X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fserver%2FAAConWS.java;h=fab12b8e42b5ae3e8e04b26ffe9dfb52d2af0be1;hb=a2619dbd95b874abd03ae551c02524fe09e9f631;hp=1ffbbf342a735d5e4bf30e4ee7af941fcb352a47;hpb=1c8cbe10ed2f25b3b36620a13d16e8cb96f6523f;p=jabaws.git

diff --git a/webservices/compbio/ws/server/AAConWS.java b/webservices/compbio/ws/server/AAConWS.java
index 1ffbbf3..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;
@@ -13,11 +12,11 @@ import org.apache.log4j.Logger;
 
 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;
@@ -57,6 +56,8 @@ public class AAConWS implements SequenceAnnotation<AACon> {
 	ConfiguredExecutable<AACon> init(List<FastaSequence> sequences)
 			throws JobSubmissionException {
 		AACon aacon = new AACon();
+		aacon.setInput(SkeletalExecutable.INPUT).setOutput(
+				SkeletalExecutable.OUTPUT);
 		return Configurator.configureExecutable(aacon, sequences);
 	}
 
@@ -67,12 +68,9 @@ public class AAConWS implements SequenceAnnotation<AACon> {
 		AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
 		ConfiguredExecutable<AACon> aacon = (ConfiguredExecutable<AACon>) asyncEngine
 				.getResults(jobId);
-		HashSet<Score> mas = aacon.getResults();
-		// ScoreManager result = new HashMap<String, HashSet<Score>>();
-		// result.put("Alignment", mas);
+		ScoreManager mas = aacon.getResults();
 		log.trace(jobId + " getConservation : " + mas);
-		// FIXME
-		return null;
+		return mas;
 	}
 	/*
 	 * @SuppressWarnings("unchecked") public JalviewAnnotation