/*
 * 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.seqfetcher;

import jalview.datamodel.Alignment;
import jalview.datamodel.DBRefSource;
import jalview.io.FormatAdapter;
import jalview.io.IdentifyFile;

import java.util.Hashtable;

/**
 * common methods for implementations of the DbSourceProxy interface.
 * 
 * @author JimP
 * 
 */
public abstract class DbSourceProxyImpl implements DbSourceProxy
{
  public DbSourceProxyImpl()
  {
    // default constructor - do nothing probably.
  }

  private Hashtable props = null;

  /*
   * (non-Javadoc)
   * 
   * @see jalview.ws.DbSourceProxy#getDbSourceProperties()
   */
  public Hashtable getDbSourceProperties()
  {
    if (props==null)
    {
      props = new Hashtable();
    }
    return props;
  }

  protected void addDbSourceProperty(Object propname)
  {
    addDbSourceProperty(propname, propname);
  }

  protected void addDbSourceProperty(Object propname, Object propvalue)
  {
    if (props == null)
    {
      props = new Hashtable();
    }
    props.put(propname, propvalue);
  }

  boolean queryInProgress = false;

  protected StringBuffer results = null;

  /*
   * (non-Javadoc)
   * 
   * @see jalview.ws.DbSourceProxy#getRawRecords()
   */
  public StringBuffer getRawRecords()
  {
    return results;
  }

  /*
   * (non-Javadoc)
   * 
   * @see jalview.ws.DbSourceProxy#queryInProgress()
   */
  public boolean queryInProgress()
  {
    return queryInProgress;
  }

  /**
   * call to set the queryInProgress flag
   * 
   */
  protected void startQuery()
  {
    queryInProgress = true;
  }

  /**
   * call to clear the queryInProgress flag
   * 
   */
  protected void stopQuery()
  {
    queryInProgress = false;
  }

  /**
   * create an alignment from raw text file...
   * 
   * @param result
   * @return null or a valid alignment
   * @throws Exception
   */
  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.toString(), "Paste",
              format);
    }
    return sequences;
  }

}