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 Vector selectRefs(java.util.Vector 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.size(); i<j; i++)
        if (dbrefs.get(i) instanceof jalview.datamodel.DBRefEntry) {
          jalview.datamodel.DBRefEntry entry = (jalview.datamodel.DBRefEntry) dbrefs.get(i);
          if (srcs.containsKey(entry.getSource()))
            res.add(entry);
        }
      if (res.size()>0)
        return res;
      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;
  }
}