/*
 * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
 * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
 * 
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
package jalview.ws.dbsources.das;

import jalview.datamodel.AlignmentI;
import jalview.datamodel.Alignment;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.ws.dbsources.DasSequenceSource;

import org.biojava.dasobert.eventmodel.SequenceEvent;
import org.biojava.dasobert.eventmodel.SequenceListener;

/**
 * Listen for sequence fetch events from a dasobert SequenceThread started with
 * a query string and collect sequences returned from the DAS sequence source.
 * 
 * @author JimP
 * 
 */
public class DasSequenceSourceListener implements SequenceListener
{

  String ourAccession = null;

  DasSequenceSource oursource = null;

  /**
   * 
   * @param source
   *                the DAS Sequence DbProxy object containing database details
   *                for this source
   * @param query
   *                the query string sent to the das source that we should be
   *                listening for.
   */
  public DasSequenceSourceListener(DasSequenceSource source, String query)
  {
    oursource = source;
    ourAccession = query;
  }

  public void clearSelection()
  {
    // TODO Auto-generated method stub

  }

  java.util.Vector seqs = null;

  public void newSequence(SequenceEvent e)
  {
    if (!e.getAccessionCode().equals(ourAccession))
    {
      System.err
              .println("Warning - received sequence event for strange accession code ("
                      + e.getAccessionCode()
                      + ") - we expected "
                      + ourAccession);

      return;
    }
    if (seqs == null)
    {
      if (e.getSequence().length() == 0)
      {
        System.err.println("Empty sequence returned for accession code ("
                + e.getAccessionCode() + ") from " + oursource.getDbName());
        called = true;
        noSequences = true;
        return;
      }
      seqs = new java.util.Vector();
    }
    Sequence sq = new Sequence(e.getAccessionCode(), e.getSequence());
    sq.addDBRef(new DBRefEntry(oursource.getDbSource(), oursource
            .getDbVersion()
            + ":" + e.getVersion(), e.getAccessionCode()));
    seqs.addElement(sq);
    called = true;
  }

  public void selectedSeqPosition(int position)
  {
    // TODO Auto-generated method stub

  }

  public void selectedSeqRange(int start, int end)
  {
    // TODO Auto-generated method stub

  }

  public void selectionLocked(boolean flag)
  {
    // TODO Auto-generated method stub

  }

  public void newObjectRequested(String accessionCode)
  {
    // TODO Auto-generated method stub

  }

  boolean noSequences = false;

  public void noObjectFound(String accessionCode)
  {
    if (accessionCode.equals(ourAccession))
    {
      noSequences = true;
      called = true;
    }
  }

  public boolean hasNoSequences()
  {
    return noSequences;
  }

  boolean called = false;

  public boolean isNotCalled()
  {
    return !called;
  }

  public AlignmentI getSequences()
  {
    if (noSequences || seqs != null && seqs.size() == 0)
      return null;
    SequenceI[] sqs = new SequenceI[seqs.size()];
    for (int i = 0, iSize = seqs.size(); i < iSize; i++)
    {
      sqs[i] = (SequenceI) seqs.elementAt(i);
    }
    Alignment al = new Alignment(sqs);
    if (oursource.getSource().hasCapability("features"))
    {
      java.util.Vector src = new java.util.Vector();
      src.addElement(oursource.getSource());
      new jalview.ws.DasSequenceFeatureFetcher(sqs, null, src, false, false);
    }

    return al;
  }

}