package jalview.io;

import jalview.gui.AlignFrame;
import jalview.schemes.ColourSchemeI;

import java.io.IOException;

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();

      new JSONFile().parse(alignmentJsonString);

      // 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, Integer.valueOf(sequence.get("start")
      // .toString()), Integer.valueOf(sequence.get("end")
      // .toString()));
      //
      // JSONArray jsonSeqArray = (JSONArray) sequence.get("features");
      // SequenceFeature[] retrievedSeqFeatures = getJalviewSequenceFeatures(
      // jsonSeqArray, seq);
      // if (retrievedSeqFeatures != null)
      // {
      // seq.setSequenceFeatures(retrievedSeqFeatures);
      // }
      // seqs.add(seq);
      //
      // }
    } catch (Exception e)
    {
      e.printStackTrace();
    }
  }

  // public SequenceFeature[] getJalviewSequenceFeatures(
  // JSONArray jsonSeqFeatures, Sequence seq)
  // {
  // SequenceFeature[] seqFeatures = null;
  // int count = 0;
  // if (jsonSeqFeatures != null)
  // {
  // seqFeatures = new SequenceFeature[jsonSeqFeatures.size()];
  // for (@SuppressWarnings("unchecked")
  // 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(seq.findPosition(begin.intValue()));
  // sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
  // 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!");
  }

}