X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fserver%2FTcoffeeWS.java;h=086d870bf9594a18c931aa194f96bb36ed0cfd85;hb=9072bd850138bedbd005509e5b14bb5e104574b4;hp=59b4c19808cd68851da609840b7b91c44d83eafe;hpb=61af8ce2cea02220228f58b30b4319f500b2f040;p=jabaws.git

diff --git a/webservices/compbio/ws/server/TcoffeeWS.java b/webservices/compbio/ws/server/TcoffeeWS.java
index 59b4c19..086d870 100644
--- a/webservices/compbio/ws/server/TcoffeeWS.java
+++ b/webservices/compbio/ws/server/TcoffeeWS.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
@@ -25,6 +25,7 @@ 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;
@@ -47,7 +48,7 @@ import compbio.metadata.WrongParameterException;
 import compbio.runner.Util;
 import compbio.runner.msa.Tcoffee;
 
-@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "TcoffeeWS")
+@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "TcoffeeWS")
 public class TcoffeeWS implements MsaWS<Tcoffee> {
 
 	private static Logger log = Logger.getLogger(TcoffeeWS.class);
@@ -66,8 +67,7 @@ public class TcoffeeWS implements MsaWS<Tcoffee> {
 			throws JobSubmissionException {
 		WSUtil.validateFastaInput(sequences);
 		ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);
-		return WSUtil
-				.align(sequences, confTcoffee, null, "align", getLimit(""));
+		return WSUtil.align(sequences, confTcoffee, log, "align", getLimit(""));
 	}
 
 	ConfiguredExecutable<Tcoffee> init(List<FastaSequence> sequences)
@@ -100,7 +100,7 @@ public class TcoffeeWS implements MsaWS<Tcoffee> {
 				Tcoffee.KEY_VALUE_SEPARATOR);
 		log.info("Setting parameters:" + params);
 		confTcoffee.addParameters(params);
-		return WSUtil.align(sequences, confTcoffee, null, "customAlign",
+		return WSUtil.align(sequences, confTcoffee, log, "customAlign",
 				getLimit(""));
 	}
 
@@ -115,7 +115,7 @@ public class TcoffeeWS implements MsaWS<Tcoffee> {
 		ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);
 		confTcoffee.addParameters(preset.getOptions());
 		Limit<Tcoffee> limit = getLimit(preset.getName());
-		return WSUtil.align(sequences, confTcoffee, null, "presetAlign", limit);
+		return WSUtil.align(sequences, confTcoffee, log, "presetAlign", limit);
 	}
 
 	@SuppressWarnings("unchecked")