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 compbio.data.msa.Category;
  22 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
  23 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
  24 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
  25
  26 public class SlivkaMsaServiceInstance extends SlivkaWSInstance implements MultipleSequenceAlignmentI
  27 {
  28   SlivkaMsaServiceInstance(SlivkaClient client, SlivkaService service, String category) {
  29     super(client, service, category);
  30     style = ServiceClient.MSAWSCLIENT;
  31   }
  32
  33   @Override
  34   public JobId align(List<SequenceI> toalign, WsParamSetI parameters, List<ArgumentI> list) throws Throwable
  35   {
  36     return super.submit(toalign, parameters, list);
  37   }
  38
  39   @Override
  40   public AlignmentI getAlignmentFor(JobId jobId) throws InvalidArgumentException, ServerError, IOError
  41   {
  42     Collection<RemoteFile> files;
  43     try
  44     {
  45       var slivkaJob = client.getJob(jobId.getJobId());
  46       files = slivkaJob.getResults();
  47       for (RemoteFile f : files)
  48       {
  49         if (f.getMediaType().equals("application/clustal"))
  50         {
  51           return new FormatAdapter().readFile(f.getContentUrl().toString(), DataSourceType.URL, FileFormat.Clustal);
  52         }
  53         else if (f.getMediaType().equals("application/fasta"))
  54         {
  55           return new FormatAdapter().readFile(f.getContentUrl().toString(), DataSourceType.URL, FileFormat.Fasta);
  56         }
  57       }
  58     } catch (IOException e)
  59     {
  60       throw new IOError(e);
  61     }
  62     return null;
  63   }
  64 }