/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ 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.datamodel;

import java.util.Iterator;
import java.util.NoSuchElementException;

/**
 * An iterator which iterates over all visible rows in an alignment
 * 
 * @author kmourao
 *
 */
public class VisibleRowsIterator implements Iterator<Integer>
{
  private int last;

  private int current;

  private int next;

  private HiddenSequences hidden;

  private AlignmentI al;

  /**
   * Create an iterator for all visible rows in the alignment
   * 
   * @param firstrow
   *          absolute row index to start from
   * @param lastrow
   *          absolute row index to end at
   * @param alignment
   *          alignment to work with
   */
  public VisibleRowsIterator(int firstrow, int lastrow,
          AlignmentI alignment)
  {
    al = alignment;
    current = firstrow;
    last = lastrow;
    hidden = al.getHiddenSequences();
    while (last > current && hidden.isHidden(last))
    {
      last--;
    }
    current = firstrow;
    while (current < last && hidden.isHidden(current))
    {
      current++;
    }
    next = current;
  }

  @Override
  public boolean hasNext()
  {
    return next <= last;
  }

  @Override
  public Integer next()
  {
    if (next > last)
    {
      throw new NoSuchElementException();
    }
    current = next;
    do
    {
      next++;
    } while (next <= last && hidden.isHidden(next));
    return current;
  }

  @Override
  public void remove()
  {
    throw new UnsupportedOperationException();
  }
}