package jalview.ws.slivkaws;

import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FormatAdapter;
import jalview.ws.api.JobId;
import jalview.ws.api.MultipleSequenceAlignmentI;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.InvalidArgumentException;
import jalview.ws.params.WsParamSetI;

import java.io.IOError;
import java.io.IOException;
import java.rmi.ServerError;
import java.util.Collection;
import java.util.List;

import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
import uk.ac.dundee.compbio.slivkaclient.SlivkaService;

public class SlivkaMsaServiceInstance extends SlivkaWSInstance implements MultipleSequenceAlignmentI
{
  SlivkaMsaServiceInstance(SlivkaClient client, SlivkaService service, String category) {
    super(client, service, category);
    style = ServiceClient.MSAWSCLIENT;
  }

  @Override
  public JobId align(List<SequenceI> toalign, WsParamSetI parameters, List<ArgumentI> list) throws Throwable
  {
    return super.submit(toalign, parameters, list);
  }

  @Override
  public AlignmentI getAlignmentFor(JobId jobId) throws InvalidArgumentException, ServerError, IOError
  {
    Collection<RemoteFile> files;
    try
    {
      var slivkaJob = client.getJob(jobId.getJobId());
      files = slivkaJob.getResults();
      for (RemoteFile f : files)
      {
        if (f.getMediaType().equals("application/clustal"))
        {
          return new FormatAdapter().readFile(f.getContentUrl().toString(), DataSourceType.URL, FileFormat.Clustal);
        }
        else if (f.getMediaType().equals("application/fasta"))
        {
          return new FormatAdapter().readFile(f.getContentUrl().toString(), DataSourceType.URL, FileFormat.Fasta);
        }
      }
    } catch (IOException e)
    {
      throw new IOError(e);
    }
    return null;
  }
}