X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fserver%2FMuscleWS.java;h=943b3c2a8c6b3b5b0e03986cb11f0f4b59fbb96e;hb=184bf3dce9500c599b5257140ec49edd80f8cea1;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..943b3c2 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
@@ -25,13 +25,16 @@ 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.data.sequence.Program;
 import compbio.engine.AsyncExecutor;
 import compbio.engine.Configurator;
 import compbio.engine.client.ConfiguredExecutable;
 import compbio.engine.client.SkeletalExecutable;
+import compbio.engine.client.EngineUtil;
 import compbio.metadata.ChunkHolder;
 import compbio.metadata.JobStatus;
 import compbio.metadata.JobSubmissionException;
@@ -43,29 +46,23 @@ import compbio.metadata.PresetManager;
 import compbio.metadata.ResultNotAvailableException;
 import compbio.metadata.RunnerConfig;
 import compbio.metadata.WrongParameterException;
-import compbio.runner.Util;
+import compbio.runner.RunnerUtil;
 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);
-
-	private static final RunnerConfig<Muscle> muscleOptions = Util
-			.getSupportedOptions(Muscle.class);
-
-	private static final PresetManager<Muscle> musclePresets = Util
-			.getPresets(Muscle.class);
-
-	private static final LimitsManager<Muscle> limitMan = compbio.engine.client.Util
-			.getLimits(new Muscle().getType());
+	private static final RunnerConfig<Muscle> muscleOptions = RunnerUtil.getSupportedOptions(Muscle.class);
+	private static final PresetManager<Muscle> musclePresets = RunnerUtil.getPresets(Muscle.class);
+	private static final LimitsManager<Muscle> limitMan = EngineUtil.getLimits(new Muscle().getType());
 
 	@Override
 	public String align(List<FastaSequence> sequences)
 			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)
@@ -89,8 +86,7 @@ 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",
-				getLimit(""));
+		return WSUtil.align(sequences, confMuscle, log, "customAlign", getLimit(""));
 	}
 
 	@Override
@@ -104,7 +100,7 @@ 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")
@@ -115,8 +111,7 @@ public class MuscleWS implements MsaWS<Muscle> {
 		ConfiguredExecutable<Muscle> muscle = (ConfiguredExecutable<Muscle>) asyncEngine
 				.getResults(jobId);
 		Alignment al = muscle.getResults();
-		// log(jobId, "getResults");
-		return al;
+		return new Alignment (al.getSequences(),Program.Muscle, '-');
 	}
 
 	@Override