package jalview.ext.treeviewer;

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

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

/**
 * Generic implementation of {@link LoadedTreeAssociationI } that tries to
 * associate tree nodes based on comparing Jalview's sequence IDs to tree node
 * names.
 * 
 * @author kjvanderheide
 *
 */
public class LoadedTreeSequenceAssociation
        implements LoadedTreeAssociationI
{
  SequenceI[] alignSequences;

  TreeI tree;

  Map<SequenceI, TreeNodeI> alignmentWithNodes;

  Map<TreeNodeI, SequenceI> nodesWithAlignment;

  public LoadedTreeSequenceAssociation(SequenceI[] alignmentSequences,
          TreeI extTree)
  {
    alignSequences = alignmentSequences;
    tree = extTree;
    alignmentWithNodes = new HashMap<>(alignSequences.length);
    nodesWithAlignment = new HashMap<>(alignSequences.length);

  }

  @Override
  public void associateNodesToSequences()

  {
    SequenceIdMatcher algnIds = new SequenceIdMatcher(alignSequences);
    SequenceI nodeSequence;
    String nodeSequenceName;

    if (!tree.isEmpty())
    {
      for (final Iterator<TreeNodeI> iter = tree
              .iterateInPreOrder(); iter
              .hasNext();)
      {
        TreeNodeI treeNode = iter.next();
        nodeSequenceName = treeNode.getNodeName();

        nodeSequence = algnIds.findIdMatch(nodeSequenceName);
        if (nodeSequence != null)
        {
          // is there already a sequence present for the node?
          // If so, does it actually match Jalview's sequence?
          if (treeNode.getSequence() != null)
          {
            if (!(treeNode.getSequence().getSequenceAsString()
                    .equals(nodeSequence.getSequenceAsString())))
            {
              System.err.println(
                      "Sequence detected in tree node that does not match corresponding Jalview sequence:"
                              + nodeSequenceName);
              // which sequence gets precedence?

            }

          }
          else
          {
          treeNode.setSequence(nodeSequence);
          }
          MappingUtils.putWithDuplicationCheck(alignmentWithNodes,
                  nodeSequence, treeNode);
          MappingUtils.putWithDuplicationCheck(nodesWithAlignment, treeNode,
                  nodeSequence);


        }

    }

    }
  }



  @Override
  public Map<SequenceI, TreeNodeI> getAlignmentWithNodes()
  {
    return alignmentWithNodes;
  }

  @Override
  public Map<TreeNodeI, SequenceI> getNodesWithAlignment()
  {
    return nodesWithAlignment;
  }


}