package jalview.io;

import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.gui.AlignFrame;
import jalview.json.binding.v1.BioJsAlignmentPojo.JalviewBioJsColorSchemeMapper;
import jalview.schemes.ColourSchemeI;

import java.io.IOException;
import java.util.Iterator;

import org.json.simple.JSONArray;
import org.json.simple.JSONObject;
import org.json.simple.parser.JSONParser;
import org.jsoup.Jsoup;
import org.jsoup.nodes.Document;
import org.jsoup.nodes.Element;

public class HtmlFile extends AlignFile
{
  // public static final String FILE_EXT = "html";
  //
  // public static final String FILE_DESC = "HTML";

  private ColourSchemeI cs;

  public HtmlFile()
  {
    super();
  }

  public HtmlFile(FileParse source) throws IOException
  {
    super(source);
  }

  public HtmlFile(String inFile, String type) throws IOException
  {
    super(inFile, type);
  }

  @SuppressWarnings("unchecked")
  @Override
  public void parse() throws IOException
  {
    try
    {
      StringBuilder htmlData = new StringBuilder();
      String currentLine;
      while ((currentLine = nextLine()) != null)
      {
        htmlData.append(currentLine);
      }

      Document doc = Jsoup.parse(htmlData.toString());
      Element content = doc.getElementById("seqData");

      String alignmentJsonString = content.val();
      JSONParser jsonParser = new JSONParser();
      JSONObject alignmentJsonObj = (JSONObject) jsonParser
              .parse(alignmentJsonString);
      JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
      String bioJsColourScheme = (String) alignmentJsonObj
              .get("globalColorScheme");
      cs = getJalviewColorScheme(bioJsColourScheme);

      for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
              .hasNext();)
      {
        JSONObject sequence = sequenceIter.next();
        String sequcenceString = sequence.get("seq").toString();
        Sequence seq = new Sequence(sequence.get("name").toString(),
                sequcenceString, 0, sequcenceString.length());

        JSONArray jsonSeqArray = (JSONArray) sequence.get("features");
        SequenceFeature[] retrievedSeqFeatures = getJalviewSequenceFeatures(jsonSeqArray);
        if (retrievedSeqFeatures != null)
        {
          seq.setSequenceFeatures(retrievedSeqFeatures);
        }
        seqs.add(seq);

      }
    } catch (Exception e)
    {
      e.printStackTrace();
    }
  }

  public SequenceFeature[] getJalviewSequenceFeatures(
          JSONArray jsonSeqFeatures)
  {
    SequenceFeature[] seqFeatures = null;
    int count = 0;
    if (jsonSeqFeatures != null)
    {
      seqFeatures = new SequenceFeature[jsonSeqFeatures.size()];
      for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
              .hasNext();)
      {

        SequenceFeature sequenceFeature = new SequenceFeature();
        JSONObject jsonFeature = seqFeatureItr.next();
        Long begin = (Long) jsonFeature.get("xStart");
        Long end = (Long) jsonFeature.get("xEnd");
        String type = (String) jsonFeature.get("text");

        String color = (String) jsonFeature.get("fillColor");

        sequenceFeature.setBegin(begin.intValue());
        sequenceFeature.setEnd(end.intValue());
        sequenceFeature.setType(type);
        seqFeatures[count++] = sequenceFeature;
      }
    }
    return seqFeatures;
  }

  public void LoadAlignmentFeatures(AlignFrame af)
  {

    af.setShowSeqFeatures(true);
    af.changeColour(cs);
    af.setMenusForViewport();
  }

  private ColourSchemeI getJalviewColorScheme(String bioJsColourSchemeName)
  {
    ColourSchemeI jalviewColor = null;
    for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
            .values())
    {
      if (cs.getBioJsName().equals(bioJsColourSchemeName))
      {
        jalviewColor = cs.getJvColourScheme();
        break;
      }
    }
    return jalviewColor;
  }

  @Override
  public String print()
  {
    throw new UnsupportedOperationException(
            "Print method of HtmlFile not yet supported!");
  }

}