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 AptxInit
{
  /**
   * 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_jalview_configuration_file", filePath };
    MainFrame aptxApp = Archaeopteryx.main(AptxArgs);

    LoadedTreeAssociation bindAptxNodes = new LoadedTreeAssociation(
            viewport.getAlignment().getSequencesArray(),
            aptxApp.getMainPanel().getCurrentTreePanel().getPhylogeny());

    bindAptxNodes.associateLeavesToSequences();

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

    return bindFrameToJalview(aptxApp);
  }

  public static MainFrame createInstanceFromUrl()
  {

    return null;
    // void readPhylogeniesFromURL() {
    // URL url = null;
    // Phylogeny[] phys = null;
    // final String message = "Please enter a complete URL, for example
    // \"http://purl.org/phylo/treebase/phylows/study/TB2:S15480?format=nexus\"";
    // final String url_string = JOptionPane
    // .showInputDialog( this,
    // message,
    // "Use URL/webservice to obtain a phylogeny",
    // JOptionPane.QUESTION_MESSAGE );
    // boolean nhx_or_nexus = false;
    // if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {
    // try {
    // url = new URL( url_string );
    // PhylogenyParser parser = null;
    // if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
    // parser = new TolParser();
    // }
    // else {
    // parser = ParserUtils
    // .createParserDependingOnUrlContents( url,
    // getConfiguration().isValidatePhyloXmlAgainstSchema() );
    // }
    // if ( parser instanceof NexusPhylogeniesParser ) {
    // nhx_or_nexus = true;
    // }
    // else if ( parser instanceof NHXParser ) {
    // nhx_or_nexus = true;
    // }
    // if ( _mainpanel.getCurrentTreePanel() != null ) {
    // _mainpanel.getCurrentTreePanel().setWaitCursor();
    // }
    // else {
    // _mainpanel.setWaitCursor();
    // }
    // final PhylogenyFactory factory =
    // ParserBasedPhylogenyFactory.getInstance();
    // phys = factory.create( url.openStream(), parser );
    // }
    // catch ( final MalformedURLException e ) {
    // JOptionPane.showMessageDialog( this,
    // "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
    // "Malformed URL",
    // JOptionPane.ERROR_MESSAGE );
    // }
    // catch ( final IOException e ) {
    // JOptionPane.showMessageDialog( this,
    // "Could not read from " + url + "\n"
    // + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
    // "Failed to read URL",
    // JOptionPane.ERROR_MESSAGE );
    // }
    // catch ( final Exception e ) {
    // JOptionPane.showMessageDialog( this,
    // ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
    // "Unexpected Exception",
    // JOptionPane.ERROR_MESSAGE );
    // }
    // finally {
    // if ( _mainpanel.getCurrentTreePanel() != null ) {
    // _mainpanel.getCurrentTreePanel().setArrowCursor();
    // }
    // else {
    // _mainpanel.setArrowCursor();
    // }
    // }
    // if ( ( phys != null ) && ( phys.length > 0 ) ) {
    // if ( nhx_or_nexus &&
    // getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
    // for( final Phylogeny phy : phys ) {
    // PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
    // }
    // }
    // AptxUtil.addPhylogeniesToTabs( phys,
    // new File( url.getFile() ).getName(),
    // new File( url.getFile() ).toString(),
    // getConfiguration(),
    // getMainPanel() );
    // _mainpanel.getControlPanel().showWhole();
    // }
    // }
    // activateSaveAllIfNeeded();
    // System.gc();
    // }

  }



  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));
    // aptxApp.setFont(Desktop.instance.getFont());
    // aptxApp.getMainPanel().setFont(Desktop.instance.getFont());

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

    return aptxApp;

  }


}