package jalview.ext.archaeopteryx;

import jalview.analysis.SequenceIdMatcher;
import jalview.datamodel.SequenceI;
import jalview.ext.forester.DataConversions;
import jalview.ext.treeviewer.ExternalLoadedTreeAssociationI;
import jalview.util.MappingUtils;

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

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

public class LoadedTreeAssociation
        implements ExternalLoadedTreeAssociationI
{
  SequenceI[] alignSequences;

  Phylogeny tree;

  Map<SequenceI, PhylogenyNode> alignmentWithNodes;

  Map<PhylogenyNode, SequenceI> nodesWithAlignment;

  public LoadedTreeAssociation(SequenceI[] alignmentSequences,
          Phylogeny aptxTree)
  {
    alignSequences = alignmentSequences;
    tree = aptxTree;
    alignmentWithNodes = new HashMap<>(alignSequences.length);
    nodesWithAlignment = new HashMap<>(alignSequences.length);

  }



  /**
   * 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()

  {
    SequenceIdMatcher algnIds = new SequenceIdMatcher(alignSequences);

    List<PhylogenyNode> leaves = tree.getExternalNodes();
    SequenceI nodeSequence;
    String nodeSequenceName;

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

      nodeSequence = algnIds.findIdMatch(nodeSequenceName);
      if (nodeSequence != null)
      {
        org.forester.phylogeny.data.Sequence foresterNodeSeq = DataConversions
                .createForesterSequence(nodeSequence, true);
        treeNode.getNodeData().setSequence(foresterNodeSeq);

        MappingUtils.putWithDuplicationCheck(alignmentWithNodes,
                nodeSequence, treeNode);
        MappingUtils.putWithDuplicationCheck(nodesWithAlignment,
                treeNode, nodeSequence);


      }

    }

  }



  public Map<SequenceI, PhylogenyNode> getAlignmentWithNodes()
  {
    return alignmentWithNodes;
  }

  public Map<PhylogenyNode, SequenceI> getNodesWithAlignment()
  {
    return nodesWithAlignment;
  }

  // {
  // 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)
  // {
  // org.forester.phylogeny.data.Sequence foresterNodeSeq =
  // ForesterDataConversions.createForesterSequence(nodeSequence, true);
  //
  // treeNode.getNodeData().setSequence(foresterNodeSeq);
  // 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.setCollapse(true); // collapse nodes that couldn't be connected
  // // to a sequence
  //
  //
  // // 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();
  //
  // }

}