X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fslivkaws%2FSlivkaMsaServiceInstance.java;h=93c0bdbb744813007abbd01dddb59272b3d22d96;hb=7e4b1da6e7cba557bb9d8e78fcd82b836d5f2d98;hp=a04cff589b58051143e95449bb42a6dc879b98f8;hpb=992a0adb0deed8313fde7cad88837355336e58a5;p=jalview.git

diff --git a/src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java b/src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
index a04cff5..93c0bdb 100644
--- a/src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
+++ b/src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
@@ -1,17 +1,22 @@
 package jalview.ws.slivkaws;
 
-import java.io.IOError;
-import java.io.IOException;
-import java.rmi.ServerError;
-import java.util.List;
-
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FormatAdapter;
 import jalview.ws.api.JobId;
 import jalview.ws.api.MultipleSequenceAlignmentI;
 import jalview.ws.params.ArgumentI;
 import jalview.ws.params.InvalidArgumentException;
 import jalview.ws.params.WsParamSetI;
+
+import java.io.IOError;
+import java.io.IOException;
+import java.rmi.ServerError;
+import java.util.List;
+
+import compbio.data.msa.Category;
 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
@@ -32,13 +37,16 @@ public class SlivkaMsaServiceInstance extends SlivkaWSInstance implements Multip
   @Override
   public AlignmentI getAlignmentFor(JobId jobId) throws InvalidArgumentException, ServerError, IOError
   {
-    List<RemoteFile> files;
     try
     {
-      files = client.getJobResults(jobId.getJobId());
+      List<RemoteFile> files = client.getJobResults(jobId.getJobId());
       for (RemoteFile f : files)
       {
-        return readAlignment(f);
+        if (f.getMimeType().equals("application/clustal") 
+            || f.getMimeType().equals("application/fasta"))
+        {
+          return readAlignment(f);
+        }
       }
     } catch (IOException e)
     {