package jalview.ws.dbsources;

import jalview.datamodel.Alignment;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.Sequence;
import jalview.ws.HttpClientUtils;
import jalview.ws.seqfetcher.DbSourceProxyImpl;

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

import org.apache.http.client.ClientProtocolException;
import org.json.simple.JSONArray;
import org.json.simple.JSONObject;
import org.json.simple.parser.JSONParser;

import com.stevesoft.pat.Regex;

public abstract class Intermine extends DbSourceProxyImpl
{
  protected int seqStart = 1;

  protected int seqEnd = 500;

  protected String domain = "7227";

  protected String name = "Intermine";

  protected String baseUrl = "";

  protected String testQuery = "";

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

  @Override
  public String getDbName()
  {
    return "INTERMINE_" + this.name;
  }

  @Override
  public String getDbVersion()
  {
    return baseUrl;
  }


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

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

  @Override
  public String getTestQuery()
  {
    return testQuery;
  }

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

  @SuppressWarnings("unchecked")
  public Alignment getAlignmentData(String baseUrl, String query,
          String domain, int seqStart, int seqEnd)
  {

    StringTokenizer queries = new StringTokenizer(query, ";");

    int count = 0;
    Sequence[] retrievedSeq = new Sequence[queries.countTokens()];
    try
    {
      while (queries.hasMoreTokens())
      {
        String uniquequery = queries.nextToken();
        String seqRef = uniquequery;
        // StringTokenizer queryParam = new StringTokenizer(uniquequery, ":");
        String[] queryParam = uniquequery.split(":");
        if (queryParam.length > 1)
        {
          seqRef = queryParam[0];
          String[] positions = queryParam[1].split("-");
          if (positions.length > 1)
          {
            seqStart = Integer.valueOf(positions[0]);
            seqEnd = Integer.valueOf(positions[1]);
          }
        }

        startQuery();
        String rawSequenceData = fetchData(baseUrl,
                seqRef, domain,
                seqStart, seqEnd, true);
        String rawAnnotationData = fetchData(baseUrl,
                uniquequery, domain, seqStart, seqEnd, false);
        stopQuery();

        String sequenceString = "";

        // System.out.println("Sequence data: " + rawSequenceData);
        // System.out.println("Annotation data : " + rawAnnotationData);
        JSONParser jsonParser = new JSONParser();
        JSONObject rawSeqJson = (JSONObject) jsonParser
                .parse(rawSequenceData);
        // JSONObject rawAnotJson = (JSONObject)
        // jsonParser.parse(rawAnnotationData);
        JSONArray rawSeqJsonArray = (JSONArray) rawSeqJson.get("features");
        for (Iterator<JSONObject> sequenceIter = rawSeqJsonArray.iterator(); sequenceIter
                .hasNext();)
        {
          // retrievedSeq = new Sequence[rawSeqJsonArray.size()];
          JSONObject feature = sequenceIter.next();
          sequenceString = feature.get("seq").toString();
          int start = Integer.valueOf(feature.get("start").toString());
          int end = Integer.valueOf(feature.get("end").toString());

          retrievedSeq[count++] = new Sequence(uniquequery, sequenceString,
                  start,
                  end);
        }
      }
    } catch (Exception e)
    {
      e.printStackTrace();
    }
    return new Alignment(retrievedSeq);
  }


  private static String fetchData(String baseUrl, String seqRef,
          String domain, int start, int end, Boolean fetchRef)
                  throws ClientProtocolException, IOException
  {
    String resourceUrl = baseUrl + "/service/jbrowse/" + domain
            + "/features/" + seqRef + "?start=" + start + "&end=" + end
            + "&reference=" + fetchRef;
    return HttpClientUtils.doHttpUrlGet(resourceUrl);
  }

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

}