package jalview.io;

import static java.nio.file.Files.readAllBytes;
import static java.nio.file.Paths.get;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignViewport;
import jalview.gui.AlignmentPanel;
import jalview.gui.FeatureRenderer;
import jalview.gui.SequenceRenderer;
import jalview.json.binding.v1.BioJsAlignmentPojo;
import jalview.json.binding.v1.BioJsSeqPojo;
import jalview.util.MessageManager;

import java.io.IOException;
import java.io.PrintWriter;

import org.jsoup.Jsoup;
import org.jsoup.nodes.Document;
import org.jsoup.nodes.Element;

import com.json.JSONException;
import com.json.JSONObject;

public class BioJsHTMLOutput
{
  private AlignViewport av;
  private FeatureRenderer fr;

  public BioJsHTMLOutput(AlignmentPanel ap, SequenceRenderer sr,
          FeatureRenderer fr1)
  {
    this.av = ap.av;

    this.fr = new FeatureRenderer(ap);
    fr.transferSettings(fr1);
    exportAsBioJsHtml();
  }

  private void exportAsBioJsHtml()
  {
    try
    {
      JalviewFileChooser jvFileChooser = getJalviewFileChooserOption();
      int fileChooserOpt = jvFileChooser.showSaveDialog(null);
      if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
      {
        jalview.bin.Cache.setProperty("LAST_DIRECTORY", jvFileChooser
                .getSelectedFile().getParent());
        String selectedFile = jvFileChooser.getSelectedFile().getPath();
        String generartedBioJs = generateBioJsAlignmentData(av
                .getAlignment());
        PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
                selectedFile));
        out.print(generartedBioJs);
        out.close();
        jalview.util.BrowserLauncher.openURL("file:///" + selectedFile);
      }
    } catch (Exception ex)
    {
      ex.printStackTrace();
    }
  }

  private JalviewFileChooser getJalviewFileChooserOption()
  {
    JalviewFileChooser chooser = new JalviewFileChooser(
            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
            { "html" }, new String[]
            { "HTML files" }, "HTML files");

    chooser.setFileView(new JalviewFileView());
    // TODO uncomment when supported by MassageManager
    // chooser.setDialogTitle(MessageManager.getString("label.save_as_biojs_html"));
    chooser.setDialogTitle("save as BioJs HTML");
    chooser.setToolTipText(MessageManager.getString("action.save"));

    return chooser;
  }

  private String generateBioJsAlignmentData(AlignmentI alignment)
          throws IOException, JSONException
  {
    BioJsAlignmentPojo bjsAlignment = new BioJsAlignmentPojo();

    int count = 0;
    for (SequenceI seq : alignment.getSequences())
    {
      bjsAlignment.getSeqs().add(
              new BioJsSeqPojo(String.valueOf(++count), seq.getName(), seq
                      .getSequenceAsString()));
    }

    String seqs = new JSONObject(bjsAlignment).getString("seqs");
    String bioJSTemplate = new String(
            readAllBytes(get("resources/templates/BioJSTemplate.txt")));

    return bioJSTemplate.replaceAll("#sequenceData#", seqs);
  }

  public static void main(String[] args) throws IOException
  {
    Document doc = Jsoup.parse(new String(
            readAllBytes(get("resources/templates/BioJSTemplate.txt"))));

    Element content = doc.getElementById("seqData");
    System.out.println(content.val());
  }

}