From: Mateusz Warowny <mmzwarowny@dundee.ac.uk>
Date: Fri, 9 Jul 2021 14:57:28 +0000 (+0200)
Subject: Merge branch 'jpred-fix' into bug/JAL-3807_jpred-with-slivka
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b6bd3fa646b6728cd59c8d0de91270ab6c70f86f;hp=872210cd099a8d81f9427fd3547775c8ec043a38;p=jalview.git

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

diff --git a/src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java b/src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
index a04cff5..8d6332c 100644
--- a/src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
+++ b/src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
@@ -1,10 +1,5 @@
 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.ws.api.JobId;
@@ -12,6 +7,12 @@ 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 uk.ac.dundee.compbio.slivkaclient.RemoteFile;
 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
@@ -32,13 +33,16 @@ 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);
+        var aln = readAlignment(f);
+        if (aln != null)
+        {
+          return aln;
+        }
       }
     } catch (IOException e)
     {
diff --git a/src/jalview/ws/slivkaws/SlivkaWSInstance.java b/src/jalview/ws/slivkaws/SlivkaWSInstance.java
index 8aa56fa..138b432 100644
--- a/src/jalview/ws/slivkaws/SlivkaWSInstance.java
+++ b/src/jalview/ws/slivkaws/SlivkaWSInstance.java
@@ -252,9 +252,9 @@ public abstract class SlivkaWSInstance extends ServiceWithParameters
   {
     final var mimetype = f.getMimeType();
     FileFormat format;
-    if (mimetype == "application/clustal")
+    if (mimetype.equals("application/clustal"))
       format = FileFormat.Clustal;
-    else if (mimetype == "application/fasta")
+    else if (mimetype.equals("application/fasta"))
       format = FileFormat.Fasta;
     else
       return null;