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.gui.JvOptionPane;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;

import java.awt.Dimension;
import java.io.File;
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.PhylogenyParser;
import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
import org.forester.io.parsers.nhx.NHXParser;
import org.forester.io.parsers.util.ParserUtils;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.util.ForesterUtil;

/**
 * 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();



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

    Phylogeny aptxTree = aptxTreeBuilder.buildTree();

    MainFrame aptxApp = createAptxFrame(aptxTree,
            calculatedTree.getAvport(), null);
            
    return aptxApp;
  }

  /**
   * Refactored from Archaeopteryx.main
   * 
   * @param filePath
   * @param viewport
   * @return
   * @throws IOException
   * @throws FileNotFoundException
   */
  public static MainFrame[] createInstancesFromFile(String filePath,
          AlignmentViewport viewport)
          throws FileNotFoundException, IOException
  {
    File treeFile = new File(filePath);
    final String err = ForesterUtil.isReadableFile(treeFile);
    if (!ForesterUtil.isEmpty(err))
    {
      JvOptionPane.showMessageDialog(Desktop.desktop, err,
              MessageManager.getString("label.problem_reading_tree_file"),
              JvOptionPane.WARNING_MESSAGE);
    }
    boolean nhx_or_nexus = false;
    final PhylogenyParser p = ParserUtils.createParserDependingOnFileType(
            treeFile, VALIDATE_PHYLOXML_XSD);
    if (p instanceof NHXParser)
    {
      nhx_or_nexus = true;
      final NHXParser nhx = (NHXParser) p;
      nhx.setReplaceUnderscores(REPLACE_NHX_UNDERSCORES);
      nhx.setIgnoreQuotes(false);
      nhx.setTaxonomyExtraction(TAXONOMY_EXTRACTION);
    }
    else if (p instanceof NexusPhylogeniesParser)
    {
      nhx_or_nexus = true;
      final NexusPhylogeniesParser nex = (NexusPhylogeniesParser) p;
      nex.setReplaceUnderscores(REPLACE_NHX_UNDERSCORES);
      nex.setIgnoreQuotes(false);
    }
//    else if (p instanceof PhyloXmlParser)
//    {
//      MainFrameApplication.warnIfNotPhyloXmlValidation(APTX_CONFIG);
//    }
    Phylogeny[] phylogenies = PhylogenyMethods.readPhylogenies(p, treeFile);
    MainFrame[] aptxFrames = new MainFrame[phylogenies.length];
    String treeTitle = treeFile.getName();

    for (int i = 0; i < phylogenies.length; i++)
      {
      Phylogeny tree = phylogenies[i];

      if (nhx_or_nexus && INTERNAL_NUMBERS_AS_CONFIDENCE)
      {
        PhylogenyMethods.transferInternalNodeNamesToConfidence(tree, "");
      }

      aptxFrames[i] = createAptxFrame(tree, viewport, treeTitle);
    }

    return aptxFrames;
    }


  public static MainFrame[] createInstancesFromUrl(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[] aptxFrames = new MainFrame[trees.length];
    for (int i = 0; i < trees.length; i++)
    {
      Phylogeny tree = trees[i];
      aptxFrames[i] = createAptxFrame(tree, viewport, treeTitle);
    }

    return aptxFrames;

  }





  public static MainFrame createAptxFrame(
          final Phylogeny aptxTree,
          final AlignmentViewport jalviewAlignport, String treeTitle)
  {
    MainFrame aptxApp = Archaeopteryx.createApplication(aptxTree,
            APTX_CONFIG, treeTitle);
    LoadedTreeAssociation bindAptxNodes = new LoadedTreeAssociation(
            jalviewAlignport.getAlignment().getSequencesArray(), aptxTree);

    bindAptxNodes.associateLeavesToSequences();
    bindNodesToJalviewSequences(aptxApp, jalviewAlignport,
            bindAptxNodes.getAlignmentWithNodes(),
            bindAptxNodes.getNodesWithAlignment());
    bindFrameToJalview(aptxApp);
    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;

  }



}