/**
 * 
 */
package jalview.ws.dbsources;

import java.util.Hashtable;

import com.stevesoft.pat.Regex;

import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.io.AppletFormatAdapter;
import jalview.io.FastaFile;
import jalview.io.StockholmFile;
import jalview.ws.seqfetcher.DbSourceProxy;
import jalview.ws.seqfetcher.DbSourceProxyImpl;
/**
 * TODO: later PFAM is a complex datasource - it could return a tree in addition to an alignment
 * TODO: create interface to pass alignment properties and tree back to sequence fetcher
 * @author JimP
 *
 */
abstract public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
{

  public Pfam()
  {
    super();
    // all extensions of this PFAM source base class are DOMAINDB sources 
    addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);
  }

  /* (non-Javadoc)
   * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
   */
  public String getAccessionSeparator()
  {
    // TODO Auto-generated method stub
    return null;
  }

  /* (non-Javadoc)
   * @see jalview.ws.DbSourceProxy#getAccessionValidator()
   */
  public Regex getAccessionValidator()
  {
    // TODO Auto-generated method stub
    return null;
  }

  /* (non-Javadoc)
   * @see jalview.ws.DbSourceProxy#getDbSource()
  public String getDbSource()
  {
    ** this doesn't work - DbSource is key for the hash of DbSourceProxy instances - 1:many mapping for DbSource to proxy will be lost.
    ** suggest : PFAM is an 'alignment' source - means proxy is higher level than a sequence source.
    return jalview.datamodel.DBRefSource.PFAM;
  }
   */

  
  /* (non-Javadoc)
   * @see jalview.ws.DbSourceProxy#getDbSourceProperties()
  public Hashtable getDbSourceProperties()
  {
    
    return null;
  }
 */
  
  /* (non-Javadoc)
   * @see jalview.ws.DbSourceProxy#getDbVersion()
   */
  public String getDbVersion()
  {
    // TODO Auto-generated method stub
    return null;
  }
  /**
   * 
   * @return PFAM URL stub for this DbSource
   */
  protected abstract String getPFAMURL();
  /* (non-Javadoc)
   * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
   */
  public AlignmentI getSequenceRecords(String queries) throws Exception
  {
    // TODO: this is not a perfect implementation. We need to be able to add individual references to each sequence in each family alignment that's retrieved. 
    startQuery();
    AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getPFAMURL()+queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,"STH");
    for (int s=0,sNum=rcds.getHeight(); s<sNum;s++)
    {
      rcds.getSequenceAt(s).addDBRef(new DBRefEntry(jalview.datamodel.DBRefSource.PFAM,
              // getDbSource(), 
              getDbVersion(), queries.trim().toUpperCase()));
      if (!getDbSource().equals(jalview.datamodel.DBRefSource.PFAM))
      {         // add the specific ref too
        rcds.getSequenceAt(s).addDBRef(
                new DBRefEntry( getDbSource(), 
                        getDbVersion(), queries.trim().toUpperCase()));
      }
    }
    stopQuery();
    return rcds;
  }

  /* (non-Javadoc)
   * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
   */
  public boolean isValidReference(String accession)
  {
    return accession.indexOf("PF")==0;
  }


  /*public String getDbName()
  {
    return "PFAM"; // getDbSource();
  } */
}