package jalview.ext.archaeopteryx;

import jalview.analysis.TreeBuilder;
import jalview.datamodel.SequenceI;
import jalview.ext.treeviewer.ExternalTreeBuilderI;
import jalview.ext.treeviewer.ExternalTreeViewerBindingI;
import jalview.gui.Desktop;
import jalview.viewmodel.AlignmentViewport;

import java.awt.Dimension;
import java.util.Map;

import org.forester.archaeopteryx.Archaeopteryx;
import org.forester.archaeopteryx.MainFrame;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyNode;

/**
 * Static class for creating Archaeopteryx tree viewer instances from calculated
 * trees and letting them be bound to Jalview.
 * 
 * @author kjvanderheide
 *
 */
public final class ArchaeopteryxInit
{
  /**
   * Test method, should generally not be used as it does not bind the tree to
   * its alignment
   * 
   * @param aptxTrees
   * @return
   */
  public static MainFrame createUnboundInstance(final Phylogeny aptxTree)
  {
    Phylogeny[] aptxTrees = { aptxTree };
    return createAptxFrame(aptxTrees);
  }

  // public static MainFrame createInstance(final Phylogeny[] aptxTrees,
  // AlignmentViewport jalviewAlignmentView)
  // {
  // return createAptxFrameInJalview(aptxTrees);
  //
  // }
  //
  // public static MainFrame createInstance(final Phylogeny aptxTree,
  // final AlignmentViewport jalviewAlignmentView)
  // {
  // Phylogeny[] aptxTrees = { aptxTree }; // future possibility to load in
  // // several trees simultaneously
  // return createAptxFrameInJalview(aptxTrees);
  //
  // }

  public static MainFrame createInstance(
          final TreeBuilder calculatedTree) // very dense method, to be split up
  {
    ExternalTreeBuilderI<Phylogeny, PhylogenyNode> aptxTreeBuilder = new ArchaeopteryxTreeBuilder(
            calculatedTree);

    Phylogeny aptxTree = aptxTreeBuilder.buildTree();
    Phylogeny[] aptxTrees = { aptxTree }; // future possibility to load in
                                          // several trees simultaneously

    MainFrame aptxApp = createAptxFrame(aptxTrees);
            
    bindNodesToJalviewSequences(aptxApp, calculatedTree.getAvport(),
            aptxTreeBuilder.getAlignmentBoundNodes(),
            aptxTreeBuilder.getNodesBoundAlignment());
    return bindFrameToJalview(aptxApp);

  }




  public static MainFrame createAptxFrame(
          final Phylogeny[] aptxTrees)
  {
    MainFrame aptxApp = Archaeopteryx.createApplication(aptxTrees,
            "_aptx_jalview_configuration_file", null);
    return aptxApp;
  }

  public static ExternalTreeViewerBindingI<?> bindNodesToJalviewSequences(
          final MainFrame aptxApp,
          final AlignmentViewport jalviewAlignViewport,
          final Map<SequenceI, PhylogenyNode> alignMappedToNodes,
          final Map<PhylogenyNode, SequenceI> nodesMappedToAlign)
  {
    return new JalviewBinding(aptxApp, jalviewAlignViewport,
            alignMappedToNodes, nodesMappedToAlign);
  }


  public static MainFrame bindFrameToJalview(final MainFrame aptxApp)
  {
    int width = 400;
    int height = 550;
    aptxApp.setMinimumSize(new Dimension(width, height));

    Desktop.addInternalFrame(aptxApp, "Archaeopteryx Tree View", true,
            width, height, true, true);

    return aptxApp;

  }


}