JAL-3807 JPred can now successfully submit and track the job.

[jalview.git] / src / jalview / ws / slivkaws / SlivkaMsaServiceInstance.java

diff --git a/src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java b/src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
index 9a33b04..a04cff5 100644 (file)
--- a/src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
+++ b/src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
@@ -1,22 +1,17 @@
 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;
@@ -43,14 +38,7 @@ public class SlivkaMsaServiceInstance extends SlivkaWSInstance implements Multip
       files = client.getJobResults(jobId.getJobId());
       for (RemoteFile f : files)
       {
-        if (f.getMimeType().equals("application/clustal"))
-        {
-          return new FormatAdapter().readFile(f.getURL().toString(), DataSourceType.URL, FileFormat.Clustal);
-        }
-        else if (f.getMimeType().equals("application/fasta"))
-        {
-          return new FormatAdapter().readFile(f.getURL().toString(), DataSourceType.URL, FileFormat.Fasta);
-        }
+        return readAlignment(f);
       }
     } catch (IOException e)
     {