package jalview.ext.archaeopteryx;

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

import org.forester.evoinference.distance.NeighborJoiningF;
import org.forester.io.parsers.SymmetricalDistanceMatrixParser;
import org.forester.msa.Msa;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyNode;

public class ArchaeopteryxTreeBuilder // cannot inherit
                                                        // TreeBuilder as that
                                                        // demands the use of
                                                        // SequenceNode (instead
                                                        // of PhylogenyNode)
{
  protected SequenceI[] sequences;

  private Phylogeny aptxTree;

  private PhylogenyNode rootNode;

  protected MatrixI distances;

  protected Msa msa;

  protected SymmetricalDistanceMatrixParser distanceParser = SymmetricalDistanceMatrixParser
          .createInstance();


  public ArchaeopteryxTreeBuilder()
  {

    this.rootNode = new PhylogenyNode();
    this.aptxTree = new Phylogeny();

  }

  public ArchaeopteryxTreeBuilder(PhylogenyNode treeRoot)
  {

    this.rootNode = treeRoot;
    this.aptxTree = new Phylogeny();

  }

  public Phylogeny buildAptxTree(TreeBuilder tree)
  {
    this.sequences = tree.getSequences();
    aptxTree.setName(
            "PLEASE FIX ME reheaheth35yheqhb3q5hyq3bt3q5u4jwqjwuh6");

    final NeighborJoiningF nj = NeighborJoiningF.createInstance(false, 5);
    distances = tree.getDistances();



    // final Phylogeny phy = nj.execute(JalviewMatrixToForesterMatrix
    // .convertJalviewToForester(distances));

    return buildAptxTree(sequences);

  }

  public Phylogeny buildAptxTree(SequenceI[] sequences)
  {

    for (SequenceI sequence : sequences)
    {
      PhylogenyNode treeNode = new PhylogenyNode(sequence.getName());
      rootNode.addAsChild(treeNode);

    }

    aptxTree.setRoot(rootNode);
    return aptxTree;

  }


  /**
   * Formats a localised title for the tree panel, like
   * <p>
   * Neighbour Joining Using BLOSUM62
   * <p>
   * For a tree loaded from file, just uses the file name
   * 
   * @return
   */
  // public String getPanelTitle()
  // {
  // if (treeTitle != null)
  // {
  // return treeTitle;
  // }
  // else
  // {
  // /*
  // * i18n description of Neighbour Joining or Average Distance method
  // */
  // String treecalcnm = MessageManager
  // .getString("label.tree_calc_" + treeType.toLowerCase());
  //
  // /*
  // * short score model name (long description can be too long)
  // */
  // String smn = substitutionMatrix;
  //
  // /*
  // * put them together as <method> Using <model>
  // */
  // final String ttl = MessageManager
  // .formatMessage("label.treecalc_title", treecalcnm, smn);
  // return ttl;
  // }
  // }
}