package jalview.ws.dbsources;

import java.util.Hashtable;

import org.biojava.dasobert.das.SequenceThread;
import org.biojava.dasobert.das2.Das2Source;
import org.biojava.dasobert.dasregistry.Das1Source;
import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
import org.biojava.dasobert.dasregistry.DasSource;
import org.biojava.dasobert.eventmodel.SequenceEvent;
import org.biojava.dasobert.eventmodel.SequenceListener;

import com.stevesoft.pat.Regex;

import jalview.ws.dbsources.das.DasSequenceSourceListener;
import jalview.ws.seqfetcher.*;
import jalview.datamodel.AlignmentI;

/**
 * an instance of this class is created for each unique DAS Sequence source (ie one capable of handling the 'sequence' for a particular MapMaster)
 *  
 * @author JimP
 *
 */
public class DasSequenceSource extends DbSourceProxyImpl implements
        DbSourceProxy
{
  protected Das1Source source=null;
  protected String dbname="DASCS";
  protected String dbrefname="das:source";
  protected DasCoordinateSystem coordsys = null;
  /**
   * create a new DbSource proxy for a DAS 1 source
   * @param dbnbame Human Readable Name to use when fetching from this source
   * @param dbrefname DbRefName for DbRefs attached to sequences retrieved from this source
   * @param source Das1Source
   * @param coordsys specific coordinate system to use for this source
   * @throws Exception if source is not capable of the 'sequence' command
   */
  public DasSequenceSource(String dbname, String dbrefname, Das1Source source,
            DasCoordinateSystem coordsys) throws Exception
  {
    if (!source.hasCapability("sequence"))
    {
      throw new Exception("Source "+source.getNickname()+" does not support the sequence command.");
    }
    this.source = source;
    this.dbname = dbname;
    this.dbrefname=dbrefname;
    this.coordsys = coordsys;
  }
  public String getAccessionSeparator()
  {
    // cope with single sequences only
    return null;
  }

  public Regex getAccessionValidator()
  {
    /** ? **/
    return Regex.perlCode("\\S+");
  }

  public String getDbName()
  {
    // TODO: map to
     return dbname+" (DAS)";
  }

  public String getDbSource()
  {
    return dbrefname;
  }

  public String getDbVersion()
  {
    return coordsys.getVersion();
  }

  public AlignmentI getSequenceRecords(String queries) throws Exception
  {
    SequenceThread seqfetcher = new org.biojava.dasobert.das.SequenceThread(queries, source);
    DasSequenceSourceListener ourlistener = new DasSequenceSourceListener(this, queries);
    seqfetcher.addSequenceListener(ourlistener);
    seqfetcher.start();
    try { Thread.sleep(5); } catch (Exception e) {};
    while (ourlistener.isNotCalled() && seqfetcher.isAlive())
    {
      try { Thread.sleep(5); } catch (Exception e) { };
    }
    if (ourlistener.isNotCalled() || ourlistener.hasNoSequences())
    {
      System.err.println("Sequence Query to "+source.getNickname()+" with '"+queries+"' returned no sequences.");
      return null;
    } else {
      return ourlistener.getSequences();
    }
  }

  public String getTestQuery()
  {
    return coordsys.getTestCode();
  }
  public boolean isValidReference(String accession)
  {
    // TODO try to validate an accession against source
    // We don't really know how to do this without querying source
    
    return true;
  }
  /**
   * @return the source
   */
  public Das1Source getSource()
  {
    return source;
  }
  /**
   * @return the coordsys
   */
  public DasCoordinateSystem getCoordsys()
  {
    return coordsys;
  }
}