package jalview.ext.archaeopteryx;

import jalview.ext.forester.io.UtilityMethods;
import jalview.ext.treeviewer.LoadedTreeAssociationI;
import jalview.ext.treeviewer.LoadedTreeSequenceAssociation;
import jalview.ext.treeviewer.TreeFrameI;
import jalview.ext.treeviewer.TreeI;
import jalview.ext.treeviewer.TreeViewerUtils;
import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;

import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.net.MalformedURLException;
import java.net.URL;

import org.forester.archaeopteryx.AptxUtil;
import org.forester.archaeopteryx.Configuration;
import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
import org.forester.archaeopteryx.webservices.WebserviceUtil;
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.phyloxml.PhyloXmlDataFormatException;
import org.forester.io.parsers.phyloxml.PhyloXmlParser;
import org.forester.io.parsers.tol.TolParser;
import org.forester.io.parsers.util.ParserUtils;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.data.Identifier;
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
{
  public final static InputStream CONFIG_LOC = AptxInit.class

          .getResourceAsStream("/_aptx_jalview_configuration_file.txt");

  public final static Configuration APTX_CONFIG = new Configuration(
          CONFIG_LOC,
          false, false);
  static
  {
    APTX_CONFIG.setBaseFontSize(Desktop.instance.getFont().getSize());
    APTX_CONFIG
            .setBaseFontFamilyName(Desktop.instance.getFont().getFamily());
  }

  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 TreeFrameI createInstanceFromNhx(String treeTitle,
          String nhxString, AlignmentViewport viewport)
          throws IOException
  {
    if (Desktop.instance != null)
    {
      Desktop.instance.startLoading(treeTitle);
    }


    Phylogeny aptxPhylogeny = Phylogeny
            .createInstanceFromNhxString(nhxString);
    aptxPhylogeny.setName(treeTitle);

    TreeFrameI aptxFrame = createAptxFrame(aptxPhylogeny, viewport,
            treeTitle);

    if (Desktop.instance != null)
    {
      Desktop.instance.stopLoading();
    }

    return aptxFrame;

  }

  /**
   * Refactored from Archaeopteryx.main
   * 
   * @param filePath
   * @param viewport
   * @return
   * @throws IOException
   * @throws FileNotFoundException
   */
  public static TreeFrameI[] createInstancesFromFile(File treeFile,
          AlignmentViewport viewport)
          throws FileNotFoundException, IOException
  {
    TreeFrameI[] aptxFrames = null;
    if (UtilityMethods.canForesterReadFile(treeFile))
    {

      if (Desktop.instance != null)
      {
        Desktop.instance.startLoading(treeFile.getCanonicalPath());
      }
      boolean nhx_or_nexus = false;
      final PhylogenyParser parser = ParserUtils
              .createParserDependingOnFileType(treeFile,
                      VALIDATE_PHYLOXML_XSD);
      if (parser instanceof NHXParser)
      {
        nhx_or_nexus = true;
        final NHXParser nhx = (NHXParser) parser;
        nhx.setReplaceUnderscores(REPLACE_NHX_UNDERSCORES);
        nhx.setIgnoreQuotes(false);
        nhx.setTaxonomyExtraction(TAXONOMY_EXTRACTION);
      }
      else if (parser instanceof NexusPhylogeniesParser)
      {
        nhx_or_nexus = true;
        final NexusPhylogeniesParser nex = (NexusPhylogeniesParser) parser;
        nex.setReplaceUnderscores(REPLACE_NHX_UNDERSCORES);
        nex.setIgnoreQuotes(false);
      }
      else if (parser instanceof PhyloXmlParser)
      {
        if (VALIDATE_PHYLOXML_XSD == false)
        {
          JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                  MessageManager.getString("error.phyloxml_validation"),
                  MessageManager.getString("label.file_open_error"),
                  JvOptionPane.WARNING_MESSAGE);
        }
      }
      Phylogeny[] trees = PhylogenyMethods.readPhylogenies(parser,
              treeFile);
      aptxFrames = new TreeFrameI[trees.length];

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

        if (nhx_or_nexus && INTERNAL_NUMBERS_AS_CONFIDENCE)
        {
          PhylogenyMethods
                  .transferInternalNodeNamesToConfidence(aptxPhylogeny, "");
        }
        String treeTitle = treeFile.getName() + "[" + i + "]";
        aptxPhylogeny.setName(treeTitle);
        aptxFrames[i] = createAptxFrame(aptxPhylogeny, viewport, treeTitle);

      }
      if (Desktop.instance != null)
      {
        Desktop.instance.stopLoading();
      }
    }
    return aptxFrames;
  }


  public static TreeFrameI[] createInstancesFromFile(
          String filePath,
          AlignmentViewport viewport)
          throws FileNotFoundException, IOException
  {
    File treeFile = new File(filePath);
    return createInstancesFromFile(treeFile, viewport);

    }

  public static TreeFrameI[] createInstancesFromUrl(URL treeUrl,
          AlignmentViewport viewport)
          throws FileNotFoundException, IOException, RuntimeException
  {
    
    String treeTitle = treeUrl.getFile();
    if (Desktop.instance != null)
    {
      Desktop.instance.startLoading(treeTitle);
    }
    Phylogeny[] trees = AptxUtil.readPhylogeniesFromUrl(treeUrl,
            VALIDATE_PHYLOXML_XSD,
             REPLACE_NHX_UNDERSCORES, INTERNAL_NUMBERS_AS_CONFIDENCE,
            TAXONOMY_EXTRACTION, MIDPOINT_REROOT);

    TreeFrameI[] aptxFrames = new TreeFrameI[trees.length];
    for (int i = 0; i < trees.length; i++)
    {
      Phylogeny aptxTree = trees[i];
      aptxFrames[i] = createAptxFrame(aptxTree, viewport, treeTitle);
    }

    if (Desktop.instance != null)
    {
      Desktop.instance.stopLoading();
    }

    return aptxFrames;

  }

  /**
   * Refactored from Forester's UrlTreeReader, this can be more efficient
   * 
   * @param databaseIndex
   * @param viewport
   * @return
   */
  public static TreeFrameI[] createInstancesFromDb(
          PhylogeniesWebserviceClient treeDbClient, String identifier,
          AlignmentViewport viewport)
  {

    URL url = null;
    Phylogeny[] trees = null;
    TreeFrameI[] aptxFrames = null;

    if ((identifier != null) && (identifier.trim().length() > 0))
    {
      if (Desktop.instance != null)
      {
        Desktop.instance.startLoading(identifier);
      }

      identifier = identifier.trim();
      if (treeDbClient.isQueryInteger())
      {
        identifier = identifier.replaceAll("^\\D+", "");

        int id;
        try
        {
          id = Integer.parseInt(identifier);
        } catch (final NumberFormatException e)
        {
          JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                  MessageManager.formatMessage(
                          "error.database_id_has_letters", new String[]
                          { identifier }),
                  MessageManager.getString("label.invalid_url"),
                  JvOptionPane.ERROR_MESSAGE);
          return new TreeFrameI[0];
        }
        identifier = id + "";
      }
      boolean exception = false;
      try
      {
        String url_str = treeDbClient.getUrl();
        url_str = url_str.replaceFirst(
                PhylogeniesWebserviceClient.QUERY_PLACEHOLDER, identifier);
        url = new URL(url_str);
        PhylogenyParser parser = null;
        switch (treeDbClient.getReturnFormat())
        {
        case TOL_XML_RESPONSE:
          parser = new TolParser();
          break;
        case NEXUS:
          parser = new NexusPhylogeniesParser();
          ((NexusPhylogeniesParser) parser).setReplaceUnderscores(true);
          break;
        case TREEBASE_TREE:
          parser = new NexusPhylogeniesParser();
          ((NexusPhylogeniesParser) parser).setReplaceUnderscores(true);
          ((NexusPhylogeniesParser) parser)
                  .setTaxonomyExtraction(NHXParser.TAXONOMY_EXTRACTION.NO);
          break;
        case TREEBASE_STUDY:
          parser = new NexusPhylogeniesParser();
          ((NexusPhylogeniesParser) parser).setReplaceUnderscores(true);
          ((NexusPhylogeniesParser) parser)
                  .setTaxonomyExtraction(NHXParser.TAXONOMY_EXTRACTION.NO);
          break;
        case NH:
          parser = new NHXParser();
          ((NHXParser) parser)
                  .setTaxonomyExtraction(NHXParser.TAXONOMY_EXTRACTION.NO);
          ((NHXParser) parser).setReplaceUnderscores(true);
          ((NHXParser) parser).setGuessRootedness(true);
          break;
        case NH_EXTRACT_TAXONOMY:
          parser = new NHXParser();
          ((NHXParser) parser).setTaxonomyExtraction(
                  NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE);
          ((NHXParser) parser).setReplaceUnderscores(false);
          ((NHXParser) parser).setGuessRootedness(true);
          break;
        case PFAM:
          parser = new NHXParser();
          ((NHXParser) parser).setTaxonomyExtraction(
                  NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT);
          ((NHXParser) parser).setReplaceUnderscores(false);
          ((NHXParser) parser).setGuessRootedness(true);
          break;
        case NHX:
          parser = new NHXParser();
          ((NHXParser) parser)
                  .setTaxonomyExtraction(NHXParser.TAXONOMY_EXTRACTION.NO);
          ((NHXParser) parser).setReplaceUnderscores(false);
          ((NHXParser) parser).setGuessRootedness(true);
          break;
        case PHYLOXML:
          parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
          break;
        default:
          throw new IllegalArgumentException(
                  "unknown format: " + treeDbClient.getReturnFormat());
        }
        //
        // if (_main_frame.getMainPanel().getCurrentTreePanel() != null)
        // {
        // _main_frame.getMainPanel().getCurrentTreePanel().setWaitCursor();
        // }
        // else
        // {
        // _main_frame.getMainPanel().setWaitCursor();
        // }
        trees = ForesterUtil.readPhylogeniesFromUrl(url, parser);
        aptxFrames = new TreeFrameI[trees.length];
      } catch (final MalformedURLException e)
      {
        exception = true;
        JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                MessageManager.formatMessage(
                        "exception.unable_to_launch_url", new String[]
                        { url.toString() }),
                MessageManager.getString("label.invalid_url"),
                JvOptionPane.ERROR_MESSAGE);
        System.err.println(e.getLocalizedMessage());
      } catch (final IOException e)
      {
        exception = true;
        JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                "Could not read from " + url + "\n"
                        + e.getLocalizedMessage(),
                "Failed to read tree from " + treeDbClient.getName() + " for "
                        + identifier,
                JvOptionPane.ERROR_MESSAGE);
        System.err.println(e.getLocalizedMessage());
      } catch (final NumberFormatException e)
      {
        exception = true;
        JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                "Could not read from " + url + "\n"
                        + e.getLocalizedMessage(),
                "Failed to read tree from " + treeDbClient.getName() + " for "
                        + identifier,
                JvOptionPane.ERROR_MESSAGE);
        System.err.println(e.getLocalizedMessage());
      } catch (final Exception e)
      {
        exception = true;
        e.printStackTrace();
        JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                e.getLocalizedMessage(), "Unexpected Exception",
                JvOptionPane.ERROR_MESSAGE);
        System.err.println(e.getLocalizedMessage());
      }
      if ((trees != null) && (trees.length > 0))
      {
        int i = 0;
        for (final Phylogeny aptxTree : trees)
        {
          if (!aptxTree.isEmpty())
          {
            if (treeDbClient.getName().equals(WebserviceUtil.TREE_FAM_NAME))
            {
              aptxTree.setRerootable(false);
              aptxTree.setRooted(true);
            }
            if (treeDbClient.getProcessingInstructions() != null)
            {
              try
              {
                WebserviceUtil.processInstructions(treeDbClient,
                        aptxTree);
              } catch (final PhyloXmlDataFormatException e)
              {
                JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                        "Error:\n" + e.getLocalizedMessage(), "Error",
                        JvOptionPane.ERROR_MESSAGE);
              }
            }
            if (treeDbClient.getNodeField() != null)
            {
              try
              {
                PhylogenyMethods.transferNodeNameToField(aptxTree,
                        treeDbClient.getNodeField(), false);
              } catch (final PhyloXmlDataFormatException e)
              {
                JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                        "Error:\n" + e.getLocalizedMessage(), "Error",
                        JvOptionPane.ERROR_MESSAGE);
              }
            }
            aptxTree.setIdentifier(
                    new Identifier(identifier, treeDbClient.getName()));
            // _main_frame.getJMenuBar().remove(_main_frame.getHelpMenu());
            // _main_frame.getMenuBarOfExternalTreeFrameI()
            // .add(_main_frame.getHelpMenu());
            // _main_frame.getMainPanel().addExternalTreeIInNewTab(ExternalTreeI,
            // _main_frame.getConfiguration(),
            // new File(url.getFile()).getName(), url.toString());


            TreeFrameI aptxApp = createAptxFrame(aptxTree,
                    viewport,
                    url.getFile());
            String my_name_for_file = "";
            if (!ForesterUtil.isEmpty(aptxTree.getName()))
            {
              my_name_for_file = new String(aptxTree.getName())
                      .replaceAll(" ", "_");
            }
            else if (aptxTree.getIdentifier() != null)
            {
              final StringBuffer sb = new StringBuffer();
              if (!ForesterUtil
                      .isEmpty(aptxTree.getIdentifier().getProvider()))
              {
                sb.append(aptxTree.getIdentifier().getProvider());
                sb.append("_");
              }
              sb.append(aptxTree.getIdentifier().getValue());
              my_name_for_file = new String(
                      sb.toString().replaceAll(" ", "_"));
            }
            aptxApp.getTreePanel()
                    .setTreeFile(new File(my_name_for_file));
            // AptxUtil.lookAtSomeTreePropertiesForAptxControlSettings(
            // aptxTree, aptxApp.getMainPanel().getControlPanel(),
            // APTX_CONFIG);
            aptxApp.getTreeControls().displayEntireTree();

            aptxApp.enableMultipleTrees();
            aptxFrames[i++] = aptxApp;
          }
        }
      }
      else if (!exception) // ..what?
      {
        JvOptionPane.showMessageDialog(null,
                ForesterUtil.wordWrap(
                        "Failed to read in tree(s) from [" + url + "]", 80),
                "Error", JvOptionPane.ERROR_MESSAGE);
      }
      if ((trees != null) && (trees.length > 0))
      {
        try
        {
          JvOptionPane.showMessageDialog(null,
                  ForesterUtil.wordWrap("Successfully read in "
                          + trees.length + " tree(s) from [" + url + "]",
                          80),
                  "Success", JvOptionPane.INFORMATION_MESSAGE);
        } catch (final Exception e)
        {
          // Not important if this fails, do nothing.
        }
      }
    }


    if (Desktop.instance != null)
    {
      Desktop.instance.stopLoading();
    }
    return aptxFrames;


  }



  public static TreeFrameI createAptxFrame(TreeI aptxTree,
          AlignmentViewport jalviewAlignport, String treeTitle)
  {
    validateConfig(APTX_CONFIG);
    TreeFrameI aptxApp = aptxTree
            .createTreeViewerFromTree(treeTitle);
    TreeI jalviewTree = aptxApp.getTree();
    LoadedTreeAssociationI bindAptxNodes = new LoadedTreeSequenceAssociation(
            jalviewAlignport.getAlignment().getSequencesArray(),
            jalviewTree);
    bindAptxNodes.associateNodesToSequences();

    TreeViewerUtils.associateNodesWithJalviewSequences(aptxApp, jalviewAlignport,
            bindAptxNodes.getAlignmentWithNodes(),
            bindAptxNodes.getNodesWithAlignment());
    TreeViewerUtils.addTreeViewFrameToJalview(aptxApp, 400, 500);

    // adaptAptxGui(aptxApp); //moved to AptxFrame
    return aptxApp;
  }


  protected static TreeFrameI createAptxFrame(
          final Phylogeny aptxTree,
          final AlignmentViewport jalviewAlignport, String treeTitle)
  {
    validateConfig(APTX_CONFIG);
    TreeFrameI aptxApp = new AptxFrame(aptxTree, APTX_CONFIG,
            treeTitle);
    TreeI jalviewTree = aptxApp.getTree();
    LoadedTreeAssociationI bindAptxNodes = new LoadedTreeSequenceAssociation(
            jalviewAlignport.getAlignment().getSequencesArray(),
            jalviewTree);
    bindAptxNodes.associateNodesToSequences();

    TreeViewerUtils.associateNodesWithJalviewSequences(aptxApp, jalviewAlignport,
            bindAptxNodes.getAlignmentWithNodes(),
            bindAptxNodes.getNodesWithAlignment());
    TreeViewerUtils.addTreeViewFrameToJalview(aptxApp, 400, 500);

    return aptxApp;
  }


  private static boolean validateConfig(Configuration aptxConfig)
  {
    if (aptxConfig == null || aptxConfig.isCouldReadConfigFile() == false)
    {
      int keepGoing = JvOptionPane.showConfirmDialog(Desktop.desktop,
              MessageManager.getString("label.aptx_config_not_found"),
              MessageManager.formatMessage("label.couldnt_locate",
                      new String[]
                      { "_aptx_jalview_configuration_file" }),
              JvOptionPane.YES_NO_CANCEL_OPTION);

      if (keepGoing == JvOptionPane.CANCEL_OPTION
              || keepGoing == JvOptionPane.CLOSED_OPTION
              || keepGoing == JvOptionPane.NO_OPTION)
      {
        return false;
      }

    }
    return true;
  }


}