package jalview.ws.jws2.jabaws2;

import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.ws.api.CancellableI;
import jalview.ws.api.JobId;
import jalview.ws.api.MultipleSequenceAlignmentI;
import jalview.ws.jws2.JabaParamStore;
import jalview.ws.jws2.JabaPreset;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.InvalidArgumentException;
import jalview.ws.params.WsParamSetI;

import java.io.IOError;
import java.rmi.ServerError;
import java.util.ArrayList;
import java.util.List;

import compbio.data.sequence.Alignment;
import compbio.data.sequence.FastaSequence;
import compbio.metadata.ResultNotAvailableException;

public class JabawsMsaInstance
        extends JabawsServiceInstance<compbio.data.msa.MsaWS>
        implements MultipleSequenceAlignmentI, CancellableI
{
  @Override
  public JobId align(List<SequenceI> toalign, WsParamSetI parameters,
          List<ArgumentI> arguments) throws Throwable
  {
    List<compbio.data.sequence.FastaSequence> seqs = new ArrayList<>();
    for (SequenceI seq : toalign)
    {
      seqs.add(new FastaSequence(seq.getName(), seq.getSequenceAsString()));
    }
    String jobid = null;
    if (parameters != null)
    {
      if (parameters instanceof JabaPreset)
      {
        jobid = service.presetAlign(seqs,
                ((JabaPreset) parameters).getJabaPreset());
      }
      else
      {
        jobid = service.customAlign(seqs, JabaParamStore
                .getJabafromJwsArgs(parameters.getArguments()));
      }
    }
    else if (arguments != null && arguments.size() > 0)
    {
      jobid = service.customAlign(seqs,
              JabaParamStore.getJabafromJwsArgs(arguments));
    }
    else
    {
      jobid = service.align(seqs);
    }

    if (jobid == null)
    {
      return null;
    }
    return new JobId(our.getServiceType(), our.getName(), jobid);
  }

  @Override
  public AlignmentI getAlignmentFor(JobId jobId)
          throws InvalidArgumentException, ServerError, IOError
  {
    Alignment alignment = null;
    try
    {
      alignment = service.getResult(jobId.getJobId());
    } catch (ResultNotAvailableException rnotav)
    {

      // TODO - migrate JABA exception
      // throw new ServerError("Couldn't get result for job",rnotav);
    }
    SequenceI[] alseqs;
    int alseq_l = 0;
    if (alignment.getSequences().size() == 0)
    {
      return null;
    }

    alseqs = new SequenceI[alignment.getSequences().size()];
    for (compbio.data.sequence.FastaSequence seq : alignment.getSequences())
    {
      alseqs[alseq_l++] = new Sequence(seq.getId(), seq.getSequence());
    }
    AlignmentI jv_al = new jalview.datamodel.Alignment(alseqs);
    jv_al.setGapCharacter(alignment.getMetadata().getGapchar());
    return jv_al;

  }

  public JabawsMsaInstance(Jws2Instance handle)
  {
    super(handle);
  }

}