src/jalview/ws2/actions/hmmer/PhmmerTask.java

   1 package jalview.ws2.actions.hmmer;
   2
   3 import static jalview.util.Comparison.GapChars;
   4
   5 import java.io.IOException;
   6 import java.util.List;
   7
   8 import jalview.analysis.AlignSeq;
   9 import jalview.bin.Console;
  10 import jalview.datamodel.AlignmentI;
  11 import jalview.datamodel.AlignmentView;
  12 import jalview.datamodel.Sequence;
  13 import jalview.ws.params.ArgumentI;
  14 import jalview.ws2.actions.AbstractPollableTask;
  15 import jalview.ws2.actions.BaseJob;
  16 import jalview.ws2.actions.ServiceInputInvalidException;
  17 import jalview.ws2.actions.api.TaskEventListener;
  18 import jalview.ws2.api.Credentials;
  19 import jalview.ws2.api.JobStatus;
  20 import jalview.ws2.client.api.AlignmentWebServiceClientI;
  21
  22 class PhmmerTask extends AbstractPollableTask<BaseJob, AlignmentI>
  23 {
  24   private final AlignmentWebServiceClientI client;
  25   private final AlignmentView view;
  26
  27   PhmmerTask(AlignmentWebServiceClientI client, List<ArgumentI> args,
  28           Credentials credentials, AlignmentView view,
  29           TaskEventListener<AlignmentI> eventListener)
  30   {
  31     super(client, args, credentials, eventListener);
  32     this.client = client;
  33     this.view = view;
  34   }
  35
  36   @Override
  37   protected List<BaseJob> prepare() throws ServiceInputInvalidException
  38   {
  39     Console.info("Preparing sequence for phmmer job");
  40     var sequence = view.getVisibleAlignment('-').getSequenceAt(0);
  41     var seq = new Sequence(sequence.getName(),
  42             AlignSeq.extractGaps(GapChars, sequence.getSequenceAsString()));
  43     var job = new BaseJob(List.of(seq))
  44     {
  45       @Override
  46       public boolean isInputValid()
  47       {
  48         return true;
  49       }
  50     };
  51     job.setStatus(JobStatus.READY);
  52     return List.of(job);
  53   }
  54
  55   @Override
  56   protected AlignmentI done() throws IOException
  57   {
  58     var job = getSubJobs().get(0);
  59     var jobId = job.getServerJob().getJobId();
  60     var status = job.getStatus();
  61     Console.info(String.format("phmmer finished job \"%s\" with status %s",
  62             jobId, status));
  63     return client.getAlignment(job.getServerJob());
  64   }
  65
  66 }