/*
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
 * Copyright (C) 2015 The Jalview Authors
 * 
 * This file is part of Jalview.
 * 
 * Jalview 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 3
 * of the License, or (at your option) any later version.
 *  
 * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.commands;

/*
 * Jalview - A Sequence Alignment Editor and Viewer Copyright (C) 2007 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
 */

import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;

public class RemoveGapsCommand extends EditCommand
{
  public RemoveGapsCommand(String description, SequenceI[] seqs,
          AlignmentI al)
  {
    this.description = description;
    int width = 0;
    for (int i = 0; i < seqs.length; i++)
    {
      if (seqs[i].getLength() > width)
      {
        width = seqs[i].getLength();
      }
    }

    findGaps(seqs, 0, width, al);
  }

  public RemoveGapsCommand(String description, SequenceI[] seqs, int start,
          int end, AlignmentI al)
  {
    this.description = description;
    findGaps(seqs, start, end, al);
  }

  void findGaps(SequenceI[] seqs, int start, int end, AlignmentI al)
  {

    int startCol = -1, endCol = -1;
    int deletedCols = 0;

    int j, jSize;

    clearEdits();

    boolean delete = true;
    char[] sequence;

    for (int s = 0; s < seqs.length; s++)
    {
      deletedCols = 0;
      startCol = -1;
      endCol = -1;
      sequence = seqs[s].getSequence(start, end + 1);

      jSize = sequence.length;
      for (j = 0; j < jSize; j++)
      {
        delete = true;

        if (!jalview.util.Comparison.isGap(sequence[j]))
        {
          if (delete)
          {
            endCol = j;
          }

          delete = false;
        }

        if (delete && startCol == -1)
        {
          startCol = j;
        }

        if (!delete && startCol > -1)
        {
          this.appendEdit(Action.DELETE_GAP, new SequenceI[] { seqs[s] },
                  start + startCol - deletedCols, endCol - startCol, al,
                  false, null);

          deletedCols += (endCol - startCol);
          startCol = -1;
          endCol = -1;
        }
      }
      if (delete && startCol > -1)
      {
        this.appendEdit(Action.DELETE_GAP, new SequenceI[] { seqs[s] },
                start + startCol - deletedCols, jSize - startCol, al,
                false, null);
      }

    }

    performEdit(0, null);
  }

}