src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java

   1 package jalview.ws.slivkaws;
   2
   3 import jalview.datamodel.AlignmentI;
   4 import jalview.datamodel.SequenceI;
   5 import jalview.ws.api.JobId;
   6 import jalview.ws.api.MultipleSequenceAlignmentI;
   7 import jalview.ws.params.ArgumentI;
   8 import jalview.ws.params.InvalidArgumentException;
   9 import jalview.ws.params.WsParamSetI;
  10
  11 import java.io.IOError;
  12 import java.io.IOException;
  13 import java.rmi.ServerError;
  14 import java.util.List;
  15
  16 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
  17 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
  18 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
  19
  20 public class SlivkaMsaServiceInstance extends SlivkaWSInstance implements MultipleSequenceAlignmentI
  21 {
  22   SlivkaMsaServiceInstance(SlivkaClient client, SlivkaService service, String category) {
  23     super(client, service, category);
  24     style = ServiceClient.MSAWSCLIENT;
  25   }
  26
  27   @Override
  28   public JobId align(List<SequenceI> toalign, WsParamSetI parameters, List<ArgumentI> list) throws Throwable
  29   {
  30     return super.submit(toalign, parameters, list);
  31   }
  32
  33   @Override
  34   public AlignmentI getAlignmentFor(JobId jobId) throws InvalidArgumentException, ServerError, IOError
  35   {
  36     try
  37     {
  38       List<RemoteFile> files = client.getJobResults(jobId.getJobId());
  39       for (RemoteFile f : files)
  40       {
  41         var aln = readAlignment(f);
  42         if (aln != null)
  43         {
  44           return aln;
  45         }
  46       }
  47     } catch (IOException e)
  48     {
  49       throw new IOError(e);
  50     }
  51     return null;
  52   }
  53 }