Merge branch 'jpred-fix' into bug/JAL-3807_jpred-with-slivka

[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 a65e93e..8d6332c 100644 (file)
--- a/src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
+++ b/src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
@@ -2,9 +2,6 @@ package jalview.ws.slivkaws;
 
 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;
@@ -22,8 +19,8 @@ import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
 
 public class SlivkaMsaServiceInstance extends SlivkaWSInstance implements MultipleSequenceAlignmentI
 {
-  SlivkaMsaServiceInstance(SlivkaClient client, SlivkaService service) {
-    super(client, service, "Sequence Alignment");
+  SlivkaMsaServiceInstance(SlivkaClient client, SlivkaService service, String category) {
+    super(client, service, category);
     style = ServiceClient.MSAWSCLIENT;
   }
 
@@ -36,19 +33,15 @@ 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)
       {
-        if (f.getMimeType().equals("application/clustal"))
+        var aln = readAlignment(f);
+        if (aln != null)
         {
-          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 aln;
         }
       }
     } catch (IOException e)