package jalview.ext.forester;

import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.math.MatrixI;

import org.forester.evoinference.matrix.distance.DistanceMatrix;
import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
import org.forester.phylogeny.PhylogenyNode;

public final class DataConversions
{
  public static org.forester.phylogeny.data.Sequence createForesterSequence(
          final SequenceI jalviewSequence, final boolean sequenceIsAligned)
  {
    org.forester.phylogeny.data.Sequence foresterSeq = new org.forester.phylogeny.data.Sequence();

    if (jalviewSequence.getDescription() != null)
    {
      foresterSeq.setName(jalviewSequence.getDescription());
    }

    // all tree sequences should be aligned already
    foresterSeq.setMolecularSequenceAligned(sequenceIsAligned);

    foresterSeq.setMolecularSequence(jalviewSequence.getSequenceAsString());
    
    // add checks for DNA or RNA (infer from forester itself?)
    if (jalviewSequence.isProtein())
    {
      try
      {
        foresterSeq.setType("protein");
      } catch (final PhyloXmlDataFormatException ignore)
      {
        // do nothing
      }

    }

    return foresterSeq;

  }

  public static SequenceI createJalviewSequence(
          PhylogenyNode foresterNode)
  {
    String seq = foresterNode.getNodeData().getSequence()
            .getMolecularSequence();
    String seqName = foresterNode.getName();

    SequenceI jalviewSeq = new Sequence(seqName, seq, 1,
            seq.length() + 1);
    return jalviewSeq.deriveSequence();


  }


  // public static org.forester.phylogeny.data.Accession
  // createForesterAccession(
  // SequenceI jalviewSequence)
  // {
  //
  //
  // org.forester.phylogeny.data.Accession foresterAcs = new
  // org.forester.phylogeny.data.Accession();
  //
  // return foresterAcs;
  // }

  public static DistanceMatrix createForesterDistanceMatrix(
          final MatrixI jalviewInputMatrix,
          final String[] matrixIdentifiers)
  {

    DistanceMatrix foresterMatrix = new ForesterMatrix(jalviewInputMatrix,
            matrixIdentifiers);
    return foresterMatrix;

  }

  public static DistanceMatrix createForesterDistanceMatrix(
          final MatrixI jalviewInputMatrix,
          final SequenceI[] matrixSequences)
  {
    DistanceMatrix foresterMatrix = new ForesterMatrix(jalviewInputMatrix,
            matrixSequences);
    return foresterMatrix;

  }


}