src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java

   1 package jalview.ws.slivkaws;
   2
   3
   4 import jalview.datamodel.AlignmentI;
   5 import jalview.datamodel.SequenceI;
   6 import jalview.io.DataSourceType;
   7 import jalview.io.FileFormat;
   8 import jalview.io.FormatAdapter;
   9 import jalview.ws.api.JobId;
  10 import jalview.ws.api.MultipleSequenceAlignmentI;
  11 import jalview.ws.params.ArgumentI;
  12 import jalview.ws.params.InvalidArgumentException;
  13 import jalview.ws.params.WsParamSetI;
  14 import java.io.IOError;
  15 import java.io.IOException;
  16 import java.rmi.ServerError;
  17 import java.util.Collection;
  18 import java.util.List;
  19
  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     Collection<RemoteFile> files;
  41     try
  42     {
  43       var slivkaJob = client.getJob(jobId.getJobId());
  44       files = slivkaJob.getResults();
  45       for (RemoteFile f : files)
  46       {
  47         if (f.getMediaType().equals("application/clustal"))
  48         {
  49           return new FormatAdapter().readFile(f.getContentUrl().toString(), DataSourceType.URL, FileFormat.Clustal);
  50         }
  51         else if (f.getMediaType().equals("application/fasta"))
  52         {
  53           return new FormatAdapter().readFile(f.getContentUrl().toString(), DataSourceType.URL, FileFormat.Fasta);
  54         }
  55       }
  56     } catch (IOException e)
  57     {
  58       throw new IOError(e);
  59     }
  60     return null;
  61   }
  62 }