/*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2006 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.util;

import java.util.*;

import jalview.datamodel.*;


public class DBRefUtils
{
    /**
     * Utilities for handling DBRef objects and their collections.
     */
    /**
     *
     * @param dbrefs Vector of DBRef objects to search
     * @param sources String[] array of source DBRef IDs to retrieve
     * @return Vector
     */
    public static DBRefEntry [] selectRefs(DBRefEntry [] dbrefs, String[] sources) {
      if (dbrefs==null)
        return null;
      if (sources==null)
        return dbrefs;
      Hashtable srcs = new Hashtable();
      Vector res=new Vector();

      for (int i=0; i<sources.length; i++)
        srcs.put(new String(sources[i]), new Integer(i));
      for (int i = 0, j = dbrefs.length; i < j; i++)
        {
          if (srcs.containsKey(dbrefs[i].getSource()))
            res.add(dbrefs[i]);
        }

      if (res.size()>0)
      {
        DBRefEntry [] reply = new DBRefEntry[res.size()];
        for(int i=0; i<res.size(); i++)
          reply[i] = (DBRefEntry)res.elementAt(i);
        return reply;
      }
      res = null;
      // there are probable  memory leaks in the hashtable!
      return null;
    }

  /**
   * isDasCoordinateSystem
   *
   * @param string String
   * @param dBRefEntry DBRefEntry
   * @return boolean true if Source DBRefEntry is compatible with DAS CoordinateSystem name
   */
  public static Hashtable DasCoordinateSystemsLookup = null;
  public static boolean isDasCoordinateSystem(String string,
                                              DBRefEntry dBRefEntry)
  {
    if (DasCoordinateSystemsLookup==null)
    { // Initialise
      DasCoordinateSystemsLookup = new Hashtable();
      DasCoordinateSystemsLookup.put("pdbresnum",
                                     jalview.datamodel.DBRefSource.PDB);
      DasCoordinateSystemsLookup.put("uniprot",
                                     jalview.datamodel.DBRefSource.UNIPROT);
    }

    String coordsys = (String) DasCoordinateSystemsLookup.get(string.toLowerCase());
    if (coordsys!=null)
      return coordsys.equals(dBRefEntry.getSource());
    return false;
  }
}