X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fserver%2FClustalWS.java;h=3ba7d62bfe1265220a8a6b641081a637bd1e8784;hb=bd6c0919476cff487ea479588d5ad9f3bdd5af1e;hp=22fad0c8eb1fe16fe5faf6d8b13a9f0142a889c7;hpb=603a6be6b9459625f535bf42c6d8ec5462e218e2;p=jabaws.git

diff --git a/webservices/compbio/ws/server/ClustalWS.java b/webservices/compbio/ws/server/ClustalWS.java
index 22fad0c..3ba7d62 100644
--- a/webservices/compbio/ws/server/ClustalWS.java
+++ b/webservices/compbio/ws/server/ClustalWS.java
@@ -1,6 +1,6 @@
-/* Copyright (c) 2009 Peter Troshin
+/* Copyright (c) 2011 Peter Troshin
  *  
- *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0   
+ *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     
  * 
  *  This library is free software; you can redistribute it and/or modify it under the terms of the
  *  Apache License version 2 as published by the Apache Software Foundation
@@ -25,12 +25,14 @@ import javax.jws.WebService;
 
 import org.apache.log4j.Logger;
 
+import compbio.data.msa.JABAService;
 import compbio.data.msa.MsaWS;
 import compbio.data.sequence.Alignment;
 import compbio.data.sequence.FastaSequence;
 import compbio.engine.AsyncExecutor;
 import compbio.engine.Configurator;
 import compbio.engine.client.ConfiguredExecutable;
+import compbio.engine.client.SkeletalExecutable;
 import compbio.metadata.ChunkHolder;
 import compbio.metadata.JobStatus;
 import compbio.metadata.JobSubmissionException;
@@ -45,7 +47,7 @@ import compbio.metadata.WrongParameterException;
 import compbio.runner.Util;
 import compbio.runner.msa.ClustalW;
 
-@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "ClustalWS")
+@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "ClustalWS")
 public class ClustalWS implements MsaWS<ClustalW> {
 
 	private static Logger log = Logger.getLogger(ClustalWS.class);
@@ -71,6 +73,9 @@ public class ClustalWS implements MsaWS<ClustalW> {
 	ConfiguredExecutable<ClustalW> init(List<FastaSequence> dataSet)
 			throws JobSubmissionException {
 		ClustalW clustal = new ClustalW();
+		clustal.setInput(SkeletalExecutable.INPUT)
+				.setOutput(SkeletalExecutable.OUTPUT)
+				.setError(SkeletalExecutable.ERROR);
 		ConfiguredExecutable<ClustalW> confClust = Configurator
 				.configureExecutable(clustal, dataSet);
 		return confClust;