/*
 * 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.datamodel;

public class SearchResults
{

  Match [] matches;

    /**
     * This method replaces the old search results which merely
     * held an alignment index of search matches. This broke
     * when sequences were moved around the alignment
     * @param seq Sequence
     * @param start int
     * @param end int
     */
  public void addResult(SequenceI seq, int start, int end)
  {
    if(matches == null)
    {
      matches = new Match[]{new Match(seq, start, end)};
      return;
    }

    int mSize = matches.length;

    Match [] tmp = new Match[mSize+1];
    int m;
    for(m=0; m<mSize; m++)
    {
      tmp[m] = matches[m];
    }

    tmp[m] = new Match(seq, start, end);

    matches = tmp;
  }

  /**
  * This Method returns the search matches which lie between the
  * start and end points of the sequence in question. It is
  * optimised for returning objects for drawing on SequenceCanvas
  */
  public int [] getResults(SequenceI sequence, int start, int end)
  {
    if(matches==null)
      return null;

    int [] result = null;
    int [] tmp = null;
    int resultLength;

    for(int m=0; m<matches.length; m++)
    {
      if( matches[m].sequence == sequence )
      {
        int matchStart = matches[m].sequence.findIndex( matches[m].start ) - 1;
        int matchEnd = matches[m].sequence.findIndex( matches[m].end ) - 1;

        if(matchStart<=end && matchEnd>=start)
        {
          if(matchStart<start)
            matchStart = start;

          if(matchEnd>end)
            matchEnd = end;


          if(result==null)
            result = new int[]{matchStart, matchEnd};
          else
          {
            resultLength = result.length;
            tmp = new int[resultLength+2];
            System.arraycopy(result,0,tmp,0,resultLength);
            result = tmp;
            result[resultLength] = matchStart;
            result[resultLength+1] = matchEnd;
          }
        }
      }
    }
    return result;
  }

  public int getSize()
  {
    return matches==null ? 0 : matches.length;
  }

  public SequenceI getResultSequence(int index)
  {    return matches[index].sequence;  }

  public int getResultStart(int index)
  {    return matches[index].start;  }

  public int getResultEnd(int index)
  {    return matches[index].end;  }

  class Match
  {
    SequenceI sequence;
    int start;
    int end;

    public Match(SequenceI seq, int start, int end)
    {
     sequence = seq;
     this.start = start;
     this.end = end;
    }
  }
}