package jalview.ws2.actions.hmmer;

import static jalview.util.Comparison.GapChars;

import java.io.IOException;
import java.util.List;

import jalview.analysis.AlignSeq;
import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.Sequence;
import jalview.ws.params.ArgumentI;
import jalview.ws2.actions.AbstractPollableTask;
import jalview.ws2.actions.BaseJob;
import jalview.ws2.actions.ServiceInputInvalidException;
import jalview.ws2.actions.api.TaskEventListener;
import jalview.ws2.api.Credentials;
import jalview.ws2.api.JobStatus;
import jalview.ws2.client.api.AlignmentWebServiceClientI;

class PhmmerTask extends AbstractPollableTask<BaseJob, AlignmentI>
{
  private final AlignmentWebServiceClientI client;
  private final AlignmentView view;

  PhmmerTask(AlignmentWebServiceClientI client, List<ArgumentI> args,
          Credentials credentials, AlignmentView view,
          TaskEventListener<AlignmentI> eventListener)
  {
    super(client, args, credentials, eventListener);
    this.client = client;
    this.view = view;
  }

  @Override
  protected List<BaseJob> prepare() throws ServiceInputInvalidException
  {
    Console.info("Preparing sequence for phmmer job");
    var sequence = view.getVisibleAlignment('-').getSequenceAt(0);
    var seq = new Sequence(sequence.getName(),
            AlignSeq.extractGaps(GapChars, sequence.getSequenceAsString()));
    var job = new BaseJob(List.of(seq))
    {
      @Override
      public boolean isInputValid()
      {
        return true;
      }
    };
    job.setStatus(JobStatus.READY);
    return List.of(job);
  }

  @Override
  protected AlignmentI done() throws IOException
  {
    var job = getSubJobs().get(0);
    var jobId = job.getServerJob().getJobId();
    var status = job.getStatus();
    Console.info(String.format("phmmer finished job \"%s\" with status %s",
            jobId, status));
    return client.getAlignment(job.getServerJob());
  }

}