package jalview.ext.archaeopteryx;

import jalview.analysis.TreeBuilder;
import jalview.datamodel.SequenceI;
import jalview.ext.forester.DataConversions;
import jalview.ext.forester.ForesterMatrix;
import jalview.ext.treeviewer.ExternalTreeBuilderI;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;

import java.util.HashMap;
import java.util.Map;

import org.forester.evoinference.matrix.distance.DistanceMatrix;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.data.NodeData;
import org.forester.phylogeny.data.Sequence;

/**
 * Class for converting trees made in Jalview (through TreeBuilder) to trees
 * compatible with Forester (Phylogeny objects).
 * 
 * Note that this currently demands a 1:1 relationship between tree nodes and
 * the sequences used for generating them.
 * 
 * @author kjvanderheide
 *
 */
public class AptxTreeBuilder
        implements ExternalTreeBuilderI<Phylogeny, PhylogenyNode>
{
  protected final SequenceI[] sequences;

  protected final DistanceMatrix distances;
  
  protected final TreeBuilder jalviewTree;
  
  public String treeTitle;

  private final Phylogeny aptxTree;

  private PhylogenyNode rootNode;

  private final Map<SequenceI, PhylogenyNode> alignmentWithNodes;

  private final Map<PhylogenyNode, SequenceI> nodesWithAlignment;

  public AptxTreeBuilder(final TreeBuilder calculatedTree)
  {
    jalviewTree = calculatedTree;
    sequences = jalviewTree.getSequences();
    distances = ForesterMatrix.convertJalviewToForester(
            jalviewTree.getDistances(), sequences);

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

    int amountOfSequences = distances.getSize();
    alignmentWithNodes = new HashMap<>(amountOfSequences);
    nodesWithAlignment = new HashMap<>(amountOfSequences);


  }

  @Override
  public Phylogeny buildTree(final PhylogenyNode treeRoot)
  {

    if (treeRoot != null)
    {
      rootNode = treeRoot;
    }

    buildTree();

    return aptxTree;

  }


  @Override
  public Phylogeny buildTree()
  {

    for (SequenceI sequence : sequences)
    {
      Sequence seq = DataConversions
              .createForesterSequence(sequence, true);
      PhylogenyNode sequenceNode = new PhylogenyNode(sequence.getName());

      NodeData nodeData = sequenceNode.getNodeData();
      nodeData.setSequence(seq);

      MappingUtils.putWithDuplicationCheck(nodesWithAlignment,
              sequenceNode, sequence);
      MappingUtils.putWithDuplicationCheck(alignmentWithNodes,
              sequence, sequenceNode);
      rootNode.addAsChild(sequenceNode);
    }


    aptxTree.setRoot(rootNode);

    treeTitle = generateTreeName();
    aptxTree.setName(treeTitle);

    return aptxTree;

  }

  @Override
  public Map<SequenceI, PhylogenyNode> getAlignmentBoundNodes()
  {
    return alignmentWithNodes;
  }

  @Override
  public Map<PhylogenyNode, SequenceI> getNodesBoundAlignment()
  {
    return nodesWithAlignment;
  }

  private Phylogeny clusterNodes()
  {
    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
   */
  @Override
  public String generateTreeName() // Move this and add selection region to the
                                   // title when applicable
  {
    if (treeTitle != null) // will currently never happen, loaded tree file will
                           // take a different path
    {
      return treeTitle;
    }
    else
    {
      /*
      * i18n description of Neighbour Joining or Average Distance method
      */
      String treecalcnm = MessageManager
              .getString("label.tree_calc_" + jalviewTree.getClass()
                      .getSimpleName().substring(0, 2).toLowerCase());
      /*
      * short score model name (long description can be too long)
      */
      String smn = jalviewTree.getScoreModel().getName();

      /*
      * put them together as <method> Using <model>
      */
      final String ttl = MessageManager
              .formatMessage("label.treecalc_title", treecalcnm, smn);
      return ttl;
    }
  }
  

}