From 1791d2710aba8bf012a83e5d18c5c1988ecc176b Mon Sep 17 00:00:00 2001
From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Tue, 24 Sep 2013 17:35:06 +0100
Subject: [PATCH] Assign JABAService.V2_SERVICE_NAMESPACE to all new services:
 JpredWS, RNAalifoldWS, MSAprobsWS, GLprobsWS

---
 webservices/compbio/ws/client/Services.java        |    8 +-
 webservices/compbio/ws/server/ClustalOWS.java      |    2 +-
 webservices/compbio/ws/server/GLprobsWS.java       |    2 +-
 webservices/compbio/ws/server/JpredWS.java         |    2 +-
 webservices/compbio/ws/server/MSAprobsWS.java      |    2 +-
 .../compbio/ws/server/resource/GLprobsWS.wsdl      |  149 +-------
 .../compbio/ws/server/resource/JpredWS.wsdl        |  149 +-------
 .../compbio/ws/server/resource/JpredWS_schema1.xsd |  374 --------------------
 .../compbio/ws/server/resource/MSAprobsWS.wsdl     |  149 +-------
 .../ws/server/resource/MSAprobsWS_schema1.xsd      |  374 --------------------
 webservices/compbio/ws/server/resource/MsaWS.wsdl  |  149 ++++++++
 .../{GLprobsWS_schema1.xsd => MsaWS_schema1.xsd}   |    0
 wsbuild.log                                        |   25 +-
 13 files changed, 190 insertions(+), 1195 deletions(-)
 delete mode 100644 webservices/compbio/ws/server/resource/JpredWS_schema1.xsd
 delete mode 100644 webservices/compbio/ws/server/resource/MSAprobsWS_schema1.xsd
 create mode 100644 webservices/compbio/ws/server/resource/MsaWS.wsdl
 rename webservices/compbio/ws/server/resource/{GLprobsWS_schema1.xsd => MsaWS_schema1.xsd} (100%)

diff --git a/webservices/compbio/ws/client/Services.java b/webservices/compbio/ws/client/Services.java
index 6815e33..87ef1d2 100644
--- a/webservices/compbio/ws/client/Services.java
+++ b/webservices/compbio/ws/client/Services.java
@@ -108,15 +108,15 @@ public enum Services {
 			case DisemblWS :
 			case GlobPlotWS :
 			case IUPredWS :
-				return JABAService.V2_SERVICE_NAMESPACE;
-			case ClustalOWS :
+			case MSAprobsWS :
+			case GLprobsWS :
 			case JpredWS :
+			case ClustalOWS :
+				return JABAService.V2_SERVICE_NAMESPACE;
 			case ClustalWS :
 			case MafftWS :
 			case MuscleWS :
 			case ProbconsWS :
-			case MSAprobsWS :
-			case GLprobsWS :
 			case TcoffeeWS :
 				return JABAService.SERVICE_NAMESPACE;
 			default :
diff --git a/webservices/compbio/ws/server/ClustalOWS.java b/webservices/compbio/ws/server/ClustalOWS.java
index 1d8e9b6..bef39a1 100644
--- a/webservices/compbio/ws/server/ClustalOWS.java
+++ b/webservices/compbio/ws/server/ClustalOWS.java
@@ -50,7 +50,7 @@ import compbio.metadata.WrongParameterException;
 import compbio.runner.RunnerUtil;
 import compbio.runner.msa.ClustalO;
 
-@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "ClustalOWS")
+@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "ClustalOWS")
 public class ClustalOWS implements MsaWS<ClustalO> {
 
 	private static Logger log = Logger.getLogger(ClustalOWS.class);
diff --git a/webservices/compbio/ws/server/GLprobsWS.java b/webservices/compbio/ws/server/GLprobsWS.java
index 91b048d..007322c 100644
--- a/webservices/compbio/ws/server/GLprobsWS.java
+++ b/webservices/compbio/ws/server/GLprobsWS.java
@@ -49,7 +49,7 @@ import compbio.metadata.WrongParameterException;
 import compbio.runner.RunnerUtil;
 import compbio.runner.msa.GLprobs;
 
-@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "GLprobsWS")
+@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "GLprobsWS")
 public class GLprobsWS implements MsaWS<GLprobs> {
 
 	private static Logger log = Logger.getLogger(GLprobsWS.class);
diff --git a/webservices/compbio/ws/server/JpredWS.java b/webservices/compbio/ws/server/JpredWS.java
index 6eb20e7..df9bba4 100644
--- a/webservices/compbio/ws/server/JpredWS.java
+++ b/webservices/compbio/ws/server/JpredWS.java
@@ -50,7 +50,7 @@ import compbio.metadata.WrongParameterException;
 import compbio.runner.RunnerUtil;
 import compbio.runner.predictors.Jpred;
 
-@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "JpredWS")
+@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "JpredWS")
 public class JpredWS implements MsaWS<Jpred> {
 
 	private static Logger log = Logger.getLogger(JpredWS.class);
diff --git a/webservices/compbio/ws/server/MSAprobsWS.java b/webservices/compbio/ws/server/MSAprobsWS.java
index 0f25069..003e702 100644
--- a/webservices/compbio/ws/server/MSAprobsWS.java
+++ b/webservices/compbio/ws/server/MSAprobsWS.java
@@ -49,7 +49,7 @@ import compbio.metadata.WrongParameterException;
 import compbio.runner.RunnerUtil;
 import compbio.runner.msa.MSAprobs;
 
-@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "MSAprobsWS")
+@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "MSAprobsWS")
 public class MSAprobsWS implements MsaWS<MSAprobs> {
 
 	private static Logger log = Logger.getLogger(MSAprobsWS.class);
diff --git a/webservices/compbio/ws/server/resource/GLprobsWS.wsdl b/webservices/compbio/ws/server/resource/GLprobsWS.wsdl
index 66288af..3f4ea80 100644
--- a/webservices/compbio/ws/server/resource/GLprobsWS.wsdl
+++ b/webservices/compbio/ws/server/resource/GLprobsWS.wsdl
@@ -1,151 +1,8 @@
 <?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 Metro/2.1 (branches/2.1-6728; 2011-02-03T14:14:58+0000) JAXWS-RI/2.2.3 JAXWS/2.2. -->
-<definitions targetNamespace="http://msa.data.compbio/01/01/2010/" name="GLprobsWS" xmlns="http://schemas.xmlsoap.org/wsdl/" xmlns:wsp="http://www.w3.org/ns/ws-policy" xmlns:tns="http://msa.data.compbio/01/01/2010/" 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">
-  <types>
-    <xsd:schema>
-      <xsd:import namespace="http://msa.data.compbio/01/01/2010/" schemaLocation="GLprobsWS_schema1.xsd"/>
-    </xsd:schema>
-  </types>
-  <message name="align">
-    <part name="parameters" element="tns:align"/>
-  </message>
-  <message name="alignResponse">
-    <part name="parameters" element="tns:alignResponse"/>
-  </message>
-  <message name="UnsupportedRuntimeException">
-    <part name="fault" element="tns:UnsupportedRuntimeException"/>
-  </message>
-  <message name="LimitExceededException">
-    <part name="fault" element="tns:LimitExceededException"/>
-  </message>
-  <message name="JobSubmissionException">
-    <part name="fault" element="tns:JobSubmissionException"/>
-  </message>
-  <message name="presetAlign">
-    <part name="parameters" element="tns:presetAlign"/>
-  </message>
-  <message name="presetAlignResponse">
-    <part name="parameters" element="tns:presetAlignResponse"/>
-  </message>
-  <message name="WrongParameterException">
-    <part name="fault" element="tns:WrongParameterException"/>
-  </message>
-  <message name="customAlign">
-    <part name="parameters" element="tns:customAlign"/>
-  </message>
-  <message name="customAlignResponse">
-    <part name="parameters" element="tns:customAlignResponse"/>
-  </message>
-  <message name="getResult">
-    <part name="parameters" element="tns:getResult"/>
-  </message>
-  <message name="getResultResponse">
-    <part name="parameters" element="tns:getResultResponse"/>
-  </message>
-  <message name="ResultNotAvailableException">
-    <part name="fault" element="tns:ResultNotAvailableException"/>
-  </message>
-  <message name="cancelJob">
-    <part name="parameters" element="tns:cancelJob"/>
-  </message>
-  <message name="cancelJobResponse">
-    <part name="parameters" element="tns:cancelJobResponse"/>
-  </message>
-  <message name="getJobStatus">
-    <part name="parameters" element="tns:getJobStatus"/>
-  </message>
-  <message name="getJobStatusResponse">
-    <part name="parameters" element="tns:getJobStatusResponse"/>
-  </message>
-  <message name="pullExecStatistics">
-    <part name="parameters" element="tns:pullExecStatistics"/>
-  </message>
-  <message name="pullExecStatisticsResponse">
-    <part name="parameters" element="tns:pullExecStatisticsResponse"/>
-  </message>
-  <message name="getRunnerOptions">
-    <part name="parameters" element="tns:getRunnerOptions"/>
-  </message>
-  <message name="getRunnerOptionsResponse">
-    <part name="parameters" element="tns:getRunnerOptionsResponse"/>
-  </message>
-  <message name="getLimit">
-    <part name="parameters" element="tns:getLimit"/>
-  </message>
-  <message name="getLimitResponse">
-    <part name="parameters" element="tns:getLimitResponse"/>
-  </message>
-  <message name="getLimits">
-    <part name="parameters" element="tns:getLimits"/>
-  </message>
-  <message name="getLimitsResponse">
-    <part name="parameters" element="tns:getLimitsResponse"/>
-  </message>
-  <message name="getPresets">
-    <part name="parameters" element="tns:getPresets"/>
-  </message>
-  <message name="getPresetsResponse">
-    <part name="parameters" element="tns:getPresetsResponse"/>
-  </message>
-  <portType name="MsaWS">
-    <operation name="align">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignRequest" message="tns:align"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignResponse" message="tns:alignResponse"/>
-      <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/UnsupportedRuntimeException"/>
-      <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/LimitExceededException"/>
-      <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/JobSubmissionException"/>
-    </operation>
-    <operation name="presetAlign">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlignRequest" message="tns:presetAlign"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlignResponse" message="tns:presetAlignResponse"/>
-      <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/UnsupportedRuntimeException"/>
-      <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/LimitExceededException"/>
-      <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/JobSubmissionException"/>
-      <fault message="tns:WrongParameterException" name="WrongParameterException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/WrongParameterException"/>
-    </operation>
-    <operation name="customAlign">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlignRequest" message="tns:customAlign"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlignResponse" message="tns:customAlignResponse"/>
-      <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/UnsupportedRuntimeException"/>
-      <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/LimitExceededException"/>
-      <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/JobSubmissionException"/>
-      <fault message="tns:WrongParameterException" name="WrongParameterException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/WrongParameterException"/>
-    </operation>
-    <operation name="getResult">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultRequest" message="tns:getResult"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultResponse" message="tns:getResultResponse"/>
-      <fault message="tns:ResultNotAvailableException" name="ResultNotAvailableException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResult/Fault/ResultNotAvailableException"/>
-    </operation>
-    <operation name="cancelJob">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/cancelJobRequest" message="tns:cancelJob"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/cancelJobResponse" message="tns:cancelJobResponse"/>
-    </operation>
-    <operation name="getJobStatus">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getJobStatusRequest" message="tns:getJobStatus"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getJobStatusResponse" message="tns:getJobStatusResponse"/>
-    </operation>
-    <operation name="pullExecStatistics">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
-    </operation>
-    <operation name="getRunnerOptions">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
-    </operation>
-    <operation name="getLimit">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitRequest" message="tns:getLimit"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitResponse" message="tns:getLimitResponse"/>
-    </operation>
-    <operation name="getLimits">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsRequest" message="tns:getLimits"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsResponse" message="tns:getLimitsResponse"/>
-    </operation>
-    <operation name="getPresets">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsRequest" message="tns:getPresets"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsResponse" message="tns:getPresetsResponse"/>
-    </operation>
-  </portType>
-  <binding name="GLprobsWSPortBinding" type="tns:MsaWS">
+<definitions targetNamespace="http://msa.data.compbio/01/12/2010/" name="GLprobsWS" 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">
+  <import namespace="http://msa.data.compbio/01/01/2010/" location="MsaWS.wsdl"/>
+  <binding name="GLprobsWSPortBinding" type="ns1:MsaWS" xmlns:ns1="http://msa.data.compbio/01/01/2010/">
     <soap:binding transport="http://schemas.xmlsoap.org/soap/http" style="document"/>
     <operation name="align">
       <soap:operation soapAction=""/>
diff --git a/webservices/compbio/ws/server/resource/JpredWS.wsdl b/webservices/compbio/ws/server/resource/JpredWS.wsdl
index 02ca1db..35dce1a 100644
--- a/webservices/compbio/ws/server/resource/JpredWS.wsdl
+++ b/webservices/compbio/ws/server/resource/JpredWS.wsdl
@@ -1,151 +1,8 @@
 <?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 Metro/2.1 (branches/2.1-6728; 2011-02-03T14:14:58+0000) JAXWS-RI/2.2.3 JAXWS/2.2. -->
-<definitions targetNamespace="http://msa.data.compbio/01/01/2010/" name="JpredWS" xmlns="http://schemas.xmlsoap.org/wsdl/" xmlns:wsp="http://www.w3.org/ns/ws-policy" xmlns:tns="http://msa.data.compbio/01/01/2010/" 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">
-  <types>
-    <xsd:schema>
-      <xsd:import namespace="http://msa.data.compbio/01/01/2010/" schemaLocation="JpredWS_schema1.xsd"/>
-    </xsd:schema>
-  </types>
-  <message name="align">
-    <part name="parameters" element="tns:align"/>
-  </message>
-  <message name="alignResponse">
-    <part name="parameters" element="tns:alignResponse"/>
-  </message>
-  <message name="UnsupportedRuntimeException">
-    <part name="fault" element="tns:UnsupportedRuntimeException"/>
-  </message>
-  <message name="LimitExceededException">
-    <part name="fault" element="tns:LimitExceededException"/>
-  </message>
-  <message name="JobSubmissionException">
-    <part name="fault" element="tns:JobSubmissionException"/>
-  </message>
-  <message name="presetAlign">
-    <part name="parameters" element="tns:presetAlign"/>
-  </message>
-  <message name="presetAlignResponse">
-    <part name="parameters" element="tns:presetAlignResponse"/>
-  </message>
-  <message name="WrongParameterException">
-    <part name="fault" element="tns:WrongParameterException"/>
-  </message>
-  <message name="customAlign">
-    <part name="parameters" element="tns:customAlign"/>
-  </message>
-  <message name="customAlignResponse">
-    <part name="parameters" element="tns:customAlignResponse"/>
-  </message>
-  <message name="getResult">
-    <part name="parameters" element="tns:getResult"/>
-  </message>
-  <message name="getResultResponse">
-    <part name="parameters" element="tns:getResultResponse"/>
-  </message>
-  <message name="ResultNotAvailableException">
-    <part name="fault" element="tns:ResultNotAvailableException"/>
-  </message>
-  <message name="cancelJob">
-    <part name="parameters" element="tns:cancelJob"/>
-  </message>
-  <message name="cancelJobResponse">
-    <part name="parameters" element="tns:cancelJobResponse"/>
-  </message>
-  <message name="getJobStatus">
-    <part name="parameters" element="tns:getJobStatus"/>
-  </message>
-  <message name="getJobStatusResponse">
-    <part name="parameters" element="tns:getJobStatusResponse"/>
-  </message>
-  <message name="pullExecStatistics">
-    <part name="parameters" element="tns:pullExecStatistics"/>
-  </message>
-  <message name="pullExecStatisticsResponse">
-    <part name="parameters" element="tns:pullExecStatisticsResponse"/>
-  </message>
-  <message name="getRunnerOptions">
-    <part name="parameters" element="tns:getRunnerOptions"/>
-  </message>
-  <message name="getRunnerOptionsResponse">
-    <part name="parameters" element="tns:getRunnerOptionsResponse"/>
-  </message>
-  <message name="getLimit">
-    <part name="parameters" element="tns:getLimit"/>
-  </message>
-  <message name="getLimitResponse">
-    <part name="parameters" element="tns:getLimitResponse"/>
-  </message>
-  <message name="getLimits">
-    <part name="parameters" element="tns:getLimits"/>
-  </message>
-  <message name="getLimitsResponse">
-    <part name="parameters" element="tns:getLimitsResponse"/>
-  </message>
-  <message name="getPresets">
-    <part name="parameters" element="tns:getPresets"/>
-  </message>
-  <message name="getPresetsResponse">
-    <part name="parameters" element="tns:getPresetsResponse"/>
-  </message>
-  <portType name="MsaWS">
-    <operation name="align">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignRequest" message="tns:align"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignResponse" message="tns:alignResponse"/>
-      <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/UnsupportedRuntimeException"/>
-      <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/LimitExceededException"/>
-      <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/JobSubmissionException"/>
-    </operation>
-    <operation name="presetAlign">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlignRequest" message="tns:presetAlign"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlignResponse" message="tns:presetAlignResponse"/>
-      <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/UnsupportedRuntimeException"/>
-      <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/LimitExceededException"/>
-      <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/JobSubmissionException"/>
-      <fault message="tns:WrongParameterException" name="WrongParameterException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/WrongParameterException"/>
-    </operation>
-    <operation name="customAlign">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlignRequest" message="tns:customAlign"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlignResponse" message="tns:customAlignResponse"/>
-      <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/UnsupportedRuntimeException"/>
-      <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/LimitExceededException"/>
-      <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/JobSubmissionException"/>
-      <fault message="tns:WrongParameterException" name="WrongParameterException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/WrongParameterException"/>
-    </operation>
-    <operation name="getResult">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultRequest" message="tns:getResult"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultResponse" message="tns:getResultResponse"/>
-      <fault message="tns:ResultNotAvailableException" name="ResultNotAvailableException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResult/Fault/ResultNotAvailableException"/>
-    </operation>
-    <operation name="cancelJob">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/cancelJobRequest" message="tns:cancelJob"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/cancelJobResponse" message="tns:cancelJobResponse"/>
-    </operation>
-    <operation name="getJobStatus">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getJobStatusRequest" message="tns:getJobStatus"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getJobStatusResponse" message="tns:getJobStatusResponse"/>
-    </operation>
-    <operation name="pullExecStatistics">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
-    </operation>
-    <operation name="getRunnerOptions">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
-    </operation>
-    <operation name="getLimit">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitRequest" message="tns:getLimit"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitResponse" message="tns:getLimitResponse"/>
-    </operation>
-    <operation name="getLimits">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsRequest" message="tns:getLimits"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsResponse" message="tns:getLimitsResponse"/>
-    </operation>
-    <operation name="getPresets">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsRequest" message="tns:getPresets"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsResponse" message="tns:getPresetsResponse"/>
-    </operation>
-  </portType>
-  <binding name="JpredWSPortBinding" type="tns:MsaWS">
+<definitions targetNamespace="http://msa.data.compbio/01/12/2010/" name="JpredWS" 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">
+  <import namespace="http://msa.data.compbio/01/01/2010/" location="MsaWS.wsdl"/>
+  <binding name="JpredWSPortBinding" type="ns1:MsaWS" xmlns:ns1="http://msa.data.compbio/01/01/2010/">
     <soap:binding transport="http://schemas.xmlsoap.org/soap/http" style="document"/>
     <operation name="align">
       <soap:operation soapAction=""/>
diff --git a/webservices/compbio/ws/server/resource/JpredWS_schema1.xsd b/webservices/compbio/ws/server/resource/JpredWS_schema1.xsd
deleted file mode 100644
index e1e8e5f..0000000
--- a/webservices/compbio/ws/server/resource/JpredWS_schema1.xsd
+++ /dev/null
@@ -1,374 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
-<xs:schema version="1.0" targetNamespace="http://msa.data.compbio/01/01/2010/" xmlns:tns="http://msa.data.compbio/01/01/2010/" xmlns:xs="http://www.w3.org/2001/XMLSchema">
-
-  <xs:element name="JobSubmissionException" type="tns:JobSubmissionException"/>
-
-  <xs:element name="LimitExceededException" type="tns:LimitExceededException"/>
-
-  <xs:element name="ResultNotAvailableException" type="tns:ResultNotAvailableException"/>
-
-  <xs:element name="UnsupportedRuntimeException" type="tns:UnsupportedRuntimeException"/>
-
-  <xs:element name="WrongParameterException" type="tns:WrongParameterException"/>
-
-  <xs:element name="align" type="tns:align"/>
-
-  <xs:element name="alignResponse" type="tns:alignResponse"/>
-
-  <xs:element name="cancelJob" type="tns:cancelJob"/>
-
-  <xs:element name="cancelJobResponse" type="tns:cancelJobResponse"/>
-
-  <xs:element name="customAlign" type="tns:customAlign"/>
-
-  <xs:element name="customAlignResponse" type="tns:customAlignResponse"/>
-
-  <xs:element name="getJobStatus" type="tns:getJobStatus"/>
-
-  <xs:element name="getJobStatusResponse" type="tns:getJobStatusResponse"/>
-
-  <xs:element name="getLimit" type="tns:getLimit"/>
-
-  <xs:element name="getLimitResponse" type="tns:getLimitResponse"/>
-
-  <xs:element name="getLimits" type="tns:getLimits"/>
-
-  <xs:element name="getLimitsResponse" type="tns:getLimitsResponse"/>
-
-  <xs:element name="getPresets" type="tns:getPresets"/>
-
-  <xs:element name="getPresetsResponse" type="tns:getPresetsResponse"/>
-
-  <xs:element name="getResult" type="tns:getResult"/>
-
-  <xs:element name="getResultResponse" type="tns:getResultResponse"/>
-
-  <xs:element name="getRunnerOptions" type="tns:getRunnerOptions"/>
-
-  <xs:element name="getRunnerOptionsResponse" type="tns:getRunnerOptionsResponse"/>
-
-  <xs:element name="limits" type="tns:limitsManager"/>
-
-  <xs:element name="presetAlign" type="tns:presetAlign"/>
-
-  <xs:element name="presetAlignResponse" type="tns:presetAlignResponse"/>
-
-  <xs:element name="presets" type="tns:presetManager"/>
-
-  <xs:element name="pullExecStatistics" type="tns:pullExecStatistics"/>
-
-  <xs:element name="pullExecStatisticsResponse" type="tns:pullExecStatisticsResponse"/>
-
-  <xs:element name="runnerConfig" type="tns:runnerConfig"/>
-
-  <xs:complexType name="align">
-    <xs:sequence>
-      <xs:element name="fastaSequences" type="tns:fastaSequence" minOccurs="0" maxOccurs="unbounded"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="fastaSequence">
-    <xs:sequence>
-      <xs:element name="id" type="xs:string" minOccurs="0"/>
-      <xs:element name="sequence" type="xs:string" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="alignResponse">
-    <xs:sequence>
-      <xs:element name="return" type="xs:string" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="UnsupportedRuntimeException">
-    <xs:sequence>
-      <xs:element name="message" type="xs:string" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="LimitExceededException">
-    <xs:sequence>
-      <xs:element name="actualNumberofSequences" type="xs:int"/>
-      <xs:element name="message" type="xs:string" minOccurs="0"/>
-      <xs:element name="numberOfSequencesAllowed" type="xs:int"/>
-      <xs:element name="sequenceLenghtActual" type="xs:int"/>
-      <xs:element name="sequenceLenghtAllowed" type="xs:int"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="JobSubmissionException">
-    <xs:sequence>
-      <xs:element name="message" type="xs:string" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="customAlign">
-    <xs:sequence>
-      <xs:element name="fastaSequences" type="tns:fastaSequence" minOccurs="0" maxOccurs="unbounded"/>
-      <xs:element name="options" type="tns:option" minOccurs="0" maxOccurs="unbounded"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="option">
-    <xs:sequence>
-      <xs:element name="description" type="xs:string"/>
-      <xs:element name="optionNames" type="xs:string" maxOccurs="unbounded"/>
-      <xs:element name="name" type="xs:string"/>
-      <xs:element name="furtherDetails" type="xs:string" minOccurs="0"/>
-      <xs:element name="defaultValue" type="xs:string" minOccurs="0"/>
-    </xs:sequence>
-    <xs:attribute name="isRequired" type="xs:boolean" use="required"/>
-  </xs:complexType>
-
-  <xs:complexType name="customAlignResponse">
-    <xs:sequence>
-      <xs:element name="return" type="xs:string" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="WrongParameterException">
-    <xs:sequence>
-      <xs:element name="message" type="xs:string" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="pullExecStatistics">
-    <xs:sequence>
-      <xs:element name="jobId" type="xs:string" minOccurs="0"/>
-      <xs:element name="position" type="xs:long"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="pullExecStatisticsResponse">
-    <xs:sequence>
-      <xs:element name="return" type="tns:chunkHolder" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="chunkHolder">
-    <xs:sequence>
-      <xs:element name="chunk" type="xs:string" minOccurs="0"/>
-      <xs:element name="position" type="xs:long"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="presetAlign">
-    <xs:sequence>
-      <xs:element name="fastaSequences" type="tns:fastaSequence" minOccurs="0" maxOccurs="unbounded"/>
-      <xs:element name="preset" type="tns:preset" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="preset">
-    <xs:sequence>
-      <xs:element name="name" type="xs:string"/>
-      <xs:element name="description" type="xs:string" minOccurs="0"/>
-      <xs:element name="optlist" minOccurs="0">
-        <xs:complexType>
-          <xs:sequence>
-            <xs:element name="option" type="xs:string" maxOccurs="unbounded"/>
-          </xs:sequence>
-        </xs:complexType>
-      </xs:element>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="presetAlignResponse">
-    <xs:sequence>
-      <xs:element name="return" type="xs:string" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="getPresets">
-    <xs:sequence/>
-  </xs:complexType>
-
-  <xs:complexType name="getPresetsResponse">
-    <xs:sequence>
-      <xs:element name="return" type="tns:presetManager" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="presetManager">
-    <xs:sequence>
-      <xs:element name="runnerClassName" type="xs:string"/>
-      <xs:element name="preset" type="tns:preset" maxOccurs="unbounded"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="getLimits">
-    <xs:sequence/>
-  </xs:complexType>
-
-  <xs:complexType name="getLimitsResponse">
-    <xs:sequence>
-      <xs:element name="return" type="tns:limitsManager" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="limitsManager">
-    <xs:sequence>
-      <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
-      <xs:element name="limit" type="tns:limit" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="limit">
-    <xs:sequence>
-      <xs:element name="preset" type="xs:string" minOccurs="0"/>
-      <xs:element name="seqNumber" type="xs:int"/>
-      <xs:element name="seqLength" type="xs:int"/>
-    </xs:sequence>
-    <xs:attribute name="isDefault" type="xs:boolean" use="required"/>
-  </xs:complexType>
-
-  <xs:complexType name="getLimit">
-    <xs:sequence>
-      <xs:element name="presetName" type="xs:string" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="getLimitResponse">
-    <xs:sequence>
-      <xs:element name="return" type="tns:limit" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="cancelJob">
-    <xs:sequence>
-      <xs:element name="jobId" type="xs:string" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="cancelJobResponse">
-    <xs:sequence>
-      <xs:element name="return" type="xs:boolean"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="getRunnerOptions">
-    <xs:sequence/>
-  </xs:complexType>
-
-  <xs:complexType name="getRunnerOptionsResponse">
-    <xs:sequence>
-      <xs:element name="return" type="tns:runnerConfig" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="runnerConfig">
-    <xs:sequence>
-      <xs:element name="options" type="tns:option" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
-      <xs:element name="parameters" type="tns:parameter" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
-      <xs:element name="prmSeparator" type="xs:string" minOccurs="0"/>
-      <xs:element name="runnerClassName" type="xs:string"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="parameter">
-    <xs:complexContent>
-      <xs:extension base="tns:option">
-        <xs:sequence>
-          <xs:element name="possibleValues" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>
-          <xs:element name="validValue" type="tns:valueConstrain" minOccurs="0"/>
-        </xs:sequence>
-      </xs:extension>
-    </xs:complexContent>
-  </xs:complexType>
-
-  <xs:complexType name="valueConstrain">
-    <xs:sequence>
-      <xs:element name="type" type="tns:type"/>
-      <xs:element name="max" type="xs:string" minOccurs="0"/>
-      <xs:element name="min" type="xs:string" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="getResult">
-    <xs:sequence>
-      <xs:element name="jobId" type="xs:string" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="getResultResponse">
-    <xs:sequence>
-      <xs:element name="return" type="tns:alignment" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="alignment">
-    <xs:sequence>
-      <xs:element name="metadata" type="tns:alignmentMetadata" minOccurs="0"/>
-      <xs:element name="sequences" type="tns:fastaSequence" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="alignmentMetadata">
-    <xs:sequence>
-      <xs:element name="program" type="tns:program" minOccurs="0"/>
-      <xs:element name="gapchar" type="xs:unsignedShort"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="jpredAlignment">
-    <xs:complexContent>
-      <xs:extension base="tns:alignment">
-        <xs:sequence/>
-      </xs:extension>
-    </xs:complexContent>
-  </xs:complexType>
-
-  <xs:complexType name="ResultNotAvailableException">
-    <xs:sequence>
-      <xs:element name="message" type="xs:string" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="getJobStatus">
-    <xs:sequence>
-      <xs:element name="jobId" type="xs:string" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="getJobStatusResponse">
-    <xs:sequence>
-      <xs:element name="return" type="tns:jobStatus" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:simpleType name="type">
-    <xs:restriction base="xs:string">
-      <xs:enumeration value="Integer"/>
-      <xs:enumeration value="Float"/>
-    </xs:restriction>
-  </xs:simpleType>
-
-  <xs:simpleType name="program">
-    <xs:restriction base="xs:string">
-      <xs:enumeration value="CLUSTAL"/>
-      <xs:enumeration value="ClustalO"/>
-      <xs:enumeration value="Mafft"/>
-      <xs:enumeration value="Muscle"/>
-      <xs:enumeration value="Tcoffee"/>
-      <xs:enumeration value="Probcons"/>
-      <xs:enumeration value="MSAprobs"/>
-      <xs:enumeration value="GLprobs"/>
-      <xs:enumeration value="Jpred"/>
-    </xs:restriction>
-  </xs:simpleType>
-
-  <xs:simpleType name="jobStatus">
-    <xs:restriction base="xs:string">
-      <xs:enumeration value="PENDING"/>
-      <xs:enumeration value="RUNNING"/>
-      <xs:enumeration value="CANCELLED"/>
-      <xs:enumeration value="FINISHED"/>
-      <xs:enumeration value="FAILED"/>
-      <xs:enumeration value="UNDEFINED"/>
-      <xs:enumeration value="STARTED"/>
-      <xs:enumeration value="SUBMITTED"/>
-      <xs:enumeration value="COLLECTED"/>
-    </xs:restriction>
-  </xs:simpleType>
-</xs:schema>
-
diff --git a/webservices/compbio/ws/server/resource/MSAprobsWS.wsdl b/webservices/compbio/ws/server/resource/MSAprobsWS.wsdl
index a50285c..002951c 100644
--- a/webservices/compbio/ws/server/resource/MSAprobsWS.wsdl
+++ b/webservices/compbio/ws/server/resource/MSAprobsWS.wsdl
@@ -1,151 +1,8 @@
 <?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 Metro/2.1 (branches/2.1-6728; 2011-02-03T14:14:58+0000) JAXWS-RI/2.2.3 JAXWS/2.2. -->
-<definitions targetNamespace="http://msa.data.compbio/01/01/2010/" name="MSAprobsWS" xmlns="http://schemas.xmlsoap.org/wsdl/" xmlns:wsp="http://www.w3.org/ns/ws-policy" xmlns:tns="http://msa.data.compbio/01/01/2010/" 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">
-  <types>
-    <xsd:schema>
-      <xsd:import namespace="http://msa.data.compbio/01/01/2010/" schemaLocation="MSAprobsWS_schema1.xsd"/>
-    </xsd:schema>
-  </types>
-  <message name="align">
-    <part name="parameters" element="tns:align"/>
-  </message>
-  <message name="alignResponse">
-    <part name="parameters" element="tns:alignResponse"/>
-  </message>
-  <message name="UnsupportedRuntimeException">
-    <part name="fault" element="tns:UnsupportedRuntimeException"/>
-  </message>
-  <message name="LimitExceededException">
-    <part name="fault" element="tns:LimitExceededException"/>
-  </message>
-  <message name="JobSubmissionException">
-    <part name="fault" element="tns:JobSubmissionException"/>
-  </message>
-  <message name="presetAlign">
-    <part name="parameters" element="tns:presetAlign"/>
-  </message>
-  <message name="presetAlignResponse">
-    <part name="parameters" element="tns:presetAlignResponse"/>
-  </message>
-  <message name="WrongParameterException">
-    <part name="fault" element="tns:WrongParameterException"/>
-  </message>
-  <message name="customAlign">
-    <part name="parameters" element="tns:customAlign"/>
-  </message>
-  <message name="customAlignResponse">
-    <part name="parameters" element="tns:customAlignResponse"/>
-  </message>
-  <message name="getResult">
-    <part name="parameters" element="tns:getResult"/>
-  </message>
-  <message name="getResultResponse">
-    <part name="parameters" element="tns:getResultResponse"/>
-  </message>
-  <message name="ResultNotAvailableException">
-    <part name="fault" element="tns:ResultNotAvailableException"/>
-  </message>
-  <message name="cancelJob">
-    <part name="parameters" element="tns:cancelJob"/>
-  </message>
-  <message name="cancelJobResponse">
-    <part name="parameters" element="tns:cancelJobResponse"/>
-  </message>
-  <message name="getJobStatus">
-    <part name="parameters" element="tns:getJobStatus"/>
-  </message>
-  <message name="getJobStatusResponse">
-    <part name="parameters" element="tns:getJobStatusResponse"/>
-  </message>
-  <message name="pullExecStatistics">
-    <part name="parameters" element="tns:pullExecStatistics"/>
-  </message>
-  <message name="pullExecStatisticsResponse">
-    <part name="parameters" element="tns:pullExecStatisticsResponse"/>
-  </message>
-  <message name="getRunnerOptions">
-    <part name="parameters" element="tns:getRunnerOptions"/>
-  </message>
-  <message name="getRunnerOptionsResponse">
-    <part name="parameters" element="tns:getRunnerOptionsResponse"/>
-  </message>
-  <message name="getLimit">
-    <part name="parameters" element="tns:getLimit"/>
-  </message>
-  <message name="getLimitResponse">
-    <part name="parameters" element="tns:getLimitResponse"/>
-  </message>
-  <message name="getLimits">
-    <part name="parameters" element="tns:getLimits"/>
-  </message>
-  <message name="getLimitsResponse">
-    <part name="parameters" element="tns:getLimitsResponse"/>
-  </message>
-  <message name="getPresets">
-    <part name="parameters" element="tns:getPresets"/>
-  </message>
-  <message name="getPresetsResponse">
-    <part name="parameters" element="tns:getPresetsResponse"/>
-  </message>
-  <portType name="MsaWS">
-    <operation name="align">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignRequest" message="tns:align"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignResponse" message="tns:alignResponse"/>
-      <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/UnsupportedRuntimeException"/>
-      <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/LimitExceededException"/>
-      <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/JobSubmissionException"/>
-    </operation>
-    <operation name="presetAlign">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlignRequest" message="tns:presetAlign"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlignResponse" message="tns:presetAlignResponse"/>
-      <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/UnsupportedRuntimeException"/>
-      <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/LimitExceededException"/>
-      <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/JobSubmissionException"/>
-      <fault message="tns:WrongParameterException" name="WrongParameterException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/WrongParameterException"/>
-    </operation>
-    <operation name="customAlign">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlignRequest" message="tns:customAlign"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlignResponse" message="tns:customAlignResponse"/>
-      <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/UnsupportedRuntimeException"/>
-      <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/LimitExceededException"/>
-      <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/JobSubmissionException"/>
-      <fault message="tns:WrongParameterException" name="WrongParameterException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/WrongParameterException"/>
-    </operation>
-    <operation name="getResult">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultRequest" message="tns:getResult"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultResponse" message="tns:getResultResponse"/>
-      <fault message="tns:ResultNotAvailableException" name="ResultNotAvailableException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResult/Fault/ResultNotAvailableException"/>
-    </operation>
-    <operation name="cancelJob">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/cancelJobRequest" message="tns:cancelJob"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/cancelJobResponse" message="tns:cancelJobResponse"/>
-    </operation>
-    <operation name="getJobStatus">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getJobStatusRequest" message="tns:getJobStatus"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getJobStatusResponse" message="tns:getJobStatusResponse"/>
-    </operation>
-    <operation name="pullExecStatistics">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
-    </operation>
-    <operation name="getRunnerOptions">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
-    </operation>
-    <operation name="getLimit">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitRequest" message="tns:getLimit"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitResponse" message="tns:getLimitResponse"/>
-    </operation>
-    <operation name="getLimits">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsRequest" message="tns:getLimits"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsResponse" message="tns:getLimitsResponse"/>
-    </operation>
-    <operation name="getPresets">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsRequest" message="tns:getPresets"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsResponse" message="tns:getPresetsResponse"/>
-    </operation>
-  </portType>
-  <binding name="MSAprobsWSPortBinding" type="tns:MsaWS">
+<definitions targetNamespace="http://msa.data.compbio/01/12/2010/" name="MSAprobsWS" 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">
+  <import namespace="http://msa.data.compbio/01/01/2010/" location="MsaWS.wsdl"/>
+  <binding name="MSAprobsWSPortBinding" type="ns1:MsaWS" xmlns:ns1="http://msa.data.compbio/01/01/2010/">
     <soap:binding transport="http://schemas.xmlsoap.org/soap/http" style="document"/>
     <operation name="align">
       <soap:operation soapAction=""/>
diff --git a/webservices/compbio/ws/server/resource/MSAprobsWS_schema1.xsd b/webservices/compbio/ws/server/resource/MSAprobsWS_schema1.xsd
deleted file mode 100644
index 5ab9459..0000000
--- a/webservices/compbio/ws/server/resource/MSAprobsWS_schema1.xsd
+++ /dev/null
@@ -1,374 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
-<xs:schema version="1.0" targetNamespace="http://msa.data.compbio/01/01/2010/" xmlns:tns="http://msa.data.compbio/01/01/2010/" xmlns:xs="http://www.w3.org/2001/XMLSchema">
-
-  <xs:element name="JobSubmissionException" type="tns:JobSubmissionException"/>
-
-  <xs:element name="LimitExceededException" type="tns:LimitExceededException"/>
-
-  <xs:element name="ResultNotAvailableException" type="tns:ResultNotAvailableException"/>
-
-  <xs:element name="UnsupportedRuntimeException" type="tns:UnsupportedRuntimeException"/>
-
-  <xs:element name="WrongParameterException" type="tns:WrongParameterException"/>
-
-  <xs:element name="align" type="tns:align"/>
-
-  <xs:element name="alignResponse" type="tns:alignResponse"/>
-
-  <xs:element name="cancelJob" type="tns:cancelJob"/>
-
-  <xs:element name="cancelJobResponse" type="tns:cancelJobResponse"/>
-
-  <xs:element name="customAlign" type="tns:customAlign"/>
-
-  <xs:element name="customAlignResponse" type="tns:customAlignResponse"/>
-
-  <xs:element name="getJobStatus" type="tns:getJobStatus"/>
-
-  <xs:element name="getJobStatusResponse" type="tns:getJobStatusResponse"/>
-
-  <xs:element name="getLimit" type="tns:getLimit"/>
-
-  <xs:element name="getLimitResponse" type="tns:getLimitResponse"/>
-
-  <xs:element name="getLimits" type="tns:getLimits"/>
-
-  <xs:element name="getLimitsResponse" type="tns:getLimitsResponse"/>
-
-  <xs:element name="getPresets" type="tns:getPresets"/>
-
-  <xs:element name="getPresetsResponse" type="tns:getPresetsResponse"/>
-
-  <xs:element name="getResult" type="tns:getResult"/>
-
-  <xs:element name="getResultResponse" type="tns:getResultResponse"/>
-
-  <xs:element name="getRunnerOptions" type="tns:getRunnerOptions"/>
-
-  <xs:element name="getRunnerOptionsResponse" type="tns:getRunnerOptionsResponse"/>
-
-  <xs:element name="limits" type="tns:limitsManager"/>
-
-  <xs:element name="presetAlign" type="tns:presetAlign"/>
-
-  <xs:element name="presetAlignResponse" type="tns:presetAlignResponse"/>
-
-  <xs:element name="presets" type="tns:presetManager"/>
-
-  <xs:element name="pullExecStatistics" type="tns:pullExecStatistics"/>
-
-  <xs:element name="pullExecStatisticsResponse" type="tns:pullExecStatisticsResponse"/>
-
-  <xs:element name="runnerConfig" type="tns:runnerConfig"/>
-
-  <xs:complexType name="getRunnerOptions">
-    <xs:sequence/>
-  </xs:complexType>
-
-  <xs:complexType name="getRunnerOptionsResponse">
-    <xs:sequence>
-      <xs:element name="return" type="tns:runnerConfig" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="runnerConfig">
-    <xs:sequence>
-      <xs:element name="options" type="tns:option" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
-      <xs:element name="parameters" type="tns:parameter" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
-      <xs:element name="prmSeparator" type="xs:string" minOccurs="0"/>
-      <xs:element name="runnerClassName" type="xs:string"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="option">
-    <xs:sequence>
-      <xs:element name="description" type="xs:string"/>
-      <xs:element name="optionNames" type="xs:string" maxOccurs="unbounded"/>
-      <xs:element name="name" type="xs:string"/>
-      <xs:element name="furtherDetails" type="xs:string" minOccurs="0"/>
-      <xs:element name="defaultValue" type="xs:string" minOccurs="0"/>
-    </xs:sequence>
-    <xs:attribute name="isRequired" type="xs:boolean" use="required"/>
-  </xs:complexType>
-
-  <xs:complexType name="parameter">
-    <xs:complexContent>
-      <xs:extension base="tns:option">
-        <xs:sequence>
-          <xs:element name="possibleValues" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>
-          <xs:element name="validValue" type="tns:valueConstrain" minOccurs="0"/>
-        </xs:sequence>
-      </xs:extension>
-    </xs:complexContent>
-  </xs:complexType>
-
-  <xs:complexType name="valueConstrain">
-    <xs:sequence>
-      <xs:element name="type" type="tns:type"/>
-      <xs:element name="max" type="xs:string" minOccurs="0"/>
-      <xs:element name="min" type="xs:string" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="getResult">
-    <xs:sequence>
-      <xs:element name="jobId" type="xs:string" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="getResultResponse">
-    <xs:sequence>
-      <xs:element name="return" type="tns:alignment" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="alignment">
-    <xs:sequence>
-      <xs:element name="metadata" type="tns:alignmentMetadata" minOccurs="0"/>
-      <xs:element name="sequences" type="tns:fastaSequence" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="alignmentMetadata">
-    <xs:sequence>
-      <xs:element name="program" type="tns:program" minOccurs="0"/>
-      <xs:element name="gapchar" type="xs:unsignedShort"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="fastaSequence">
-    <xs:sequence>
-      <xs:element name="id" type="xs:string" minOccurs="0"/>
-      <xs:element name="sequence" type="xs:string" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="jpredAlignment">
-    <xs:complexContent>
-      <xs:extension base="tns:alignment">
-        <xs:sequence/>
-      </xs:extension>
-    </xs:complexContent>
-  </xs:complexType>
-
-  <xs:complexType name="ResultNotAvailableException">
-    <xs:sequence>
-      <xs:element name="message" type="xs:string" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="getJobStatus">
-    <xs:sequence>
-      <xs:element name="jobId" type="xs:string" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="getJobStatusResponse">
-    <xs:sequence>
-      <xs:element name="return" type="tns:jobStatus" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="pullExecStatistics">
-    <xs:sequence>
-      <xs:element name="jobId" type="xs:string" minOccurs="0"/>
-      <xs:element name="position" type="xs:long"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="pullExecStatisticsResponse">
-    <xs:sequence>
-      <xs:element name="return" type="tns:chunkHolder" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="chunkHolder">
-    <xs:sequence>
-      <xs:element name="chunk" type="xs:string" minOccurs="0"/>
-      <xs:element name="position" type="xs:long"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="customAlign">
-    <xs:sequence>
-      <xs:element name="fastaSequences" type="tns:fastaSequence" minOccurs="0" maxOccurs="unbounded"/>
-      <xs:element name="options" type="tns:option" minOccurs="0" maxOccurs="unbounded"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="customAlignResponse">
-    <xs:sequence>
-      <xs:element name="return" type="xs:string" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="UnsupportedRuntimeException">
-    <xs:sequence>
-      <xs:element name="message" type="xs:string" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="LimitExceededException">
-    <xs:sequence>
-      <xs:element name="actualNumberofSequences" type="xs:int"/>
-      <xs:element name="message" type="xs:string" minOccurs="0"/>
-      <xs:element name="numberOfSequencesAllowed" type="xs:int"/>
-      <xs:element name="sequenceLenghtActual" type="xs:int"/>
-      <xs:element name="sequenceLenghtAllowed" type="xs:int"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="JobSubmissionException">
-    <xs:sequence>
-      <xs:element name="message" type="xs:string" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="WrongParameterException">
-    <xs:sequence>
-      <xs:element name="message" type="xs:string" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="align">
-    <xs:sequence>
-      <xs:element name="fastaSequences" type="tns:fastaSequence" minOccurs="0" maxOccurs="unbounded"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="alignResponse">
-    <xs:sequence>
-      <xs:element name="return" type="xs:string" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="getPresets">
-    <xs:sequence/>
-  </xs:complexType>
-
-  <xs:complexType name="getPresetsResponse">
-    <xs:sequence>
-      <xs:element name="return" type="tns:presetManager" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="presetManager">
-    <xs:sequence>
-      <xs:element name="runnerClassName" type="xs:string"/>
-      <xs:element name="preset" type="tns:preset" maxOccurs="unbounded"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="preset">
-    <xs:sequence>
-      <xs:element name="name" type="xs:string"/>
-      <xs:element name="description" type="xs:string" minOccurs="0"/>
-      <xs:element name="optlist" minOccurs="0">
-        <xs:complexType>
-          <xs:sequence>
-            <xs:element name="option" type="xs:string" maxOccurs="unbounded"/>
-          </xs:sequence>
-        </xs:complexType>
-      </xs:element>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="getLimits">
-    <xs:sequence/>
-  </xs:complexType>
-
-  <xs:complexType name="getLimitsResponse">
-    <xs:sequence>
-      <xs:element name="return" type="tns:limitsManager" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="limitsManager">
-    <xs:sequence>
-      <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
-      <xs:element name="limit" type="tns:limit" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="limit">
-    <xs:sequence>
-      <xs:element name="preset" type="xs:string" minOccurs="0"/>
-      <xs:element name="seqNumber" type="xs:int"/>
-      <xs:element name="seqLength" type="xs:int"/>
-    </xs:sequence>
-    <xs:attribute name="isDefault" type="xs:boolean" use="required"/>
-  </xs:complexType>
-
-  <xs:complexType name="getLimit">
-    <xs:sequence>
-      <xs:element name="presetName" type="xs:string" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="getLimitResponse">
-    <xs:sequence>
-      <xs:element name="return" type="tns:limit" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="cancelJob">
-    <xs:sequence>
-      <xs:element name="jobId" type="xs:string" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="cancelJobResponse">
-    <xs:sequence>
-      <xs:element name="return" type="xs:boolean"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="presetAlign">
-    <xs:sequence>
-      <xs:element name="fastaSequences" type="tns:fastaSequence" minOccurs="0" maxOccurs="unbounded"/>
-      <xs:element name="preset" type="tns:preset" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:complexType name="presetAlignResponse">
-    <xs:sequence>
-      <xs:element name="return" type="xs:string" minOccurs="0"/>
-    </xs:sequence>
-  </xs:complexType>
-
-  <xs:simpleType name="type">
-    <xs:restriction base="xs:string">
-      <xs:enumeration value="Integer"/>
-      <xs:enumeration value="Float"/>
-    </xs:restriction>
-  </xs:simpleType>
-
-  <xs:simpleType name="program">
-    <xs:restriction base="xs:string">
-      <xs:enumeration value="CLUSTAL"/>
-      <xs:enumeration value="ClustalO"/>
-      <xs:enumeration value="Mafft"/>
-      <xs:enumeration value="Muscle"/>
-      <xs:enumeration value="Tcoffee"/>
-      <xs:enumeration value="Probcons"/>
-      <xs:enumeration value="MSAprobs"/>
-      <xs:enumeration value="GLprobs"/>
-      <xs:enumeration value="Jpred"/>
-    </xs:restriction>
-  </xs:simpleType>
-
-  <xs:simpleType name="jobStatus">
-    <xs:restriction base="xs:string">
-      <xs:enumeration value="PENDING"/>
-      <xs:enumeration value="RUNNING"/>
-      <xs:enumeration value="CANCELLED"/>
-      <xs:enumeration value="FINISHED"/>
-      <xs:enumeration value="FAILED"/>
-      <xs:enumeration value="UNDEFINED"/>
-      <xs:enumeration value="STARTED"/>
-      <xs:enumeration value="SUBMITTED"/>
-      <xs:enumeration value="COLLECTED"/>
-    </xs:restriction>
-  </xs:simpleType>
-</xs:schema>
-
diff --git a/webservices/compbio/ws/server/resource/MsaWS.wsdl b/webservices/compbio/ws/server/resource/MsaWS.wsdl
new file mode 100644
index 0000000..9481416
--- /dev/null
+++ b/webservices/compbio/ws/server/resource/MsaWS.wsdl
@@ -0,0 +1,149 @@
+<?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 Metro/2.1 (branches/2.1-6728; 2011-02-03T14:14:58+0000) JAXWS-RI/2.2.3 JAXWS/2.2. -->
+<definitions targetNamespace="http://msa.data.compbio/01/01/2010/" xmlns="http://schemas.xmlsoap.org/wsdl/" xmlns:tns="http://msa.data.compbio/01/01/2010/" xmlns:xsd="http://www.w3.org/2001/XMLSchema">
+  <types>
+    <xsd:schema>
+      <xsd:import namespace="http://msa.data.compbio/01/01/2010/" schemaLocation="MsaWS_schema1.xsd"/>
+    </xsd:schema>
+  </types>
+  <message name="align">
+    <part name="parameters" element="tns:align"/>
+  </message>
+  <message name="alignResponse">
+    <part name="parameters" element="tns:alignResponse"/>
+  </message>
+  <message name="UnsupportedRuntimeException">
+    <part name="fault" element="tns:UnsupportedRuntimeException"/>
+  </message>
+  <message name="LimitExceededException">
+    <part name="fault" element="tns:LimitExceededException"/>
+  </message>
+  <message name="JobSubmissionException">
+    <part name="fault" element="tns:JobSubmissionException"/>
+  </message>
+  <message name="presetAlign">
+    <part name="parameters" element="tns:presetAlign"/>
+  </message>
+  <message name="presetAlignResponse">
+    <part name="parameters" element="tns:presetAlignResponse"/>
+  </message>
+  <message name="WrongParameterException">
+    <part name="fault" element="tns:WrongParameterException"/>
+  </message>
+  <message name="customAlign">
+    <part name="parameters" element="tns:customAlign"/>
+  </message>
+  <message name="customAlignResponse">
+    <part name="parameters" element="tns:customAlignResponse"/>
+  </message>
+  <message name="getResult">
+    <part name="parameters" element="tns:getResult"/>
+  </message>
+  <message name="getResultResponse">
+    <part name="parameters" element="tns:getResultResponse"/>
+  </message>
+  <message name="ResultNotAvailableException">
+    <part name="fault" element="tns:ResultNotAvailableException"/>
+  </message>
+  <message name="cancelJob">
+    <part name="parameters" element="tns:cancelJob"/>
+  </message>
+  <message name="cancelJobResponse">
+    <part name="parameters" element="tns:cancelJobResponse"/>
+  </message>
+  <message name="getJobStatus">
+    <part name="parameters" element="tns:getJobStatus"/>
+  </message>
+  <message name="getJobStatusResponse">
+    <part name="parameters" element="tns:getJobStatusResponse"/>
+  </message>
+  <message name="pullExecStatistics">
+    <part name="parameters" element="tns:pullExecStatistics"/>
+  </message>
+  <message name="pullExecStatisticsResponse">
+    <part name="parameters" element="tns:pullExecStatisticsResponse"/>
+  </message>
+  <message name="getRunnerOptions">
+    <part name="parameters" element="tns:getRunnerOptions"/>
+  </message>
+  <message name="getRunnerOptionsResponse">
+    <part name="parameters" element="tns:getRunnerOptionsResponse"/>
+  </message>
+  <message name="getLimit">
+    <part name="parameters" element="tns:getLimit"/>
+  </message>
+  <message name="getLimitResponse">
+    <part name="parameters" element="tns:getLimitResponse"/>
+  </message>
+  <message name="getLimits">
+    <part name="parameters" element="tns:getLimits"/>
+  </message>
+  <message name="getLimitsResponse">
+    <part name="parameters" element="tns:getLimitsResponse"/>
+  </message>
+  <message name="getPresets">
+    <part name="parameters" element="tns:getPresets"/>
+  </message>
+  <message name="getPresetsResponse">
+    <part name="parameters" element="tns:getPresetsResponse"/>
+  </message>
+  <portType name="MsaWS">
+    <operation name="align">
+      <input ns1:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignRequest" message="tns:align" xmlns:ns1="http://www.w3.org/2007/05/addressing/metadata"/>
+      <output ns2:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignResponse" message="tns:alignResponse" xmlns:ns2="http://www.w3.org/2007/05/addressing/metadata"/>
+      <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" ns3:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/UnsupportedRuntimeException" xmlns:ns3="http://www.w3.org/2007/05/addressing/metadata"/>
+      <fault message="tns:LimitExceededException" name="LimitExceededException" ns4:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/LimitExceededException" xmlns:ns4="http://www.w3.org/2007/05/addressing/metadata"/>
+      <fault message="tns:JobSubmissionException" name="JobSubmissionException" ns5:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/JobSubmissionException" xmlns:ns5="http://www.w3.org/2007/05/addressing/metadata"/>
+    </operation>
+    <operation name="presetAlign">
+      <input ns6:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlignRequest" message="tns:presetAlign" xmlns:ns6="http://www.w3.org/2007/05/addressing/metadata"/>
+      <output ns7:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlignResponse" message="tns:presetAlignResponse" xmlns:ns7="http://www.w3.org/2007/05/addressing/metadata"/>
+      <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" ns8:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/UnsupportedRuntimeException" xmlns:ns8="http://www.w3.org/2007/05/addressing/metadata"/>
+      <fault message="tns:LimitExceededException" name="LimitExceededException" ns9:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/LimitExceededException" xmlns:ns9="http://www.w3.org/2007/05/addressing/metadata"/>
+      <fault message="tns:JobSubmissionException" name="JobSubmissionException" ns10:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/JobSubmissionException" xmlns:ns10="http://www.w3.org/2007/05/addressing/metadata"/>
+      <fault message="tns:WrongParameterException" name="WrongParameterException" ns11:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/WrongParameterException" xmlns:ns11="http://www.w3.org/2007/05/addressing/metadata"/>
+    </operation>
+    <operation name="customAlign">
+      <input ns12:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlignRequest" message="tns:customAlign" xmlns:ns12="http://www.w3.org/2007/05/addressing/metadata"/>
+      <output ns13:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlignResponse" message="tns:customAlignResponse" xmlns:ns13="http://www.w3.org/2007/05/addressing/metadata"/>
+      <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" ns14:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/UnsupportedRuntimeException" xmlns:ns14="http://www.w3.org/2007/05/addressing/metadata"/>
+      <fault message="tns:LimitExceededException" name="LimitExceededException" ns15:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/LimitExceededException" xmlns:ns15="http://www.w3.org/2007/05/addressing/metadata"/>
+      <fault message="tns:JobSubmissionException" name="JobSubmissionException" ns16:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/JobSubmissionException" xmlns:ns16="http://www.w3.org/2007/05/addressing/metadata"/>
+      <fault message="tns:WrongParameterException" name="WrongParameterException" ns17:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/WrongParameterException" xmlns:ns17="http://www.w3.org/2007/05/addressing/metadata"/>
+    </operation>
+    <operation name="getResult">
+      <input ns18:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultRequest" message="tns:getResult" xmlns:ns18="http://www.w3.org/2007/05/addressing/metadata"/>
+      <output ns19:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultResponse" message="tns:getResultResponse" xmlns:ns19="http://www.w3.org/2007/05/addressing/metadata"/>
+      <fault message="tns:ResultNotAvailableException" name="ResultNotAvailableException" ns20:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResult/Fault/ResultNotAvailableException" xmlns:ns20="http://www.w3.org/2007/05/addressing/metadata"/>
+    </operation>
+    <operation name="cancelJob">
+      <input ns21:Action="http://msa.data.compbio/01/01/2010/MsaWS/cancelJobRequest" message="tns:cancelJob" xmlns:ns21="http://www.w3.org/2007/05/addressing/metadata"/>
+      <output ns22:Action="http://msa.data.compbio/01/01/2010/MsaWS/cancelJobResponse" message="tns:cancelJobResponse" xmlns:ns22="http://www.w3.org/2007/05/addressing/metadata"/>
+    </operation>
+    <operation name="getJobStatus">
+      <input ns23:Action="http://msa.data.compbio/01/01/2010/MsaWS/getJobStatusRequest" message="tns:getJobStatus" xmlns:ns23="http://www.w3.org/2007/05/addressing/metadata"/>
+      <output ns24:Action="http://msa.data.compbio/01/01/2010/MsaWS/getJobStatusResponse" message="tns:getJobStatusResponse" xmlns:ns24="http://www.w3.org/2007/05/addressing/metadata"/>
+    </operation>
+    <operation name="pullExecStatistics">
+      <input ns25:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsRequest" message="tns:pullExecStatistics" xmlns:ns25="http://www.w3.org/2007/05/addressing/metadata"/>
+      <output ns26:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse" xmlns:ns26="http://www.w3.org/2007/05/addressing/metadata"/>
+    </operation>
+    <operation name="getRunnerOptions">
+      <input ns27:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsRequest" message="tns:getRunnerOptions" xmlns:ns27="http://www.w3.org/2007/05/addressing/metadata"/>
+      <output ns28:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse" xmlns:ns28="http://www.w3.org/2007/05/addressing/metadata"/>
+    </operation>
+    <operation name="getLimit">
+      <input ns29:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitRequest" message="tns:getLimit" xmlns:ns29="http://www.w3.org/2007/05/addressing/metadata"/>
+      <output ns30:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitResponse" message="tns:getLimitResponse" xmlns:ns30="http://www.w3.org/2007/05/addressing/metadata"/>
+    </operation>
+    <operation name="getLimits">
+      <input ns31:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsRequest" message="tns:getLimits" xmlns:ns31="http://www.w3.org/2007/05/addressing/metadata"/>
+      <output ns32:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsResponse" message="tns:getLimitsResponse" xmlns:ns32="http://www.w3.org/2007/05/addressing/metadata"/>
+    </operation>
+    <operation name="getPresets">
+      <input ns33:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsRequest" message="tns:getPresets" xmlns:ns33="http://www.w3.org/2007/05/addressing/metadata"/>
+      <output ns34:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsResponse" message="tns:getPresetsResponse" xmlns:ns34="http://www.w3.org/2007/05/addressing/metadata"/>
+    </operation>
+  </portType>
+</definitions>
+
diff --git a/webservices/compbio/ws/server/resource/GLprobsWS_schema1.xsd b/webservices/compbio/ws/server/resource/MsaWS_schema1.xsd
similarity index 100%
rename from webservices/compbio/ws/server/resource/GLprobsWS_schema1.xsd
rename to webservices/compbio/ws/server/resource/MsaWS_schema1.xsd
diff --git a/wsbuild.log b/wsbuild.log
index 35dff38..9ab338d 100644
--- a/wsbuild.log
+++ b/wsbuild.log
@@ -2,8 +2,31 @@
 build-server:
    [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/AAConWS.wsdl
    [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/AAConWS_schema1.xsd
+   [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/ClustalWS.wsdl
+   [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/ClustalWS_schema1.xsd
+   [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/DisemblWS.wsdl
+   [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/DisemblWS_schema1.xsd
+   [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/GLprobsWS.wsdl
+   [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/GlobPlotWS.wsdl
+   [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/GlobPlotWS_schema1.xsd
+   [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/IUPredWS.wsdl
+   [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/IUPredWS_schema1.xsd
    [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/JpredWS.wsdl
-   [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/JpredWS_schema1.xsd
+   [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/JronnWS.wsdl
+   [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/JronnWS_schema1.xsd
+   [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/MSAprobsWS.wsdl
+   [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/MafftWS.wsdl
+   [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/MafftWS_schema1.xsd
+   [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/MsaWS.wsdl
+   [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/MsaWS_schema1.xsd
+   [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/MuscleWS.wsdl
+   [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/MuscleWS_schema1.xsd
+   [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/RNAalifoldWS.wsdl
+   [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/RNAalifoldWS_schema1.xsd
+   [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/RegistryWS.wsdl
+   [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/RegistryWS_schema1.xsd
+   [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/TcoffeeWS.wsdl
+   [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/TcoffeeWS_schema1.xsd
     [wsgen] command line: wsgen -classpath /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/classes:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/commons-beanutils-1.7.0.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/commons-collections-3.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/commons-lang-2.3.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/commons-logging-1.1.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/compbio-annotations-1.0.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/compbio-ga-1.1.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/compbio-util-1.4.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/derby-10.8.2.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/displaytag-1.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/displaytag-export-poi-1.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/drmaa.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/itext-1.4.7.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/jstl-1.1.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/log4j-1.2.15.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/poi-3.2-FINAL-20081019.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/standard-1.1.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/webservices-api.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/webservices-rt.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/webservices-tools.jar -d /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/classes -Xendorsed -keep -wsdl -r /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource -s /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices -verbose compbio.ws.server.JpredWS
     [wsgen] Note: 	ap round: 1
     [wsgen] [ProcessedMethods Interface: compbio.data.msa.MsaWS<T>]
-- 
1.7.10.2