src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java

   1 package jalview.ws.slivkaws;
   2
   3 import jalview.bin.Cache;
   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
  15 import java.io.IOError;
  16 import java.io.IOException;
  17 import java.rmi.ServerError;
  18 import java.util.Collection;
  19 import java.util.List;
  20
  21 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
  22 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
  23 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
  24
  25 public class SlivkaMsaServiceInstance extends SlivkaWSInstance implements MultipleSequenceAlignmentI
  26 {
  27   SlivkaMsaServiceInstance(SlivkaClient client, SlivkaService service, String category) {
  28     super(client, service, category);
  29     style = ServiceClient.MSAWSCLIENT;
  30   }
  31
  32   @Override
  33   public JobId align(List<SequenceI> toalign, WsParamSetI parameters, List<ArgumentI> list) throws Throwable
  34   {
  35     return super.submit(toalign, parameters, list);
  36   }
  37
  38   @Override
  39   public AlignmentI getAlignmentFor(JobId jobId) throws InvalidArgumentException, ServerError, IOError
  40   {
  41     Collection<RemoteFile> files;
  42     try
  43     {
  44       var slivkaJob = client.getJob(jobId.getJobId());
  45       files = slivkaJob.getResults();
  46       for (RemoteFile f : files)
  47       {
  48         if (f.getMediaType().equals("application/clustal"))
  49         {
  50           return new FormatAdapter().readFile(f.getContentUrl().toString(), DataSourceType.URL, FileFormat.Clustal);
  51         }
  52         else if (f.getMediaType().equals("application/fasta"))
  53         {
  54           return new FormatAdapter().readFile(f.getContentUrl().toString(), DataSourceType.URL, FileFormat.Fasta);
  55         }
  56       }
  57     } catch (IOException e)
  58     {
  59       throw new IOError(e);
  60     }
  61     return null;
  62   }
  63 }