package jalview.analysis;

import jalview.datamodel.SequenceI;
import java.util.Hashtable;

/**
 * <p>Title: </p>
 *
 * <p>Description: </p>
 *
 * <p>Copyright: Copyright (c) 2004</p>
 *
 * <p>Company: Dundee University</p>
 *
 * @author not attributable
 * @version 1.0
 */
public class SeqsetUtils
{
    /**
     * Store essential properties of a sequence in a hashtable for later recovery
     *  Keys are Name, Start, End, SeqFeatures, PdbId
     * @param seq SequenceI
     * @return Hashtable
     */
    public static Hashtable SeqCharacterHash(SequenceI seq) {
    Hashtable sqinfo = new Hashtable();
    sqinfo.put("Name", seq.getName());
    sqinfo.put("Start", new Integer(seq.getStart()));
    sqinfo.put("End", new Integer(seq.getEnd()));
    sqinfo.put("SeqFeatures", seq.getSequenceFeatures());
    sqinfo.put("PdbId", (seq.getPDBId()!=null) ? seq.getPDBId() : new String("") );
    return sqinfo;
  }
  /**
   * Recover essential properties of a sequence from a hashtable
   * TODO: replace these methods with something more elegant.
   * @param sq SequenceI
   * @param sqinfo Hashtable
   * @return boolean
   */
  public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo) {
    boolean namePresent = true;
    String oldname = (String) sqinfo.get("Name");
    Integer start = (Integer) sqinfo.get("Start");
    Integer end = (Integer) sqinfo.get("End");
    java.util.Vector sfeatures = (java.util.Vector) sqinfo.get("SeqFeatures");
    String pdbid = (String) sqinfo.get("PdbId");
    if (oldname==null)
      namePresent = false;
    else
      sq.setName(oldname);
    if (!pdbid.equals(""))
      sq.setPDBId(pdbid);

    if ((start!=null) && (end!=null)) {
      sq.setStart(start.intValue());
      sq.setEnd(end.intValue());
    }
    if (sfeatures!=null)
      sq.setSequenceFeatures(sfeatures);
    return namePresent;
  }

  /**
   * Form of the unique name used in uniquify for the i'th sequence in an ordered vector of sequences.
   * @param i int
   * @return String
   */
  public static String unique_name(int i) {
      return new String("Sequence"+i);
  }

  public static Hashtable uniquify(SequenceI[] sequences, boolean write_names)
  {
    // Generate a safely named sequence set and a hash to recover the sequence names
    Hashtable map = new Hashtable();
    String[] un_names = new String[sequences.length];
    if (!write_names)

    for (int i = 0; i < sequences.length; i++)
    {
      String safename = new String("Sequence" + i);
      map.put(safename, SeqCharacterHash(sequences[i]));
      if (write_names)
        sequences[i].setName(safename);
    }
    return map;
  }

  public static boolean deuniquify(Hashtable map, SequenceI[] sequences)
  {
    // recover unsafe sequence names for a sequence set
    boolean allfound = true;
    for (int i = 0; i < sequences.length; i++)
    {
      if (map.containsKey(sequences[i].getName()))
      {
        Hashtable sqinfo = (Hashtable) map.get(sequences[i].getName());
        SeqCharacterUnhash(sequences[i], sqinfo);
      }
      else
      {
        allfound = false;
      }
    }
    return allfound;
  }

}