package jalview.ext.forester.io;

import jalview.ext.archaeopteryx.ArchaeopteryxInit;
import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
import jalview.util.MessageManager;

import java.io.File;
import java.io.IOException;

import org.forester.archaeopteryx.Archaeopteryx;
import org.forester.archaeopteryx.MainFrame;
import org.forester.util.ForesterUtil;

public class ForesterTreeParser implements ExternalTreeParserI<MainFrame>
{
  private final String filePath;

  private final File file;

  public ForesterTreeParser(final String treeFilePath)
  {
    final String possibleError = ForesterUtil.isReadableFile(treeFilePath);
    if (possibleError != null)
    {
      JvOptionPane.showMessageDialog(Desktop.desktop, possibleError,
              MessageManager.getString("label.problem_reading_tree_file"),
              JvOptionPane.WARNING_MESSAGE);

    }
    filePath = treeFilePath;
    file = new File(filePath);


  }

  public ForesterTreeParser(final File treeFile) throws IOException
  {
    final String possibleError = ForesterUtil.isReadableFile(treeFile);
    if (possibleError != null)
    {
      JvOptionPane.showMessageDialog(Desktop.desktop, possibleError,
              MessageManager.getString("label.problem_reading_tree_file"),
              JvOptionPane.WARNING_MESSAGE);

    }
    file = treeFile;
    filePath = file.getCanonicalPath();
  }

  @Override
  public MainFrame loadTree()
  {
    String[] AptxArgs = new String[] { "-c",
        "_aptx_jalview_configuration_file", filePath };
    MainFrame aptx = Archaeopteryx.main(AptxArgs);
    ArchaeopteryxInit.bindFrameToJalview(aptx);
    return aptx;


  }

}

/**
 * Mostly refactored from Archaeopteryx.main() and
 * MainFrameApplication.readPhylogeniesFromFile()
 */
// boolean nhx_or_nexus = false;
// Configuration config = new Configuration(
// "_aptx_jalview_configuration_file", false, false, false);
// try
// {
// final PhylogenyParser p = ParserUtils.createParserDependingOnFileType(
// file, config.isValidatePhyloXmlAgainstSchema());
//
// if (p instanceof NHXParser)
// {
// nhx_or_nexus = true;
// final NHXParser nhx = (NHXParser) p;
// nhx.setReplaceUnderscores(false);
// nhx.setIgnoreQuotes(false);
// nhx.setTaxonomyExtraction(config.getTaxonomyExtraction());
// }
// else if (p instanceof NexusPhylogeniesParser)
// {
// nhx_or_nexus = true;
// final NexusPhylogeniesParser nex = (NexusPhylogeniesParser) p;
// nex.setReplaceUnderscores(config.isReplaceUnderscoresInNhParsing());
// nex.setIgnoreQuotes(false);
// }
// else if (p instanceof PhyloXmlParser)
// {
//
// }
// Phylogeny[] phylogenies = PhylogenyMethods.readPhylogenies(p, file);
// if (nhx_or_nexus
// && config.isInternalNumberAreConfidenceForNhParsing())
// {
// for (final Phylogeny phy : phylogenies)
// {
// PhylogenyMethods.transferInternalNodeNamesToConfidence(phy, "");
//
// }
// }
// }
//
// catch (IOException e)
// {
// // TODO Auto-generated catch block
// e.printStackTrace();
// }
// }