X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fserver%2FProbconsWS.java;h=586352bae4fb39b14ef76c32fb35f3d7c12e4db4;hb=175c6382f4b2838916a98a2d87f1a4fff0103ea6;hp=85e8a705c44e1b290ad530258e11363b3cb6b60f;hpb=2a269830633463e5016d5c92ed672d9e312c9776;p=jabaws.git

diff --git a/webservices/compbio/ws/server/ProbconsWS.java b/webservices/compbio/ws/server/ProbconsWS.java
index 85e8a70..586352b 100644
--- a/webservices/compbio/ws/server/ProbconsWS.java
+++ b/webservices/compbio/ws/server/ProbconsWS.java
@@ -61,7 +61,7 @@ public class ProbconsWS implements MsaWS<Probcons> {
 	private static final RunnerConfig<Probcons> probconsOptions = Util
 			.getSupportedOptions(Probcons.class);
 
-	private static final LimitsManager<Probcons> limitMan = compbio.runner.Util
+	private static final LimitsManager<Probcons> limitMan = compbio.engine.client.Util
 			.getLimits(new Probcons().getType());
 
 	@Override
@@ -76,7 +76,6 @@ public class ProbconsWS implements MsaWS<Probcons> {
 	ConfiguredExecutable<Probcons> init(List<FastaSequence> dataSet)
 			throws JobSubmissionException {
 		Probcons probcons = new Probcons();
-		probcons.setInput("fasta.in").setOutput("alignment.out");
 		return Configurator.configureExecutable(probcons, dataSet);
 	}
 
@@ -123,6 +122,10 @@ public class ProbconsWS implements MsaWS<Probcons> {
 
 	@Override
 	public Limit<Probcons> getLimit(String presetName) {
+		if (limitMan == null) {
+			// Limit is not defined
+			return null;
+		}
 		return limitMan.getLimitByName(presetName);
 	}