Web services refactoring & bug fixing

[jabaws.git] / webservices / compbio / ws / server / MafftWS.java

diff --git a/webservices/compbio/ws/server/MafftWS.java b/webservices/compbio/ws/server/MafftWS.java
index eda824a..12805af 100644 (file)
--- a/webservices/compbio/ws/server/MafftWS.java
+++ b/webservices/compbio/ws/server/MafftWS.java
@@ -31,6 +31,7 @@ import compbio.data.sequence.FastaSequence;
 import compbio.engine.AsyncExecutor;\r
 import compbio.engine.Configurator;\r
 import compbio.engine.client.ConfiguredExecutable;\r
+import compbio.engine.client.SkeletalExecutable;\r
 import compbio.metadata.ChunkHolder;\r
 import compbio.metadata.JobStatus;\r
 import compbio.metadata.JobSubmissionException;\r
@@ -70,6 +71,9 @@ public class MafftWS implements MsaWS<Mafft> {
        ConfiguredExecutable<Mafft> init(List<FastaSequence> dataSet)\r
                        throws JobSubmissionException {\r
                Mafft mafft = new Mafft();\r
+               mafft.setInput(SkeletalExecutable.INPUT)\r
+                               .setOutput(SkeletalExecutable.OUTPUT)\r
+                               .setError(SkeletalExecutable.ERROR);\r
                return Configurator.configureExecutable(mafft, dataSet);\r
        }\r
 \r