X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=webservices%2Fcompbio%2Fws%2Fserver%2FMafftWS.java;h=f293ae79d154209d638e330d86b4379e7e8d32d8;hb=da8c820a7fb2edecb190589f3dc9c362e57a2f24;hp=12805af17e733a0061ffe77c798c9dd73476facf;hpb=61af8ce2cea02220228f58b30b4319f500b2f040;p=jabaws.git

diff --git a/webservices/compbio/ws/server/MafftWS.java b/webservices/compbio/ws/server/MafftWS.java
index 12805af..f293ae7 100644
--- a/webservices/compbio/ws/server/MafftWS.java
+++ b/webservices/compbio/ws/server/MafftWS.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;
@@ -46,7 +47,7 @@ import compbio.metadata.WrongParameterException;
 import compbio.runner.Util;
 import compbio.runner.msa.Mafft;
 
-@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "MafftWS")
+@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "MafftWS")
 public class MafftWS implements MsaWS<Mafft> {
 
 	private static Logger log = Logger.getLogger(MafftWS.class);
@@ -65,7 +66,7 @@ public class MafftWS implements MsaWS<Mafft> {
 			throws JobSubmissionException {
 		WSUtil.validateFastaInput(sequences);
 		ConfiguredExecutable<Mafft> confMafft = init(sequences);
-		return WSUtil.align(sequences, confMafft, null, "align", getLimit(""));
+		return WSUtil.align(sequences, confMafft, log, "align", getLimit(""));
 	}
 
 	ConfiguredExecutable<Mafft> init(List<FastaSequence> dataSet)
@@ -87,7 +88,7 @@ public class MafftWS implements MsaWS<Mafft> {
 				Mafft.KEY_VALUE_SEPARATOR);
 		log.info("Setting parameters: " + params);
 		confMafft.addParameters(params);
-		return WSUtil.align(sequences, confMafft, null, "customAlign",
+		return WSUtil.align(sequences, confMafft, log, "customAlign",
 				getLimit(""));
 	}
 
@@ -105,7 +106,7 @@ public class MafftWS implements MsaWS<Mafft> {
 		// particular preset is not found
 		Limit<Mafft> limit = getLimit(preset.getName());
 
-		return WSUtil.align(sequences, confMafft, null, "presetAlign", limit);
+		return WSUtil.align(sequences, confMafft, log, "presetAlign", limit);
 	}
 
 	@SuppressWarnings("unchecked")