package jalview.ext.archaeopteryx;

import jalview.analysis.SequenceIdMatcher;
import jalview.datamodel.SequenceI;

import java.util.ArrayList;
import java.util.List;

import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyNode;

public class JalviewToAptxAssociation
        implements JalviewToSequenceAssociationI<Phylogeny>
{
  SequenceI[] alignSequences;

  Phylogeny tree;

  public JalviewToAptxAssociation(SequenceI[] alignmentSequences,
          Phylogeny aptxTree)
  {
    alignSequences = alignmentSequences;
    tree = aptxTree;

  }



  /**
   * Tries to match sequences from Jalview with tree nodes in Archaeopteryx and
   * fills in the tree node with sequence data if a match is found.
   * 
   * Partially refactored from the old Jalview TreeModel
   * associateLeavesToSequences method.
   *
   * @param seqs
   * @param aptxTree
   */
  @Override
  public void associateLeavesToSequences(SequenceI[] seqs,
          Phylogeny aptxTree)
  {
    SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);

    List<PhylogenyNode> leaves = aptxTree.getExternalNodes();

    int namesleft = seqs.length;
    SequenceI nodeSequence;
    String nodeSequenceName;
    List<SequenceI> one2many = new ArrayList<>();
    // int countOne2Many = 0;

    for (PhylogenyNode treeNode : leaves)
    {
      nodeSequenceName = treeNode.getName();
      nodeSequence = null;

      if (namesleft > -1)
      {
        nodeSequence = algnIds.findIdMatch(nodeSequenceName);
      }

      if (nodeSequence != null)
      {

        //treeNode.setElement(nodeSequence);
        if (one2many.contains(nodeSequence))
        {
          // countOne2Many++;
          if (jalview.bin.Cache.log.isDebugEnabled())
          {
            jalview.bin.Cache.log.debug("One 2 many relationship for"
             +nodeSequence.getName());
          }
        }
        else
        {
          one2many.add(nodeSequence);
          namesleft--;
        }
      }
      else
      {
       // treeNode.setElement( new Sequence(nodeSequenceName, "THISISAPLACEHOLDER"));
        // treeNode.setPlaceholder(true);
      }
    }
    // if (jalview.bin.Cache.log.isDebugEnabled() && countOne2Many>0) {
    // jalview.bin.Cache.log.debug("There were "+countOne2Many+" alignment
    // sequence ids (out of "+one2many.size()+" unique ids) linked to two or
    // more leaves.");
    // }
    // one2many.clear();

  }
}