src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java

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