X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fserver%2FProbconsWS.java;h=d4fa3df27be0b801740902f6de75f9474f5ae4de;hb=bd6c0919476cff487ea479588d5ad9f3bdd5af1e;hp=4ab7a348c06f39e34b0a29be5b394dd333871850;hpb=61af8ce2cea02220228f58b30b4319f500b2f040;p=jabaws.git

diff --git a/webservices/compbio/ws/server/ProbconsWS.java b/webservices/compbio/ws/server/ProbconsWS.java
index 4ab7a34..d4fa3df 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
@@ -25,6 +25,7 @@ import javax.jws.WebService;
 
 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;
@@ -46,32 +47,28 @@ 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> {
 
 	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.engine.client.Util
-			.getLimits(new Probcons().getType());
+	private static final RunnerConfig<Probcons> probconsOptions = Util.getSupportedOptions(Probcons.class);
+	private static final LimitsManager<Probcons> limitMan = compbio.engine.client.Util.getLimits(new Probcons().getType());
 
 	@Override
 	public String align(List<FastaSequence> sequences)
 			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(SkeletalExecutable.INPUT)
-				.setOutput(SkeletalExecutable.OUTPUT)
-				.setError(SkeletalExecutable.ERROR);
+		probcons.setInput(SkeletalExecutable.INPUT);
+		probcons.setOutput(SkeletalExecutable.OUTPUT);
+		probcons.setError(SkeletalExecutable.ERROR);
 		return Configurator.configureExecutable(probcons, dataSet);
 	}
 
@@ -81,12 +78,10 @@ public class ProbconsWS implements MsaWS<Probcons> {
 			WrongParameterException {
 		WSUtil.validateFastaInput(sequences);
 		ConfiguredExecutable<Probcons> confProbcons = init(sequences);
-		List<String> params = WSUtil.getCommands(options,
-				Probcons.KEY_VALUE_SEPARATOR);
+		List<String> params = WSUtil.getCommands(options, Probcons.KEY_VALUE_SEPARATOR);
 		log.info("Setting parameters:" + params);
 		confProbcons.addParameters(params);
-		return WSUtil.align(sequences, confProbcons, null, "customAlign",
-				getLimit(""));
+		return WSUtil.align(sequences, confProbcons, log, "customAlign",getLimit(""));
 	}
 
 	@Override
@@ -100,8 +95,7 @@ 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")
@@ -109,8 +103,7 @@ public class ProbconsWS implements MsaWS<Probcons> {
 	public Alignment getResult(String jobId) throws ResultNotAvailableException {
 		WSUtil.validateJobId(jobId);
 		AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
-		ConfiguredExecutable<Probcons> probcons = (ConfiguredExecutable<Probcons>) asyncEngine
-				.getResults(jobId);
+		ConfiguredExecutable<Probcons> probcons = (ConfiguredExecutable<Probcons>) asyncEngine.getResults(jobId);
 		Alignment al = probcons.getResults();
 		// log(jobId, "getResults");
 		return al;
@@ -134,8 +127,7 @@ public class ProbconsWS implements MsaWS<Probcons> {
 	public ChunkHolder pullExecStatistics(String jobId, long position) {
 		WSUtil.validateJobId(jobId);
 		// TODO check if output is the one to return
-		String file = Configurator.getWorkDirectory(jobId) + File.separator
-				+ new Probcons().getError();
+		String file = Configurator.getWorkDirectory(jobId) + File.separator + new Probcons().getError();
 		return WSUtil.pullFile(file, position);
 	}