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.io.FileNotFoundException;
import java.io.IOException;
import java.net.URL;
import java.util.Map;

import org.forester.archaeopteryx.AptxUtil;
import org.forester.archaeopteryx.Archaeopteryx;
import org.forester.archaeopteryx.Configuration;
import org.forester.archaeopteryx.MainFrame;
import org.forester.io.parsers.nhx.NHXParser;
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 AptxInit
{

  private final static Configuration APTX_CONFIG = new Configuration(
          "_aptx_jalview_configuration_file", false, false, false);

  private final static boolean VALIDATE_PHYLOXML_XSD = APTX_CONFIG
          .isValidatePhyloXmlAgainstSchema();

  private final static boolean REPLACE_NHX_UNDERSCORES = APTX_CONFIG
          .isReplaceUnderscoresInNhParsing();

  private final static boolean INTERNAL_NUMBERS_AS_CONFIDENCE = APTX_CONFIG
          .isInternalNumberAreConfidenceForNhParsing();

  private final static boolean MIDPOINT_REROOT = APTX_CONFIG
          .isMidpointReroot();

  private final static NHXParser.TAXONOMY_EXTRACTION TAXONOMY_EXTRACTION = APTX_CONFIG
          .getTaxonomyExtraction();

  /**
   * 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 AptxTreeBuilder(
            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 createInstanceFromFile(String filePath,
          AlignmentViewport viewport)
  {
    String[] AptxArgs = new String[] { "-c",
        APTX_CONFIG.getConfigFilename(), filePath };
    MainFrame aptxApp = Archaeopteryx.main(AptxArgs);

    int tabCount = aptxApp.getMainPanel().getTabbedPane().getTabCount();

    for (int i = 0; i < tabCount; i++)
    {
      // roundabout way to select each tree because getComponentAt(i) requires
      // casting to TreePanel which doesn't work
      aptxApp.getMainPanel().getTabbedPane().setSelectedIndex(i);
      Phylogeny tree = aptxApp.getMainPanel().getCurrentTreePanel()
              .getPhylogeny();

    LoadedTreeAssociation bindAptxNodes = new LoadedTreeAssociation(
            viewport.getAlignment().getSequencesArray(),
              tree);

    bindAptxNodes.associateLeavesToSequences();

    bindNodesToJalviewSequences(aptxApp, viewport,
            bindAptxNodes.getAlignmentWithNodes(),
            bindAptxNodes.getNodesWithAlignment());
    }
    return bindFrameToJalview(aptxApp);
  }

  public static MainFrame createInstanceFromUrl(URL treeUrl,
          AlignmentViewport viewport)
          throws FileNotFoundException, IOException, RuntimeException
  {
    String treeTitle = treeUrl.getFile();
    Phylogeny[] trees = AptxUtil.readPhylogeniesFromUrl(treeUrl,
            VALIDATE_PHYLOXML_XSD,
             REPLACE_NHX_UNDERSCORES, INTERNAL_NUMBERS_AS_CONFIDENCE,
            TAXONOMY_EXTRACTION, MIDPOINT_REROOT);
    MainFrame aptxApp = Archaeopteryx.createApplication(trees, APTX_CONFIG,
            treeTitle);

    for (Phylogeny tree : trees)
    {
      LoadedTreeAssociation bindAptxNodes = new LoadedTreeAssociation(
              viewport.getAlignment().getSequencesArray(), tree);

      bindAptxNodes.associateLeavesToSequences();
      bindNodesToJalviewSequences(aptxApp, viewport,
              bindAptxNodes.getAlignmentWithNodes(),
              bindAptxNodes.getNodesWithAlignment());

    }

    return bindFrameToJalview(aptxApp);

  }




  public static MainFrame createAptxFrame(
          final Phylogeny[] aptxTrees)
  {
    MainFrame aptxApp = Archaeopteryx.createApplication(aptxTrees,
            APTX_CONFIG, 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));
    // aptxApp.setFont(Desktop.instance.getFont());
    // aptxApp.getMainPanel().setFont(Desktop.instance.getFont());

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

    return aptxApp;

  }



}