package jalview.io;

import jalview.datamodel.Sequence;

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";

	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 = "{\"seqs\":" + content.val() + "}";
			JSONParser jsonParser = new JSONParser();
			JSONObject alignmentJsonObj = (JSONObject) jsonParser.parse(alignmentJsonString);
			JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");

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

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

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

}