package jalview.io;

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.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.PrintWriter;
import java.net.URL;

import com.json.JSONException;

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())
    {
      StringBuilder name = new StringBuilder();
      name.append(seq.getName()).append("/").append(seq.getStart())
              .append("-").append(seq.getEnd());
      bjsAlignment.getSeqs().add(
              new BioJsSeqPojo(String.valueOf(++count), name.toString(),
                      seq.getSequenceAsString()));
    }

    String seqs = new com.json.JSONObject(bjsAlignment).getString("seqs");
    // String bioJSTemplate = new String(
    // java.nio.file.Files.readAllBytes(java.nio.file.Paths
    // .get("resources/templates/BioJSTemplate.txt")));
    String bioJSTemplate = getBioJsTemplateAsString(alignment);

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


  public static String getBioJsTemplateAsString(AlignmentI bio)
          throws IOException
  {
     StringBuilder sb = new StringBuilder();
    URL url = bio.getClass().getResource(
            "/templates/BioJSTemplate.txt");
    if (url != null)
    {
      try
      {
        BufferedReader reader = new BufferedReader(new InputStreamReader(
                url.openStream()));
        String line;
        String lineSeparator = System.getProperty("line.separator");
        while ((line = reader.readLine()) != null)
        {
          sb.append(line).append(lineSeparator);
        }
      } catch (Exception ex)
      {
        ex.printStackTrace();
      }
    }

    return sb.toString();
  }

}