/*
* 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.Vector;
import java.util.Hashtable;
import jalview.datamodel.SequenceI;

/**
 * <p>Title: </p>
 * SequenceIdMatcher
 * <p>Description: </p>
 * Routine which does approximate Sequence Id resolution by name using string containment rather than equivalence
 * <p>Copyright: Copyright (c) 2004</p>
 *
 * <p>Company: Dundee University</p>
 *
 * @author not attributable
 * @version 1.0
 */
public class SequenceIdMatcher
{

  private class SeqIdName
  {
    String id;

    SeqIdName(String s)
    {
      id = new String(s);
    }

    public int hashCode()
    {
      return (id.substring(0, 4).hashCode());
    }

    public boolean equals(Object s)
    {
      if (s instanceof SeqIdName)
      {
        return this.equals( (SeqIdName) s);
      }
      else
      {
        if (s instanceof String)
        {
          return this.equals( (String) s);
        }
      }
      return false;
    }

    public boolean equals(SeqIdName s)
    {
      if (id.startsWith(s.id) || s.id.startsWith(id))
      {
        return true;
      }
      return false;
    }

    public boolean equals(String s)
    {
      if (id.startsWith(s) || s.startsWith(id))
      {
        return true;
      }
      return false;
    }
  }

  private Hashtable names;

  public SequenceIdMatcher(SequenceI[] seqs)
  {
    names = new Hashtable();
    for (int i = 0; i < seqs.length; i++)
    {
      names.put(new SeqIdName(seqs[i].getName()), seqs[i]);
    }
  }

  SequenceI findIdMatch(SequenceI seq)
  {
    SeqIdName nam = new SeqIdName(seq.getName());
    if (names.containsKey(nam))
    {
      return (SequenceI) names.get(nam);
    }
    return null;
  }

  SequenceI findIdMatch(String seqnam)
  {
    SeqIdName nam = new SeqIdName(seqnam);
    if (names.containsKey(nam))
    {
      return (SequenceI) names.get(nam);
    }
    return null;
  }

  /**
   * findIdMatch
   *
   * Return pointers to sequences (or sequence object containers)
   * which have same Id as a given set of different sequence objects
   *
   * @param seqs SequenceI[]
   * @return SequenceI[]
   */

  SequenceI[] findIdMatch(SequenceI[] seqs)
  {
    SequenceI[] namedseqs = new SequenceI[seqs.length];

    int i = 0;
    SeqIdName nam;
    if (seqs.length > 0)
    {
      do
      {
        nam = new SeqIdName(seqs[i].getName());
        if (names.containsKey(nam))
        {
          namedseqs[i] = (SequenceI) names.get(nam);
        }
        else
        {
          namedseqs[i] = null;
        }
      }
      while (i++ < seqs.length);
    }
    return namedseqs;
  }

}