X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fserver%2FMuscleWS.java;h=a9d6c5205b7b3833728610552a0fcf3851a8b2c9;hb=23fb18b3f14a1b396f0c61f2ea4559fec758cb1d;hp=0e5d3ef644808c8a85df2e236a5b31d1b7ee9c59;hpb=603a6be6b9459625f535bf42c6d8ec5462e218e2;p=jabaws.git

diff --git a/webservices/compbio/ws/server/MuscleWS.java b/webservices/compbio/ws/server/MuscleWS.java
index 0e5d3ef..a9d6c52 100644
--- a/webservices/compbio/ws/server/MuscleWS.java
+++ b/webservices/compbio/ws/server/MuscleWS.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.Muscle;
 
-@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "MuscleWS")
+@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "MuscleWS")
 public class MuscleWS implements MsaWS<Muscle> {
 
 	private static Logger log = Logger.getLogger(MuscleWS.class);
@@ -65,7 +66,7 @@ public class MuscleWS implements MsaWS<Muscle> {
 			throws JobSubmissionException {
 		WSUtil.validateFastaInput(sequences);
 		ConfiguredExecutable<Muscle> confMuscle = init(sequences);
-		return WSUtil.align(sequences, confMuscle, null, "align", getLimit(""));
+		return WSUtil.align(sequences, confMuscle, log, "align", getLimit(""));
 	}
 
 	ConfiguredExecutable<Muscle> init(List<FastaSequence> sequences)
@@ -89,7 +90,7 @@ public class MuscleWS implements MsaWS<Muscle> {
 		List<String> params = WSUtil.getCommands(options,
 				Muscle.KEY_VALUE_SEPARATOR);
 		confMuscle.addParameters(params);
-		return WSUtil.align(sequences, confMuscle, null, "customAlign",
+		return WSUtil.align(sequences, confMuscle, log, "customAlign",
 				getLimit(""));
 	}
 
@@ -104,7 +105,7 @@ public class MuscleWS implements MsaWS<Muscle> {
 		ConfiguredExecutable<Muscle> confMuscle = init(sequences);
 		confMuscle.addParameters(preset.getOptions());
 		Limit<Muscle> limit = getLimit(preset.getName());
-		return WSUtil.align(sequences, confMuscle, null, "presetAlign", limit);
+		return WSUtil.align(sequences, confMuscle, log, "presetAlign", limit);
 	}
 
 	@SuppressWarnings("unchecked")