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
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
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