X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fserver%2FTcoffeeWS.java;h=ee1c1c609f95ac535eae6098f1345d0e8ae31816;hb=68fe46f278b4ec408d6c68677bd56199aac749b3;hp=5608a531533b6e068109eb66382521f83800dc59;hpb=f2ed5ce799ceb51f32daa98c9d6c8fe936bf2195;p=jabaws.git

diff --git a/webservices/compbio/ws/server/TcoffeeWS.java b/webservices/compbio/ws/server/TcoffeeWS.java
index 5608a53..ee1c1c6 100644
--- a/webservices/compbio/ws/server/TcoffeeWS.java
+++ b/webservices/compbio/ws/server/TcoffeeWS.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
@@ -21,20 +21,21 @@ 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.data.sequence.Program;
 import compbio.engine.AsyncExecutor;
 import compbio.engine.Configurator;
 import compbio.engine.client.ConfiguredExecutable;
 import compbio.engine.client.Executable;
 import compbio.engine.client.SkeletalExecutable;
+import compbio.engine.client.EngineUtil;
 import compbio.metadata.ChunkHolder;
 import compbio.metadata.JobStatus;
 import compbio.metadata.JobSubmissionException;
@@ -46,41 +47,32 @@ import compbio.metadata.PresetManager;
 import compbio.metadata.ResultNotAvailableException;
 import compbio.metadata.RunnerConfig;
 import compbio.metadata.WrongParameterException;
-import compbio.runner.Util;
+import compbio.runner.RunnerUtil;
 import compbio.runner.msa.Tcoffee;
 
-@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "TcoffeeWS")
+@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "TcoffeeWS")
 public class TcoffeeWS implements MsaWS<Tcoffee> {
 
-	// Ask for resource injection
-	@Resource
-	WebServiceContext wsContext;
-
-	private static Logger statLog = Logger.getLogger("TcoffeeWS-stats");
-
 	private static Logger log = Logger.getLogger(TcoffeeWS.class);
-
-	private static final RunnerConfig<Tcoffee> tcoffeeOptions = Util
-			.getSupportedOptions(Tcoffee.class);
-
-	private static final PresetManager<Tcoffee> tcoffeePresets = Util
-			.getPresets(Tcoffee.class);
-
-	private static final LimitsManager<Tcoffee> limitMan = compbio.runner.Util
-			.getLimits(new Tcoffee().getType());
+	private static final RunnerConfig<Tcoffee> tcoffeeOptions = RunnerUtil.getSupportedOptions(Tcoffee.class);
+	private static final PresetManager<Tcoffee> tcoffeePresets = RunnerUtil.getPresets(Tcoffee.class);
+	private static final LimitsManager<Tcoffee> limitMan = EngineUtil.getLimits(new Tcoffee().getType());
 
 	@Override
 	public String align(List<FastaSequence> sequences)
 			throws JobSubmissionException {
 		WSUtil.validateFastaInput(sequences);
 		ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);
-		return WSUtil
-				.align(sequences, confTcoffee, null, "align", getLimit(""));
+		return WSUtil.align(sequences, confTcoffee, log, "align", getLimit(""));
 	}
 
 	ConfiguredExecutable<Tcoffee> init(List<FastaSequence> sequences)
 			throws JobSubmissionException {
 		Tcoffee tcoffee = new Tcoffee();
+		tcoffee.setInput(SkeletalExecutable.INPUT)
+				.setOutput(SkeletalExecutable.OUTPUT)
+				.setError(SkeletalExecutable.ERROR);
+
 		ConfiguredExecutable<Tcoffee> confCoffee = Configurator
 				.configureExecutable(tcoffee, sequences);
 		if (confCoffee.getExecProvider() == Executable.ExecProvider.Cluster) {
@@ -100,12 +92,10 @@ public class TcoffeeWS implements MsaWS<Tcoffee> {
 
 		WSUtil.validateFastaInput(sequences);
 		ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);
-		List<String> params = WSUtil.getCommands(options,
-				Tcoffee.KEY_VALUE_SEPARATOR);
+		List<String> params = WSUtil.getCommands(options, Tcoffee.KEY_VALUE_SEPARATOR);
 		log.info("Setting parameters:" + params);
 		confTcoffee.addParameters(params);
-		return WSUtil.align(sequences, confTcoffee, null, "customAlign",
-				getLimit(""));
+		return WSUtil.align(sequences, confTcoffee, log, "customAlign", getLimit(""));
 	}
 
 	@Override
@@ -119,7 +109,7 @@ public class TcoffeeWS implements MsaWS<Tcoffee> {
 		ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);
 		confTcoffee.addParameters(preset.getOptions());
 		Limit<Tcoffee> limit = getLimit(preset.getName());
-		return WSUtil.align(sequences, confTcoffee, null, "presetAlign", limit);
+		return WSUtil.align(sequences, confTcoffee, log, "presetAlign", limit);
 	}
 
 	@SuppressWarnings("unchecked")
@@ -130,8 +120,7 @@ public class TcoffeeWS implements MsaWS<Tcoffee> {
 		ConfiguredExecutable<Tcoffee> tcoffee = (ConfiguredExecutable<Tcoffee>) asyncEngine
 				.getResults(jobId);
 		Alignment al = tcoffee.getResults();
-		// log(jobId, "getResults");
-		return al;
+		return new Alignment (al.getSequences(), Program.Tcoffee, '-');
 	}
 
 	@Override