-/* 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
import java.io.File;\r
import java.util.List;\r
\r
-import javax.annotation.Resource;\r
import javax.jws.WebService;\r
-import javax.xml.ws.WebServiceContext;\r
\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
import compbio.engine.AsyncExecutor;\r
import compbio.engine.Configurator;\r
import compbio.engine.client.ConfiguredExecutable;\r
+import compbio.engine.client.SkeletalExecutable;\r
import compbio.metadata.ChunkHolder;\r
import compbio.metadata.JobStatus;\r
import compbio.metadata.JobSubmissionException;\r
import compbio.runner.Util;\r
import compbio.runner.msa.Probcons;\r
\r
-@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "ProbconsWS")\r
+@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "ProbconsWS")\r
public class ProbconsWS implements MsaWS<Probcons> {\r
\r
- // Ask for resource injection\r
- @Resource\r
- WebServiceContext wsContext;\r
-\r
- private static Logger statLog = Logger.getLogger("ProbconsWS-stats");\r
-\r
private static Logger log = Logger.getLogger(ProbconsWS.class);\r
\r
private static final RunnerConfig<Probcons> probconsOptions = Util\r
throws JobSubmissionException {\r
WSUtil.validateFastaInput(sequences);\r
ConfiguredExecutable<Probcons> confProbcons = init(sequences);\r
- return WSUtil.align(sequences, confProbcons, null, "align",\r
- getLimit(""));\r
+ return WSUtil\r
+ .align(sequences, confProbcons, log, "align", getLimit(""));\r
}\r
\r
ConfiguredExecutable<Probcons> init(List<FastaSequence> dataSet)\r
throws JobSubmissionException {\r
Probcons probcons = new Probcons();\r
+ probcons.setInput(SkeletalExecutable.INPUT)\r
+ .setOutput(SkeletalExecutable.OUTPUT)\r
+ .setError(SkeletalExecutable.ERROR);\r
return Configurator.configureExecutable(probcons, dataSet);\r
}\r
\r
Probcons.KEY_VALUE_SEPARATOR);\r
log.info("Setting parameters:" + params);\r
confProbcons.addParameters(params);\r
- return WSUtil.align(sequences, confProbcons, null, "customAlign",\r
+ return WSUtil.align(sequences, confProbcons, log, "customAlign",\r
getLimit(""));\r
}\r
\r
ConfiguredExecutable<Probcons> confProbcons = init(sequences);\r
confProbcons.addParameters(preset.getOptions());\r
Limit<Probcons> limit = getLimit(preset.getName());\r
- return WSUtil\r
- .align(sequences, confProbcons, null, "presetAlign", limit);\r
+ return WSUtil.align(sequences, confProbcons, log, "presetAlign", limit);\r
}\r
\r
@SuppressWarnings("unchecked")\r