X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=webservices%2Fcompbio%2Fws%2Fserver%2FProbconsWS.java;h=71f47302ea3fbf9a58d0f5a806b598885f665be2;hb=fa61eaad52ffe5ee0db449c3dd9ec5fa67aec43f;hp=bfad95a31b91dedb2e3a5bb27815a7df493c98af;hpb=24b1f578d0752ca4e3ee410031af5678b3ff1189;p=jabaws.git

diff --git a/webservices/compbio/ws/server/ProbconsWS.java b/webservices/compbio/ws/server/ProbconsWS.java
index bfad95a..71f4730 100644
--- a/webservices/compbio/ws/server/ProbconsWS.java
+++ b/webservices/compbio/ws/server/ProbconsWS.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
@@ -21,18 +21,18 @@ package compbio.ws.server;
 import java.io.File;
 import java.util.List;
 
-import javax.annotation.Resource;
 import javax.jws.WebService;
-import javax.xml.ws.WebServiceContext;
 
 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.engine.AsyncExecutor;
 import compbio.engine.Configurator;
 import compbio.engine.client.ConfiguredExecutable;
+import compbio.engine.client.SkeletalExecutable;
 import compbio.metadata.ChunkHolder;
 import compbio.metadata.JobStatus;
 import compbio.metadata.JobSubmissionException;
@@ -47,21 +47,15 @@ import compbio.metadata.WrongParameterException;
 import compbio.runner.Util;
 import compbio.runner.msa.Probcons;
 
-@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "ProbconsWS")
+@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "ProbconsWS")
 public class ProbconsWS implements MsaWS<Probcons> {
 
-	// Ask for resource injection
-	@Resource
-	WebServiceContext wsContext;
-
-	private static Logger statLog = Logger.getLogger("ProbconsWS-stats");
-
 	private static Logger log = Logger.getLogger(ProbconsWS.class);
 
 	private static final RunnerConfig<Probcons> probconsOptions = Util
 			.getSupportedOptions(Probcons.class);
 
-	private static final LimitsManager<Probcons> limitMan = compbio.runner.Util
+	private static final LimitsManager<Probcons> limitMan = compbio.engine.client.Util
 			.getLimits(new Probcons().getType());
 
 	@Override
@@ -69,14 +63,16 @@ public class ProbconsWS implements MsaWS<Probcons> {
 			throws JobSubmissionException {
 		WSUtil.validateFastaInput(sequences);
 		ConfiguredExecutable<Probcons> confProbcons = init(sequences);
-		return WSUtil.align(sequences, confProbcons, null, "align",
-				getLimit(""));
+		return WSUtil
+				.align(sequences, confProbcons, log, "align", getLimit(""));
 	}
 
 	ConfiguredExecutable<Probcons> init(List<FastaSequence> dataSet)
 			throws JobSubmissionException {
 		Probcons probcons = new Probcons();
-		probcons.setInput("fasta.in").setOutput("alignment.out");
+		probcons.setInput(SkeletalExecutable.INPUT)
+				.setOutput(SkeletalExecutable.OUTPUT)
+				.setError(SkeletalExecutable.ERROR);
 		return Configurator.configureExecutable(probcons, dataSet);
 	}
 
@@ -90,7 +86,7 @@ public class ProbconsWS implements MsaWS<Probcons> {
 				Probcons.KEY_VALUE_SEPARATOR);
 		log.info("Setting parameters:" + params);
 		confProbcons.addParameters(params);
-		return WSUtil.align(sequences, confProbcons, null, "customAlign",
+		return WSUtil.align(sequences, confProbcons, log, "customAlign",
 				getLimit(""));
 	}
 
@@ -105,8 +101,7 @@ public class ProbconsWS implements MsaWS<Probcons> {
 		ConfiguredExecutable<Probcons> confProbcons = init(sequences);
 		confProbcons.addParameters(preset.getOptions());
 		Limit<Probcons> limit = getLimit(preset.getName());
-		return WSUtil
-				.align(sequences, confProbcons, null, "presetAlign", limit);
+		return WSUtil.align(sequences, confProbcons, log, "presetAlign", limit);
 	}
 
 	@SuppressWarnings("unchecked")