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[jabaws.git] / webservices / compbio / ws / server / MuscleWS.java

diff --git a/webservices/compbio/ws/server/MuscleWS.java b/webservices/compbio/ws/server/MuscleWS.java
index 0e5d3ef..a9d6c52 100644 (file)
--- a/webservices/compbio/ws/server/MuscleWS.java
+++ b/webservices/compbio/ws/server/MuscleWS.java
@@ -1,6 +1,6 @@
-/* Copyright (c) 2009 Peter Troshin\r
+/* Copyright (c) 2011 Peter Troshin\r
  *  \r
- *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0   \r
+ *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     \r
  * \r
  *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
  *  Apache License version 2 as published by the Apache Software Foundation\r
@@ -25,6 +25,7 @@ import javax.jws.WebService;
 \r
 import org.apache.log4j.Logger;\r
 \r
+import compbio.data.msa.JABAService;\r
 import compbio.data.msa.MsaWS;\r
 import compbio.data.sequence.Alignment;\r
 import compbio.data.sequence.FastaSequence;\r
@@ -46,7 +47,7 @@ import compbio.metadata.WrongParameterException;
 import compbio.runner.Util;\r
 import compbio.runner.msa.Muscle;\r
 \r
-@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "MuscleWS")\r
+@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "MuscleWS")\r
 public class MuscleWS implements MsaWS<Muscle> {\r
 \r
        private static Logger log = Logger.getLogger(MuscleWS.class);\r
@@ -65,7 +66,7 @@ public class MuscleWS implements MsaWS<Muscle> {
                        throws JobSubmissionException {\r
                WSUtil.validateFastaInput(sequences);\r
                ConfiguredExecutable<Muscle> confMuscle = init(sequences);\r
-               return WSUtil.align(sequences, confMuscle, null, "align", getLimit(""));\r
+               return WSUtil.align(sequences, confMuscle, log, "align", getLimit(""));\r
        }\r
 \r
        ConfiguredExecutable<Muscle> init(List<FastaSequence> sequences)\r
@@ -89,7 +90,7 @@ public class MuscleWS implements MsaWS<Muscle> {
                List<String> params = WSUtil.getCommands(options,\r
                                Muscle.KEY_VALUE_SEPARATOR);\r
                confMuscle.addParameters(params);\r
-               return WSUtil.align(sequences, confMuscle, null, "customAlign",\r
+               return WSUtil.align(sequences, confMuscle, log, "customAlign",\r
                                getLimit(""));\r
        }\r
 \r
@@ -104,7 +105,7 @@ public class MuscleWS implements MsaWS<Muscle> {
                ConfiguredExecutable<Muscle> confMuscle = init(sequences);\r
                confMuscle.addParameters(preset.getOptions());\r
                Limit<Muscle> limit = getLimit(preset.getName());\r
-               return WSUtil.align(sequences, confMuscle, null, "presetAlign", limit);\r
+               return WSUtil.align(sequences, confMuscle, log, "presetAlign", limit);\r
        }\r
 \r
        @SuppressWarnings("unchecked")\r