/*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 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.analysis;

import java.util.*;

import jalview.datamodel.*;

/**
 * <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;
  }
}