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.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.Annotation;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
import jalview.ws.params.ArgumentI;
import jalview.ws2.actions.BaseJob;
import jalview.ws2.actions.BaseTask;
import jalview.ws2.actions.ServiceInputInvalidException;
import jalview.ws2.api.Credentials;
import jalview.ws2.api.JobStatus;
import jalview.ws2.client.api.AlignmentWebServiceClientI;

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

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

  @Override
  protected List<BaseJob> prepareJobs() 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 collectResult(List<BaseJob> jobs) throws IOException
  {
    var job = jobs.get(0);
    var status = job.getStatus();
    Console.info(String.format("phmmer finished job \"%s\" with status %s",
            job.getServerJob().getJobId(), status));
    if (status != JobStatus.COMPLETED)
      return null;
    var outputAlignment = client.getAlignment(job.getServerJob());
    var querySeq = job.getInputSequences().get(0).deriveSequence();
    {
      AlignmentAnnotation refpos = null;
      for (var annot : outputAlignment.getAlignmentAnnotation())
      {
        if (annot.sequenceRef == null && annot.label.equals("Reference Positions"))
        {
          refpos = annot;
          break;
        }
      }
      if (refpos != null)
      {
        querySeq = alignQeuryToReferencePositions(querySeq, refpos);
      }
    }
    outputAlignment.insertSequenceAt(0, querySeq);
    return outputAlignment;
  }

  private SequenceI alignQeuryToReferencePositions(SequenceI query, AlignmentAnnotation refpos)
  {
    var sequenceBuilder = new StringBuilder();
    var index = 0;
    for (Annotation a : refpos.annotations)
    {
      // TODO: we assume that the number of "x" annotations is equal to the number
      // of residues. may need a safeguard against invalid input
      if (a != null && a.displayCharacter.equals("x"))
      {
        char c;
        do
          c = query.getCharAt(index++);
        while (Comparison.isGap(c));
        sequenceBuilder.append(c);
      }
      else
      {
        sequenceBuilder.append(Comparison.GAP_DASH);
      }
    }
    query.setSequence(sequenceBuilder.toString());
    return query;
  }
}