X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fserver%2FMuscleWS.java;h=943b3c2a8c6b3b5b0e03986cb11f0f4b59fbb96e;hb=184bf3dce9500c599b5257140ec49edd80f8cea1;hp=a9d6c5205b7b3833728610552a0fcf3851a8b2c9;hpb=23fb18b3f14a1b396f0c61f2ea4559fec758cb1d;p=jabaws.git

diff --git a/webservices/compbio/ws/server/MuscleWS.java b/webservices/compbio/ws/server/MuscleWS.java
index a9d6c52..943b3c2 100644
--- a/webservices/compbio/ws/server/MuscleWS.java
+++ b/webservices/compbio/ws/server/MuscleWS.java
@@ -29,10 +29,12 @@ 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;
@@ -44,22 +46,16 @@ 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 = 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)
@@ -90,8 +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, log, "customAlign",
-				getLimit(""));
+		return WSUtil.align(sequences, confMuscle, log, "customAlign", getLimit(""));
 	}
 
 	@Override
@@ -116,8 +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