package jalview.ext.forester;

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

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

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());
    }
    foresterSeq.setMolecularSequenceAligned(sequenceIsAligned); // all tree
                                                              // sequences
                                                              // should
                                                   // be aligned already
    foresterSeq.setMolecularSequence(jalviewSequence.getSequenceAsString());
    if (jalviewSequence.isProtein()) // add checks for DNA or RNA (infer from
                                     // forester itself?)
    {
      try
      {
        foresterSeq.setType("protein");
      } catch (final PhyloXmlDataFormatException ignore)
      {
        // do nothing
      }

    }

    return foresterSeq;

  }


  // 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)
  {
    if (jalviewInputMatrix.width() != jalviewInputMatrix.height())
    {
      // some kind of warning?
    }

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

  }

  public static DistanceMatrix createForesterDistanceMatrix(
          final MatrixI jalviewInputMatrix,
          final SequenceI[] matrixSequences)
  {
    if (jalviewInputMatrix.width() != jalviewInputMatrix.height())
    {
      // some kind of warning?
    }
    DistanceMatrix foresterMatrix = new ForesterMatrix(jalviewInputMatrix,
            matrixSequences);
    return foresterMatrix;

  }
}