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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 a9d6c52..943b3c2 100644 (file)
--- 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;\r
 import compbio.data.sequence.Alignment;\r
 import compbio.data.sequence.FastaSequence;\r
+import compbio.data.sequence.Program;\r
 import compbio.engine.AsyncExecutor;\r
 import compbio.engine.Configurator;\r
 import compbio.engine.client.ConfiguredExecutable;\r
 import compbio.engine.client.SkeletalExecutable;\r
+import compbio.engine.client.EngineUtil;\r
 import compbio.metadata.ChunkHolder;\r
 import compbio.metadata.JobStatus;\r
 import compbio.metadata.JobSubmissionException;\r
@@ -44,22 +46,16 @@ import compbio.metadata.PresetManager;
 import compbio.metadata.ResultNotAvailableException;\r
 import compbio.metadata.RunnerConfig;\r
 import compbio.metadata.WrongParameterException;\r
-import compbio.runner.Util;\r
+import compbio.runner.RunnerUtil;\r
 import compbio.runner.msa.Muscle;\r
 \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
-\r
-       private static final RunnerConfig<Muscle> muscleOptions = Util\r
-                       .getSupportedOptions(Muscle.class);\r
-\r
-       private static final PresetManager<Muscle> musclePresets = Util\r
-                       .getPresets(Muscle.class);\r
-\r
-       private static final LimitsManager<Muscle> limitMan = compbio.engine.client.Util\r
-                       .getLimits(new Muscle().getType());\r
+       private static final RunnerConfig<Muscle> muscleOptions = RunnerUtil.getSupportedOptions(Muscle.class);\r
+       private static final PresetManager<Muscle> musclePresets = RunnerUtil.getPresets(Muscle.class);\r
+       private static final LimitsManager<Muscle> limitMan = EngineUtil.getLimits(new Muscle().getType());\r
 \r
        @Override\r
        public String align(List<FastaSequence> sequences)\r
@@ -90,8 +86,7 @@ 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, log, "customAlign",\r
-                               getLimit(""));\r
+               return WSUtil.align(sequences, confMuscle, log, "customAlign", getLimit(""));\r
        }\r
 \r
        @Override\r
@@ -116,8 +111,7 @@ public class MuscleWS implements MsaWS<Muscle> {
                ConfiguredExecutable<Muscle> muscle = (ConfiguredExecutable<Muscle>) asyncEngine\r
                                .getResults(jobId);\r
                Alignment al = muscle.getResults();\r
-               // log(jobId, "getResults");\r
-               return al;\r
+               return new Alignment (al.getSequences(),Program.Muscle, '-');\r
        }\r
 \r
        @Override\r