package jalview.ws.dbsources;

import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.Sequence;
import jalview.io.FormatAdapter;
import jalview.io.IdentifyFile;
import jalview.ws.intermine.IntermineFetchClient;
import jalview.ws.seqfetcher.DbSourceProxyImpl;

import java.util.Iterator;

import org.json.simple.JSONArray;
import org.json.simple.JSONObject;

import com.stevesoft.pat.Regex;

public class Intermine extends DbSourceProxyImpl // implements DbSourceProxy
{

  @Override
  public String getDbSource()
  {
    return DBRefSource.INTERMINE;
  }

  @Override
  public String getDbName()
  {
    return "Intermine";
  }

  @Override
  public String getDbVersion()
  {
    return "0";
  }

  @Override
  public String getAccessionSeparator()
  {
    return null;
  }

  @Override
  public Regex getAccessionValidator()
  {
    return null;
  }


  @Override
  public String getTestQuery()
  {
    // TODO Auto-generated method stub
    return "http://www.flymine.org/query/service/jbrowse/7227/features/2L?start=100000&end=100200&reference=true";
  }

  @Override
  public boolean isValidReference(String accession)
  {
    return false;
  }

  @SuppressWarnings("unchecked")
  @Override
  public AlignmentI getSequenceRecords(String query) throws Exception
  {
    startQuery();
    String jsonString = IntermineFetchClient.fetchData(query);
    Sequence[] retrievedSeq = null;
    String sequence = "";
    String name = "";
    System.out.println("Found json: " + jsonString);
    org.json.simple.parser.JSONParser jsonParser = new org.json.simple.parser.JSONParser();
    try
    {
      JSONObject jobj = (JSONObject) jsonParser.parse(jsonString);
      JSONArray responses = (JSONArray) jobj.get("features");
      int count = 0;
      for (Iterator<JSONObject> rvals = responses.iterator(); rvals
              .hasNext();)
      {
        retrievedSeq = new Sequence[responses.size()];

        JSONObject feature = rvals.next();
        // name = feature.get("name").toString();
        name = "name";
        sequence = feature.get("seq").toString();
        int start = Integer.valueOf(feature.get("start").toString());
        int end = Integer.valueOf(feature.get("end").toString());

        retrievedSeq[count++] = new Sequence(name, sequence, start, end);

        System.out.println("Sequence : " + sequence);

      }
    } catch (Exception e)
    {
      e.printStackTrace();
    }
    stopQuery();
    return parseResult(retrievedSeq);
  }

  @Override
  protected Alignment parseResult(String result) throws Exception
  {
    Alignment sequences = null;
    String format = new IdentifyFile().Identify(result, "Paste");
    if (FormatAdapter.isValidFormat(format))
    {
      sequences = new FormatAdapter().readFile(result, "Paste",
              format);
    }
    return sequences;
  }


  private Alignment parseResult(Sequence[] seqs)
  {
    Alignment sequences = new Alignment(seqs);
    return sequences;
  }


  @Override
  public int getTier()
  {
    return 0;
  }

}