X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fserver%2FAAConWS.java;h=fab12b8e42b5ae3e8e04b26ffe9dfb52d2af0be1;hb=a2619dbd95b874abd03ae551c02524fe09e9f631;hp=a32533ff91033f12f8bdbd66405e32a7e68ee537;hpb=6582e82919b0d3697fe5e96f1be6a369f90a2d93;p=jabaws.git

diff --git a/webservices/compbio/ws/server/AAConWS.java b/webservices/compbio/ws/server/AAConWS.java
index a32533f..fab12b8 100644
--- a/webservices/compbio/ws/server/AAConWS.java
+++ b/webservices/compbio/ws/server/AAConWS.java
@@ -2,7 +2,6 @@ package compbio.ws.server;
 
 import java.io.File;
 import java.util.Arrays;
-import java.util.HashSet;
 import java.util.List;
 
 import javax.annotation.Resource;
@@ -11,12 +10,13 @@ import javax.xml.ws.WebServiceContext;
 
 import org.apache.log4j.Logger;
 
-import compbio.data.msa.Annotation;
+import compbio.data.msa.SequenceAnnotation;
 import compbio.data.sequence.FastaSequence;
-import compbio.data.sequence.Score;
+import compbio.data.sequence.ScoreManager;
 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;
@@ -33,8 +33,8 @@ import compbio.metadata.WrongParameterException;
 import compbio.runner.Util;
 import compbio.runner.conservation.AACon;
 
-@WebService(endpointInterface = "compbio.data.msa.Annotation", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "AAConWS")
-public class AAConWS implements Annotation<AACon> {
+@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "AAConWS")
+public class AAConWS implements SequenceAnnotation<AACon> {
 
 	// Ask for resource injection
 	@Resource
@@ -50,21 +50,25 @@ public class AAConWS implements Annotation<AACon> {
 	private static final PresetManager<AACon> aaconPresets = Util
 			.getPresets(AACon.class);
 
+	private static final LimitsManager<AACon> limitMan = compbio.engine.client.Util
+			.getLimits(new AACon().getType());
+
 	ConfiguredExecutable<AACon> init(List<FastaSequence> sequences)
 			throws JobSubmissionException {
 		AACon aacon = new AACon();
-		aacon.setInput("fasta.in").setOutput("aacon.out");
+		aacon.setInput(SkeletalExecutable.INPUT).setOutput(
+				SkeletalExecutable.OUTPUT);
 		return Configurator.configureExecutable(aacon, sequences);
 	}
 
 	@Override
-	public HashSet<Score> getAnnotation(String jobId)
+	public ScoreManager getAnnotation(String jobId)
 			throws ResultNotAvailableException {
 		WSUtil.validateJobId(jobId);
 		AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
 		ConfiguredExecutable<AACon> aacon = (ConfiguredExecutable<AACon>) asyncEngine
 				.getResults(jobId);
-		HashSet<Score> mas = aacon.getResults();
+		ScoreManager mas = aacon.getResults();
 		log.trace(jobId + " getConservation : " + mas);
 		return mas;
 	}
@@ -77,12 +81,16 @@ public class AAConWS implements Annotation<AACon> {
 
 	@Override
 	public Limit<AACon> getLimit(String presetName) {
-		return new AACon().getLimit(presetName);
+		if (limitMan == null) {
+			// Limit is not defined
+			return null;
+		}
+		return limitMan.getLimitByName(presetName);
 	}
 
 	@Override
 	public LimitsManager<AACon> getLimits() {
-		return new AACon().getLimits();
+		return limitMan;
 	}
 
 	@Override