Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

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

diff --git a/src/jalview/ws/slivkaws/SlivkaJPredServiceInstance.java b/src/jalview/ws/slivkaws/SlivkaJPredServiceInstance.java
deleted file mode 100644 (file)
index 3958198..0000000
--- a/src/jalview/ws/slivkaws/SlivkaJPredServiceInstance.java
+++ /dev/null
@@ -1,98 +0,0 @@
-package jalview.ws.slivkaws;
-
-import java.io.IOError;
-import java.io.IOException;
-import java.util.Collection;
-import java.util.List;
-
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceI;
-import jalview.io.DataSourceType;
-import jalview.io.JPredFile;
-import jalview.ws.api.JPredServiceI;
-import jalview.ws.api.JobId;
-import jalview.ws.params.ArgumentI;
-import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
-import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
-import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
-
-public class SlivkaJPredServiceInstance extends SlivkaWSInstance
-    implements JPredServiceI
-{
-
-  private class InputFormatParameter implements ArgumentI
-  {
-    String value = "";
-
-    @Override
-    public String getName()
-    {
-      return "format";
-    }
-
-    @Override
-    public String getValue()
-    {
-      return value;
-    }
-
-    @Override
-    public void setValue(String selectedItem)
-    {
-      value = selectedItem;
-    }
-  }
-
-
-  public SlivkaJPredServiceInstance(SlivkaClient client,
-      SlivkaService service, String action)
-  {
-    super(client, service, action);
-    style = ServiceClient.JPREDWSCLIENT;
-  }
-
-  @Override
-  public JobId predict(List<SequenceI> sequences, boolean msa) throws Throwable
-  {
-    // Hack allowing to send both single and msa jobs
-    // until msa and single sequence services are separated.
-    var arg = new InputFormatParameter();
-    arg.setValue(msa ? "fasta" : "seq");
-    return super.submit(sequences, null, List.of(arg));
-  }
-
-  @Override
-  public AlignmentI getAlignment(JobId jobId) throws Exception
-  {
-    Collection<RemoteFile> files;
-    try {
-      var job = client.getJob(jobId.getJobId());
-      files = job.getResults();
-      for (RemoteFile f : files) {
-        var alignment = readAlignment(f);
-        if (alignment != null)
-        {
-          return alignment;
-        }
-      }
-    }
-    catch (IOException e) {
-      throw new IOError(e);
-    }
-    return null;
-  }
-
-  @Override
-  public JPredFile getPrediction(JobId jobId) throws Exception
-  {
-    Collection<RemoteFile> files = client.getJob(jobId.getJobId()).getResults();
-    for (RemoteFile f : files)
-    {
-      if (f.getLabel().equals("concise"))
-      {
-        return new JPredFile(f.getContentUrl(), DataSourceType.URL);
-      }
-    }
-    return null;
-  }
-}