X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fserver%2FMafftWS.java;h=f293ae79d154209d638e330d86b4379e7e8d32d8;hb=23fb18b3f14a1b396f0c61f2ea4559fec758cb1d;hp=0c8347da0d158716597153acc6fe8691409f49dd;hpb=2a269830633463e5016d5c92ed672d9e312c9776;p=jabaws.git

diff --git a/webservices/compbio/ws/server/MafftWS.java b/webservices/compbio/ws/server/MafftWS.java
index 0c8347d..f293ae7 100644
--- a/webservices/compbio/ws/server/MafftWS.java
+++ b/webservices/compbio/ws/server/MafftWS.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;
@@ -47,15 +47,9 @@ import compbio.metadata.WrongParameterException;
 import compbio.runner.Util;
 import compbio.runner.msa.Mafft;
 
-@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "MafftWS")
+@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "MafftWS")
 public class MafftWS implements MsaWS<Mafft> {
 
-	// Ask for resource injection
-	@Resource
-	WebServiceContext wsContext;
-
-	private static Logger statLog = Logger.getLogger("MafftWS-stats");
-
 	private static Logger log = Logger.getLogger(MafftWS.class);
 
 	private static final RunnerConfig<Mafft> mafftOptions = Util
@@ -64,7 +58,7 @@ public class MafftWS implements MsaWS<Mafft> {
 	private static final PresetManager<Mafft> mafftPresets = Util
 			.getPresets(Mafft.class);
 
-	private static final LimitsManager<Mafft> limitMan = compbio.runner.Util
+	private static final LimitsManager<Mafft> limitMan = compbio.engine.client.Util
 			.getLimits(new Mafft().getType());
 
 	@Override
@@ -72,13 +66,15 @@ public class MafftWS implements MsaWS<Mafft> {
 			throws JobSubmissionException {
 		WSUtil.validateFastaInput(sequences);
 		ConfiguredExecutable<Mafft> confMafft = init(sequences);
-		return WSUtil.align(sequences, confMafft, null, "align", getLimit(""));
+		return WSUtil.align(sequences, confMafft, log, "align", getLimit(""));
 	}
 
 	ConfiguredExecutable<Mafft> init(List<FastaSequence> dataSet)
 			throws JobSubmissionException {
 		Mafft mafft = new Mafft();
-		mafft.setInput("fasta.in").setOutput("fasta.out");
+		mafft.setInput(SkeletalExecutable.INPUT)
+				.setOutput(SkeletalExecutable.OUTPUT)
+				.setError(SkeletalExecutable.ERROR);
 		return Configurator.configureExecutable(mafft, dataSet);
 	}
 
@@ -92,7 +88,7 @@ public class MafftWS implements MsaWS<Mafft> {
 				Mafft.KEY_VALUE_SEPARATOR);
 		log.info("Setting parameters: " + params);
 		confMafft.addParameters(params);
-		return WSUtil.align(sequences, confMafft, null, "customAlign",
+		return WSUtil.align(sequences, confMafft, log, "customAlign",
 				getLimit(""));
 	}
 
@@ -110,7 +106,7 @@ public class MafftWS implements MsaWS<Mafft> {
 		// particular preset is not found
 		Limit<Mafft> limit = getLimit(preset.getName());
 
-		return WSUtil.align(sequences, confMafft, null, "presetAlign", limit);
+		return WSUtil.align(sequences, confMafft, log, "presetAlign", limit);
 	}
 
 	@SuppressWarnings("unchecked")
@@ -127,6 +123,10 @@ public class MafftWS implements MsaWS<Mafft> {
 
 	@Override
 	public Limit<Mafft> getLimit(String presetName) {
+		if (limitMan == null) {
+			// Limit is not defined
+			return null;
+		}
 		return limitMan.getLimitByName(presetName);
 	}