X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fserver%2FTcoffeeWS.java;h=086d870bf9594a18c931aa194f96bb36ed0cfd85;hb=9072bd850138bedbd005509e5b14bb5e104574b4;hp=74c172385b457059679d08d8a1a26c44043bbd8c;hpb=24b1f578d0752ca4e3ee410031af5678b3ff1189;p=jabaws.git

diff --git a/webservices/compbio/ws/server/TcoffeeWS.java b/webservices/compbio/ws/server/TcoffeeWS.java
index 74c1723..086d870 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
@@ -21,12 +21,11 @@ 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;
@@ -49,15 +48,9 @@ import compbio.metadata.WrongParameterException;
 import compbio.runner.Util;
 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
@@ -66,7 +59,7 @@ public class TcoffeeWS implements MsaWS<Tcoffee> {
 	private static final PresetManager<Tcoffee> tcoffeePresets = Util
 			.getPresets(Tcoffee.class);
 
-	private static final LimitsManager<Tcoffee> limitMan = compbio.runner.Util
+	private static final LimitsManager<Tcoffee> limitMan = compbio.engine.client.Util
 			.getLimits(new Tcoffee().getType());
 
 	@Override
@@ -74,14 +67,16 @@ public class TcoffeeWS implements MsaWS<Tcoffee> {
 			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("fasta.in").setOutput("fasta.out");
+		tcoffee.setInput(SkeletalExecutable.INPUT)
+				.setOutput(SkeletalExecutable.OUTPUT)
+				.setError(SkeletalExecutable.ERROR);
+
 		ConfiguredExecutable<Tcoffee> confCoffee = Configurator
 				.configureExecutable(tcoffee, sequences);
 		if (confCoffee.getExecProvider() == Executable.ExecProvider.Cluster) {
@@ -105,7 +100,7 @@ public class TcoffeeWS implements MsaWS<Tcoffee> {
 				Tcoffee.KEY_VALUE_SEPARATOR);
 		log.info("Setting parameters:" + params);
 		confTcoffee.addParameters(params);
-		return WSUtil.align(sequences, confTcoffee, null, "customAlign",
+		return WSUtil.align(sequences, confTcoffee, log, "customAlign",
 				getLimit(""));
 	}
 
@@ -120,7 +115,7 @@ 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")