Score> scores;
 
 		private ScoreHolder() {
 			// JAXB Default constructor should not be used otherwise
@@ -146,7 +145,7 @@ public class ScoreManager {
 
 		ScoreHolder(String id, Set<Score> scores) {
 			this.id = id;
-			this.scores = scores;
+			this.scores = new HashSet<Score>(scores);
 		}
 
 		public void writeOut(OutputStream outStream) throws IOException {
@@ -158,13 +157,12 @@ public class ScoreManager {
 
 		public Score getScoreByMethod(Enum<?> method) {
 			for (Score sc : scores) {
-				if (method == sc.getMethod()) {
+				if (method.toString().equals(sc.getMethod())) {
 					return sc;
 				}
 			}
 			return null;
 		}
-
 		public int getNumberOfScores() {
 			return scores.size();
 		}
@@ -200,7 +198,6 @@ public class ScoreManager {
 				return false;
 			return true;
 		}
-		
-		
+
 	}
 }
diff --git a/how_to_add_new_webservice.txt b/how_to_add_new_webservice.txt
index cb11ba4..529aa42 100644
--- a/how_to_add_new_webservice.txt
+++ b/how_to_add_new_webservice.txt
@@ -38,6 +38,10 @@ Check that
   - you do not have interfaces to serialize. JAXB cannot serialize them.
   - you have a default no args constructor (can be private if you do not need it)
   - JAXB cannot serialize a Map, use custom data structure instead!
+  - Enum cannot be serialized as its abstract class (do not confuse with enum which is fine)
+  - Fields serialization leave a little more space for manuevre, so use it. If you do you then 
+  can accept and return interfaces, e.g. List, Map; abstract classes etc, from your methods. 
+  
 If you have the data on the server side, but nothing is coming through to the client, 
 this is a JAXB serialization problem. They tend to be very silent and thus hard to debug. Check your 
 data structure can be serialized! 
diff --git a/testsrc/compbio/data/sequence/SequenceUtilTester.java b/testsrc/compbio/data/sequence/SequenceUtilTester.java
index 682bcad..b6e74ae 100644
--- a/testsrc/compbio/data/sequence/SequenceUtilTester.java
+++ b/testsrc/compbio/data/sequence/SequenceUtilTester.java
@@ -232,11 +232,12 @@ public class SequenceUtilTester {
 			}
 			for (Score score : scores) {
 
-				if (score.getMethod() == (Enum<?>) GlobProtResult.Disorder) {
+				if (score.getMethod()
+						.equals(GlobProtResult.Disorder.toString())) {
 					assertEquals(score.getRanges().size(), 7);
 					assertTrue(score.getScores().isEmpty());
 				}
-				if (score.getMethod() == (Enum<?>) GlobProtResult.Dydx) {
+				if (GlobProtResult.valueOf(score.getMethod()) == GlobProtResult.Dydx) {
 					assertFalse(score.getScores().isEmpty());
 					assertTrue(score.getRanges().isEmpty());
 				}
diff --git a/webservices/compbio/data/msa/jaxws/GetAnnotationResponse.java b/webservices/compbio/data/msa/jaxws/GetAnnotationResponse.java
index d7adf3c..749551e 100644
--- a/webservices/compbio/data/msa/jaxws/GetAnnotationResponse.java
+++ b/webservices/compbio/data/msa/jaxws/GetAnnotationResponse.java
@@ -1,8 +1,6 @@
 
 package compbio.data.msa.jaxws;
 
-import java.util.HashMap;
-import java.util.HashSet;
 import javax.xml.bind.annotation.XmlAccessType;
 import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlElement;
@@ -15,14 +13,14 @@ import javax.xml.bind.annotation.XmlType;
 public class GetAnnotationResponse {
 
     @XmlElement(name = "return", namespace = "")
-    private HashMap<String, HashSet<compbio.data.sequence.Score>> _return;
+    private compbio.data.sequence.ScoreManager _return;
 
     /**
      * 
      * @return
-     *     returns HashMap<String,HashSet<Score>>
+     *     returns ScoreManager
      */
-    public HashMap<String, HashSet<compbio.data.sequence.Score>> getReturn() {
+    public compbio.data.sequence.ScoreManager getReturn() {
         return this._return;
     }
 
@@ -31,7 +29,7 @@ public class GetAnnotationResponse {
      * @param _return
      *     the value for the _return property
      */
-    public void setReturn(HashMap<String, HashSet<compbio.data.sequence.Score>> _return) {
+    public void setReturn(compbio.data.sequence.ScoreManager _return) {
         this._return = _return;
     }
 
diff --git a/webservices/compbio/data/msa/jaxws/JobSubmissionExceptionBean.java b/webservices/compbio/data/msa/jaxws/JobSubmissionExceptionBean.java
index 30950b4..b2d62d6 100644
--- a/webservices/compbio/data/msa/jaxws/JobSubmissionExceptionBean.java
+++ b/webservices/compbio/data/msa/jaxws/JobSubmissionExceptionBean.java
@@ -9,8 +9,8 @@ import javax.xml.bind.annotation.XmlType;
 
 /**
  * This class was generated by the JAX-WS RI.
- * JAX-WS RI 2.2.1-hudson-28-
- * Generated source version: 2.2.1
+ * JAX-WS RI 2.1.6 in JDK 6
+ * Generated source version: 2.1.6
  * 
  */
 @XmlRootElement(name = "JobSubmissionException", namespace = "http://msa.data.compbio/01/12/2010/")
diff --git a/webservices/compbio/data/msa/jaxws/LimitExceededExceptionBean.java b/webservices/compbio/data/msa/jaxws/LimitExceededExceptionBean.java
index c9c3a4e..e1bf0bf 100644
--- a/webservices/compbio/data/msa/jaxws/LimitExceededExceptionBean.java
+++ b/webservices/compbio/data/msa/jaxws/LimitExceededExceptionBean.java
@@ -9,8 +9,8 @@ import javax.xml.bind.annotation.XmlType;
 
 /**
  * This class was generated by the JAX-WS RI.
- * JAX-WS RI 2.2.1-hudson-28-
- * Generated source version: 2.2.1
+ * JAX-WS RI 2.1.6 in JDK 6
+ * Generated source version: 2.1.6
  * 
  */
 @XmlRootElement(name = "LimitExceededException", namespace = "http://msa.data.compbio/01/12/2010/")
diff --git a/webservices/compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.java b/webservices/compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.java
index be8a26d..7016909 100644
--- a/webservices/compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.java
+++ b/webservices/compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.java
@@ -9,8 +9,8 @@ import javax.xml.bind.annotation.XmlType;
 
 /**
  * This class was generated by the JAX-WS RI.
- * JAX-WS RI 2.2.1-hudson-28-
- * Generated source version: 2.2.1
+ * JAX-WS RI 2.1.6 in JDK 6
+ * Generated source version: 2.1.6
  * 
  */
 @XmlRootElement(name = "ResultNotAvailableException", namespace = "http://msa.data.compbio/01/12/2010/")
diff --git a/webservices/compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.java b/webservices/compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.java
index 5e1268a..fa77aae 100644
--- a/webservices/compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.java
+++ b/webservices/compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.java
@@ -9,8 +9,8 @@ import javax.xml.bind.annotation.XmlType;
 
 /**
  * This class was generated by the JAX-WS RI.
- * JAX-WS RI 2.2.1-hudson-28-
- * Generated source version: 2.2.1
+ * JAX-WS RI 2.1.6 in JDK 6
+ * Generated source version: 2.1.6
  * 
  */
 @XmlRootElement(name = "UnsupportedRuntimeException", namespace = "http://msa.data.compbio/01/12/2010/")
diff --git a/webservices/compbio/data/msa/jaxws/WrongParameterExceptionBean.java b/webservices/compbio/data/msa/jaxws/WrongParameterExceptionBean.java
index 62be910..fc22bd0 100644
--- a/webservices/compbio/data/msa/jaxws/WrongParameterExceptionBean.java
+++ b/webservices/compbio/data/msa/jaxws/WrongParameterExceptionBean.java
@@ -9,8 +9,8 @@ import javax.xml.bind.annotation.XmlType;
 
 /**
  * This class was generated by the JAX-WS RI.
- * JAX-WS RI 2.2.1-hudson-28-
- * Generated source version: 2.2.1
+ * JAX-WS RI 2.1.6 in JDK 6
+ * Generated source version: 2.1.6
  * 
  */
 @XmlRootElement(name = "WrongParameterException", namespace = "http://msa.data.compbio/01/12/2010/")
diff --git a/webservices/compbio/ws/server/resource/AAConWS.wsdl b/webservices/compbio/ws/server/resource/AAConWS.wsdl
index dffcb48..c9c8412 100644
--- a/webservices/compbio/ws/server/resource/AAConWS.wsdl
+++ b/webservices/compbio/ws/server/resource/AAConWS.wsdl
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8" standalone="yes"?>
-<!-- Generated by JAX-WS RI at http://jax-ws.dev.java.net. RI's version is JAX-WS RI 2.2.1-hudson-28-. -->
-<definitions targetNamespace="http://msa.data.compbio/01/12/2010/" name="AAConWS" xmlns="http://schemas.xmlsoap.org/wsdl/" xmlns:wsp="http://www.w3.org/ns/ws-policy" xmlns:tns="http://msa.data.compbio/01/12/2010/" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:wsp1_2="http://schemas.xmlsoap.org/ws/2004/09/policy" xmlns:soap="http://schemas.xmlsoap.org/wsdl/soap/" xmlns:wsam="http://www.w3.org/2007/05/addressing/metadata" xmlns:wsu="http://docs.oasis-open.org/wss/2004/01/oasis-200401-wss-wssecurity-utility-1.0.xsd">
+<!-- Generated by JAX-WS RI at http://jax-ws.dev.java.net. RI's version is JAX-WS RI 2.1.6 in JDK 6. -->
+<definitions targetNamespace="http://msa.data.compbio/01/12/2010/" name="AAConWS" xmlns="http://schemas.xmlsoap.org/wsdl/" xmlns:tns="http://msa.data.compbio/01/12/2010/" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:soap="http://schemas.xmlsoap.org/wsdl/soap/">
   <types>
     <xsd:schema>
       <xsd:import namespace="http://msa.data.compbio/01/12/2010/" schemaLocation="AAConWS_schema1.xsd"/>
@@ -89,60 +89,60 @@
   </message>
   <portType name="SequenceAnnotation">
     <operation name="analize">
-      <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/analizeRequest" message="tns:analize"/>
-      <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/analizeResponse" message="tns:analizeResponse"/>
-      <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/analize/Fault/UnsupportedRuntimeException"/>
-      <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/analize/Fault/LimitExceededException"/>
-      <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/analize/Fault/JobSubmissionException"/>
+      <input message="tns:analize"/>
+      <output message="tns:analizeResponse"/>
+      <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException"/>
+      <fault message="tns:LimitExceededException" name="LimitExceededException"/>
+      <fault message="tns:JobSubmissionException" name="JobSubmissionException"/>
     </operation>
     <operation name="customAnalize">
-      <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/customAnalizeRequest" message="tns:customAnalize"/>
-      <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/customAnalizeResponse" message="tns:customAnalizeResponse"/>
-      <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/customAnalize/Fault/UnsupportedRuntimeException"/>
-      <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/customAnalize/Fault/LimitExceededException"/>
-      <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/customAnalize/Fault/JobSubmissionException"/>
-      <fault message="tns:WrongParameterException" name="WrongParameterException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/customAnalize/Fault/WrongParameterException"/>
+      <input message="tns:customAnalize"/>
+      <output message="tns:customAnalizeResponse"/>
+      <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException"/>
+      <fault message="tns:LimitExceededException" name="LimitExceededException"/>
+      <fault message="tns:JobSubmissionException" name="JobSubmissionException"/>
+      <fault message="tns:WrongParameterException" name="WrongParameterException"/>
     </operation>
     <operation name="presetAnalize">
-      <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/presetAnalizeRequest" message="tns:presetAnalize"/>
-      <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/presetAnalizeResponse" message="tns:presetAnalizeResponse"/>
-      <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/presetAnalize/Fault/UnsupportedRuntimeException"/>
-      <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/presetAnalize/Fault/LimitExceededException"/>
-      <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/presetAnalize/Fault/JobSubmissionException"/>
-      <fault message="tns:WrongParameterException" name="WrongParameterException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/presetAnalize/Fault/WrongParameterException"/>
+      <input message="tns:presetAnalize"/>
+      <output message="tns:presetAnalizeResponse"/>
+      <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException"/>
+      <fault message="tns:LimitExceededException" name="LimitExceededException"/>
+      <fault message="tns:JobSubmissionException" name="JobSubmissionException"/>
+      <fault message="tns:WrongParameterException" name="WrongParameterException"/>
     </operation>
     <operation name="getAnnotation">
-      <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getAnnotationRequest" message="tns:getAnnotation"/>
-      <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getAnnotationResponse" message="tns:getAnnotationResponse"/>
-      <fault message="tns:ResultNotAvailableException" name="ResultNotAvailableException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getAnnotation/Fault/ResultNotAvailableException"/>
+      <input message="tns:getAnnotation"/>
+      <output message="tns:getAnnotationResponse"/>
+      <fault message="tns:ResultNotAvailableException" name="ResultNotAvailableException"/>
     </operation>
     <operation name="pullExecStatistics">
-      <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
-      <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
+      <input message="tns:pullExecStatistics"/>
+      <output message="tns:pullExecStatisticsResponse"/>
     </operation>
     <operation name="cancelJob">
-      <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/cancelJobRequest" message="tns:cancelJob"/>
-      <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/cancelJobResponse" message="tns:cancelJobResponse"/>
+      <input message="tns:cancelJob"/>
+      <output message="tns:cancelJobResponse"/>
     </operation>
     <operation name="getJobStatus">
-      <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getJobStatusRequest" message="tns:getJobStatus"/>
-      <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getJobStatusResponse" message="tns:getJobStatusResponse"/>
+      <input message="tns:getJobStatus"/>
+      <output message="tns:getJobStatusResponse"/>
     </operation>
     <operation name="getPresets">
-      <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getPresetsRequest" message="tns:getPresets"/>
-      <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getPresetsResponse" message="tns:getPresetsResponse"/>
+      <input message="tns:getPresets"/>
+      <output message="tns:getPresetsResponse"/>
     </operation>
     <operation name="getLimit">
-      <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitRequest" message="tns:getLimit"/>
-      <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitResponse" message="tns:getLimitResponse"/>
+      <input message="tns:getLimit"/>
+      <output message="tns:getLimitResponse"/>
     </operation>
     <operation name="getLimits">
-      <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitsRequest" message="tns:getLimits"/>
-      <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitsResponse" message="tns:getLimitsResponse"/>
+      <input message="tns:getLimits"/>
+      <output message="tns:getLimitsResponse"/>
     </operation>
     <operation name="getRunnerOptions">
-      <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
-      <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
+      <input message="tns:getRunnerOptions"/>
+      <output message="tns:getRunnerOptionsResponse"/>
     </operation>
   </portType>
   <binding name="AAConWSPortBinding" type="tns:SequenceAnnotation">
diff --git a/webservices/compbio/ws/server/resource/AAConWS_schema1.xsd b/webservices/compbio/ws/server/resource/AAConWS_schema1.xsd
index 77fe8df..038af26 100644
--- a/webservices/compbio/ws/server/resource/AAConWS_schema1.xsd
+++ b/webservices/compbio/ws/server/resource/AAConWS_schema1.xsd
@@ -204,20 +204,36 @@
 
   <xs:complexType name="getAnnotationResponse">
     <xs:sequence>
-      <xs:element name="return" type="tns:hashMap" minOccurs="0"/>
+      <xs:element name="return" type="tns:scoreManager" minOccurs="0"/>
     </xs:sequence>
   </xs:complexType>
 
-  <xs:complexType name="hashMap">
-    <xs:complexContent>
-      <xs:extension base="tns:abstractMap">
-        <xs:sequence/>
-      </xs:extension>
-    </xs:complexContent>
+  <xs:complexType name="scoreManager">
+    <xs:sequence>
+      <xs:element name="seqScores" type="tns:scoreHolder" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+    </xs:sequence>
   </xs:complexType>
 
-  <xs:complexType name="abstractMap" abstract="true">
-    <xs:sequence/>
+  <xs:complexType name="scoreHolder">
+    <xs:sequence>
+      <xs:element name="id" type="xs:string" minOccurs="0"/>
+      <xs:element name="scores" type="tns:score" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="score">
+    <xs:sequence>
+      <xs:element name="method" type="xs:string" minOccurs="0"/>
+      <xs:element name="ranges" type="tns:range" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+      <xs:element name="scores" type="xs:float" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="range">
+    <xs:sequence>
+      <xs:element name="from" type="xs:int"/>
+      <xs:element name="to" type="xs:int"/>
+    </xs:sequence>
   </xs:complexType>
 
   <xs:complexType name="ResultNotAvailableException">
diff --git a/webservices/compbio/ws/server/resource/DisemblWS_schema1.xsd b/webservices/compbio/ws/server/resource/DisemblWS_schema1.xsd
index 6185886..97d6989 100644
--- a/webservices/compbio/ws/server/resource/DisemblWS_schema1.xsd
+++ b/webservices/compbio/ws/server/resource/DisemblWS_schema1.xsd
@@ -271,20 +271,36 @@
 
   <xs:complexType name="getAnnotationResponse">
     <xs:sequence>
-      <xs:element name="return" type="tns:hashMap" minOccurs="0"/>
+      <xs:element name="return" type="tns:scoreManager" minOccurs="0"/>
     </xs:sequence>
   </xs:complexType>
 
-  <xs:complexType name="hashMap">
-    <xs:complexContent>
-      <xs:extension base="tns:abstractMap">
-        <xs:sequence/>
-      </xs:extension>
-    </xs:complexContent>
+  <xs:complexType name="scoreManager">
+    <xs:sequence>
+      <xs:element name="seqScores" type="tns:scoreHolder" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+    </xs:sequence>
   </xs:complexType>
 
-  <xs:complexType name="abstractMap" abstract="true">
-    <xs:sequence/>
+  <xs:complexType name="scoreHolder">
+    <xs:sequence>
+      <xs:element name="id" type="xs:string" minOccurs="0"/>
+      <xs:element name="scores" type="tns:score" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="score">
+    <xs:sequence>
+      <xs:element name="method" type="xs:string" minOccurs="0"/>
+      <xs:element name="ranges" type="tns:range" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+      <xs:element name="scores" type="xs:float" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="range">
+    <xs:sequence>
+      <xs:element name="from" type="xs:int"/>
+      <xs:element name="to" type="xs:int"/>
+    </xs:sequence>
   </xs:complexType>
 
   <xs:complexType name="ResultNotAvailableException">
diff --git a/webservices/compbio/ws/server/resource/GlobPlotWS_schema1.xsd b/webservices/compbio/ws/server/resource/GlobPlotWS_schema1.xsd
index 109e3fb..858d2c2 100644
--- a/webservices/compbio/ws/server/resource/GlobPlotWS_schema1.xsd
+++ b/webservices/compbio/ws/server/resource/GlobPlotWS_schema1.xsd
@@ -69,20 +69,36 @@
 
   <xs:complexType name="getAnnotationResponse">
     <xs:sequence>
-      <xs:element name="return" type="tns:hashMap" minOccurs="0"/>
+      <xs:element name="return" type="tns:scoreManager" minOccurs="0"/>
     </xs:sequence>
   </xs:complexType>
 
-  <xs:complexType name="hashMap">
-    <xs:complexContent>
-      <xs:extension base="tns:abstractMap">
-        <xs:sequence/>
-      </xs:extension>
-    </xs:complexContent>
+  <xs:complexType name="scoreManager">
+    <xs:sequence>
+      <xs:element name="seqScores" type="tns:scoreHolder" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+    </xs:sequence>
   </xs:complexType>
 
-  <xs:complexType name="abstractMap" abstract="true">
-    <xs:sequence/>
+  <xs:complexType name="scoreHolder">
+    <xs:sequence>
+      <xs:element name="id" type="xs:string" minOccurs="0"/>
+      <xs:element name="scores" type="tns:score" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="score">
+    <xs:sequence>
+      <xs:element name="method" type="xs:string" minOccurs="0"/>
+      <xs:element name="ranges" type="tns:range" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+      <xs:element name="scores" type="xs:float" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="range">
+    <xs:sequence>
+      <xs:element name="from" type="xs:int"/>
+      <xs:element name="to" type="xs:int"/>
+    </xs:sequence>
   </xs:complexType>
 
   <xs:complexType name="ResultNotAvailableException">
diff --git a/webservices/compbio/ws/server/resource/JronnWS_schema1.xsd b/webservices/compbio/ws/server/resource/JronnWS_schema1.xsd
index 77fe8df..038af26 100644
--- a/webservices/compbio/ws/server/resource/JronnWS_schema1.xsd
+++ b/webservices/compbio/ws/server/resource/JronnWS_schema1.xsd
@@ -204,20 +204,36 @@
 
   <xs:complexType name="getAnnotationResponse">
     <xs:sequence>
-      <xs:element name="return" type="tns:hashMap" minOccurs="0"/>
+      <xs:element name="return" type="tns:scoreManager" minOccurs="0"/>
     </xs:sequence>
   </xs:complexType>
 
-  <xs:complexType name="hashMap">
-    <xs:complexContent>
-      <xs:extension base="tns:abstractMap">
-        <xs:sequence/>
-      </xs:extension>
-    </xs:complexContent>
+  <xs:complexType name="scoreManager">
+    <xs:sequence>
+      <xs:element name="seqScores" type="tns:scoreHolder" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+    </xs:sequence>
   </xs:complexType>
 
-  <xs:complexType name="abstractMap" abstract="true">
-    <xs:sequence/>
+  <xs:complexType name="scoreHolder">
+    <xs:sequence>
+      <xs:element name="id" type="xs:string" minOccurs="0"/>
+      <xs:element name="scores" type="tns:score" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="score">
+    <xs:sequence>
+      <xs:element name="method" type="xs:string" minOccurs="0"/>
+      <xs:element name="ranges" type="tns:range" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+      <xs:element name="scores" type="xs:float" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="range">
+    <xs:sequence>
+      <xs:element name="from" type="xs:int"/>
+      <xs:element name="to" type="xs:int"/>
+    </xs:sequence>
   </xs:complexType>
 
   <xs:complexType name="ResultNotAvailableException">
diff --git a/wsbuild.xml b/wsbuild.xml
index dad6d25..bf55aaa 100644
--- a/wsbuild.xml
+++ b/wsbuild.xml
@@ -26,8 +26,9 @@
 	<property name="disembl.wsdl" location="${wsdl.dir}/DisemblWS.wsdl" />
 	<property name="globplot.wsdl" location="${wsdl.dir}/GlobPlotWS.wsdl" />
 	<property name="jronn.wsdl" location="${wsdl.dir}/JronnWS.wsdl" />
+	
 
-	<taskdef name="wsgen" classname="com.sun.tools.ws.ant.WsGen">
+	<taskdef name="wsgen" onerror="report" classname="com.sun.tools.ws.ant.WsGen">
 		<classpath refid="project.classpath" />
 	</taskdef>
 
@@ -47,6 +48,7 @@
 			<!-- destdir - Where to put generated classes -->
 			<!-- sourcedestdir -  Where to put generated source files -->
 			<!-- resourcedestdir - Where to put generated source files -->
+
 		<wsgen sei="compbio.ws.server.AAConWS" 
 					sourcedestdir="${basedir}/webservices" 
 					destdir="${classes}" 
@@ -58,6 +60,7 @@
 					<classpath refid="classes.path" />
 					<classpath refid="project.classpath" />
 		</wsgen>
+
 		<wsgen sei="compbio.ws.server.ClustalWS" 
 					sourcedestdir="${basedir}/webservices" 
 					destdir="${classes}" 
@@ -102,6 +105,7 @@
 						<classpath refid="classes.path" />
 						<classpath refid="project.classpath" />
 		</wsgen>
+		
 		<wsgen sei="compbio.ws.server.DisemblWS" 
 						sourcedestdir="${basedir}/webservices" 
 						destdir="${classes}" 
-- 
1.7.10.2