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.io.DataSourceType;
   6 import jalview.io.FileFormat;
   7 import jalview.io.FormatAdapter;
   8 import jalview.ws.api.JobId;
   9 import jalview.ws.api.MultipleSequenceAlignmentI;
  10 import jalview.ws.params.ArgumentI;
  11 import jalview.ws.params.InvalidArgumentException;
  12 import jalview.ws.params.WsParamSetI;
  13
  14 import java.io.IOError;
  15 import java.io.IOException;
  16 import java.rmi.ServerError;
  17 import java.util.List;
  18
  19 import compbio.data.msa.Category;
  20 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
  21 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
  22 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
  23
  24 public class SlivkaMsaServiceInstance extends SlivkaWSInstance implements MultipleSequenceAlignmentI
  25 {
  26   SlivkaMsaServiceInstance(SlivkaClient client, SlivkaService service, String category) {
  27     super(client, service, category);
  28     style = ServiceClient.MSAWSCLIENT;
  29   }
  30
  31   @Override
  32   public JobId align(List<SequenceI> toalign, WsParamSetI parameters, List<ArgumentI> list) throws Throwable
  33   {
  34     return super.submit(toalign, parameters, list);
  35   }
  36
  37   @Override
  38   public AlignmentI getAlignmentFor(JobId jobId) throws InvalidArgumentException, ServerError, IOError
  39   {
  40     try
  41     {
  42       List<RemoteFile> files = client.getJobResults(jobId.getJobId());
  43       for (RemoteFile f : files)
  44       {
  45         if (f.getMimeType().equals("application/clustal")
  46             || f.getMimeType().equals("application/fasta"))
  47         {
  48           return readAlignment(f);
  49         }
  50       }
  51     } catch (IOException e)
  52     {
  53       throw new IOError(e);
  54     }
  55     return null;
  56   }
  57 }