package jalview.ws2.actions.secstructpred;

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

import jalview.analysis.AlignmentAnnotationUtils;
import jalview.api.AlignViewportI;
import jalview.bin.Console;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.io.AlignFile;
import jalview.io.JPredFile;
import jalview.io.JnetAnnotationMaker;
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.SecStructPredWebServiceClientI;

public class SecStructPredTask extends BaseTask<BaseJob, AlignmentI>
{
  private final SecStructPredWebServiceClientI client;

  private final AlignmentView alignmentView;

  private final AlignmentI currentView;

  private final char gapChar;

  SecStructPredTask(SecStructPredWebServiceClientI client, List<ArgumentI> args,
      Credentials credentials, AlignViewportI viewport)
  {
    super(client, args, credentials);
    this.client = client;
    this.alignmentView = viewport.getAlignmentView(true);
    this.currentView = viewport.getAlignment();
    this.gapChar = viewport.getGapCharacter();
  }

  @Override
  protected List<BaseJob> prepareJobs() throws ServiceInputInvalidException
  {
    AlignmentI alignment = alignmentView
        .getVisibleAlignment(Comparison.GAP_DASH);
    var job = new BaseJob(alignment.getSequences())
    {
      @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); // There shouldn't be more than one job
    var status = job.getStatus();
    Console
        .info(String
            .format("sec str pred job \"%s\" finished with status %s",
                job.getServerJob().getJobId(), status));
    if (status != JobStatus.COMPLETED)
      return null;
    JPredFile predictionFile = client.getPredictionFile(job.getServerJob());
    AlignFile alignmentFile = client.getAlignmentFile(job.getServerJob());
    // Object[] alnAndHiddenCols =
    // alignmentView.getAlignmentAndHiddenColumns(gapChar);
    // SequenceI[] sequences = (SequenceI[]) alnAndHiddenCols[0];
    var sequences = alignmentFile.getSeqsAsArray();
    // HiddenColumns hiddenCols = (HiddenColumns) alnAndHiddenCols[1];
    var aln = new Alignment(sequences);
    int firstSeq = 0;
    aln.setDataset(currentView.getDataset());
    try
    {
      JnetAnnotationMaker.add_annotation(predictionFile, aln, firstSeq, false);
    } catch (Exception e)
    {
      throw new IOException(e);
    }

    for (AlignmentAnnotation alnAnnot : aln.getAlignmentAnnotation())
    {
      if (alnAnnot.sequenceRef != null)
      {
        AlignmentAnnotationUtils
            .replaceAnnotationOnAlignmentWith(alnAnnot, alnAnnot.label,
                getClass().getSimpleName());
      }
    }
    aln.setSeqrep(aln.getSequenceAt(firstSeq));
    return aln;
  }

}