src/jalview/ws/slivkaws/SlivkaJPredServiceInstance.java

   1 package jalview.ws.slivkaws;
   2
   3 import java.io.IOError;
   4 import java.io.IOException;
   5 import java.util.List;
   6
   7 import jalview.datamodel.AlignmentI;
   8 import jalview.datamodel.SequenceI;
   9 import jalview.io.DataSourceType;
  10 import jalview.io.JPredFile;
  11 import jalview.ws.api.JPredMutlipleAlignmentServiceI;
  12 import jalview.ws.api.JobId;
  13 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
  14 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
  15 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
  16
  17 public class SlivkaJPredServiceInstance extends SlivkaWSInstance
  18     implements JPredMutlipleAlignmentServiceI
  19 {
  20
  21   public SlivkaJPredServiceInstance(SlivkaClient client,
  22       SlivkaService service, String action)
  23   {
  24     super(client, service, action);
  25     style = ServiceClient.JPREDWSCLIENT;
  26   }
  27
  28   @Override
  29   public JobId align(List<SequenceI> sequences) throws Throwable
  30   {
  31     return super.submit(sequences, null, null);
  32   }
  33
  34   @Override
  35   public AlignmentI getAlignment(JobId jobId) throws Exception
  36   {
  37     List<RemoteFile> files;
  38     try {
  39       files = client.getJobResults(jobId.getJobId());
  40       for (RemoteFile f : files) {
  41         var alignment = readAlignment(f);
  42         if (alignment != null)
  43         {
  44           return alignment;
  45         }
  46       }
  47     }
  48     catch (IOException e) {
  49       throw new IOError(e);
  50     }
  51     return null;
  52   }
  53
  54   @Override
  55   public JPredFile getPrediction(JobId jobId) throws Exception
  56   {
  57     List<RemoteFile> files = client.getJobResults(jobId.getJobId());
  58     for (RemoteFile f : files)
  59     {
  60       if (f.getLabel().equals("concise"))
  61       {
  62         return new JPredFile(f.getURL(), DataSourceType.URL);
  63       }
  64     }
  65     return null;
  66   }
  67 }