/*
 * 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.List;
import java.util.concurrent.atomic.AtomicReference;

public class HiddenColumnsCursor
{
  // absolute position of first hidden column
  private int firstColumn;

  private List<int[]> hiddenColumns;

  // AtomicReference to hold the current region index and hidden column count
  // Could be done with synchronisation but benchmarking shows this way is 2x
  // faster
  private final AtomicReference<HiddenCursorPosition> cursorPos = new AtomicReference<>(
          new HiddenCursorPosition(0, 0));

  protected HiddenColumnsCursor()
  {

  }

  /**
   * Reset the cursor with a new hidden columns collection. Calls to resetCursor
   * should be made from within a writeLock in the HiddenColumns class - since
   * changes to the hiddenColumns collection require a writeLock the lock should
   * already exist.
   * 
   * @param hiddenCols
   */
  protected void resetCursor(List<int[]> hiddenCols)
  {
    hiddenColumns = hiddenCols;
    if ((hiddenCols != null) && (!hiddenCols.isEmpty()))
    {
      firstColumn = hiddenColumns.get(0)[0];
      HiddenCursorPosition oldpos = cursorPos.get();
      HiddenCursorPosition newpos = new HiddenCursorPosition(0, 0);
      cursorPos.compareAndSet(oldpos, newpos);
    }
  }

  /**
   * Delete the region the cursor is currently at. Avoids having to reset the
   * cursor just because we deleted a region.
   * 
   * Calls to updateForDeletedRegion should be made from within a writeLock in
   * the HiddenColumns class - since changes to the hiddenColumns collection
   * require a writeLock the lock should already exist.
   *
   * @param hiddenCols
   */
  protected void updateForDeletedRegion(List<int[]> hiddenCols)
  {

    if ((hiddenCols != null) && (!hiddenCols.isEmpty()))
    {
      // if there is a region to the right of the current region,
      // nothing changes; otherwise
      // we deleted the last region (index=hiddenCols.size()-1)
      // or the index was at the end of the alignment (index=hiddenCols.size())
      HiddenCursorPosition oldpos = cursorPos.get();

      int index = oldpos.getRegionIndex();
      if (index >= hiddenColumns.size() - 1)
      {
        // deleted last region, index is now end of alignment
        index = hiddenCols.size();
      }

      // update the cursor position
      HiddenCursorPosition newpos = new HiddenCursorPosition(index,
              oldpos.getHiddenSoFar());
      cursorPos.compareAndSet(oldpos, newpos);
    }
    hiddenColumns = hiddenCols;
  }

  /**
   * Get the index of the region that column is within (if column is hidden) or
   * which is to the right of column (if column is visible). If no hidden
   * columns are to the right, will return size of hiddenColumns. If hidden
   * columns is empty returns -1.
   * 
   * @param column
   *          absolute position of a column in the alignment
   * @return region index
   */
  protected HiddenCursorPosition findRegionForColumn(int column)
  {
    if (hiddenColumns == null)
    {
      return null;
    }

    HiddenCursorPosition oldpos = cursorPos.get();
    int index = oldpos.getRegionIndex();
    int hiddenCount = oldpos.getHiddenSoFar();

    if (index == hiddenColumns.size())
    {
      // went past the end of hiddenColumns collection last time
      index--;
      int[] region = hiddenColumns.get(index);
      hiddenCount -= region[1] - region[0] + 1;
    }

    if ((hiddenColumns.get(index)[0] <= column)
            && hiddenColumns.get(index)[1] >= column)
    {
      // column is in the current region
      // we hit the jackpot
      // don't need to move index
    }
    else if (column < firstColumn)
    {
      index = 0;
      hiddenCount = 0;
    }
    // column is after current region
    else if (column > hiddenColumns.get(index)[1]) // includes if column >
                                                   // lastColumn
    {
      // iterate from where we are now, if we're lucky we'll be close by
      // (but still better than iterating from 0)
      // stop when we find the region *before* column
      // i.e. the next region starts after column or if not, ends after column
      while ((index < hiddenColumns.size())
              && (column > hiddenColumns.get(index)[1]))
      {
        int[] region = hiddenColumns.get(index);
        hiddenCount += region[1] - region[0] + 1;
        index++;
      }
    }

    // column is before current region
    else if (column < hiddenColumns.get(index)[0])
    {
      // column is before or in the previous region
      if ((index > 0) && (hiddenColumns.get(index - 1)[1] >= column))
      {
        while ((index > 0) && (hiddenColumns.get(index - 1)[1] >= column))
        {
          index--;
          int[] region = hiddenColumns.get(index);
          hiddenCount -= region[1] - region[0] + 1;
        }
      }
    }
    HiddenCursorPosition newpos = new HiddenCursorPosition(index,
            hiddenCount);
    cursorPos.compareAndSet(oldpos, newpos);
    return newpos;
  }

  /**
   * Get the number of hidden columns in regions before column i.e. excludes
   * hidden columns in the region column is in, if any
   * 
   * @param column
   *          index of column in visible alignment
   * @return
   */
  protected HiddenCursorPosition getHiddenOffset(int column)
  {
    if (hiddenColumns == null)
    {
      return null;
    }

    HiddenCursorPosition oldpos = cursorPos.get();
    int index = oldpos.getRegionIndex();
    int hiddenCount = oldpos.getHiddenSoFar();

    if (column < firstColumn)
    {
      index = 0;
      hiddenCount = 0;
    }
    else if ((index < hiddenColumns.size())
            && (hiddenColumns.get(index)[0] <= column + hiddenCount))
    {
      // iterate from where we are now, if we're lucky we'll be close by
      // (but still better than iterating from 0)
      while ((index < hiddenColumns.size())
              && (hiddenColumns.get(index)[0] <= column + hiddenCount))
      {
        int[] region = hiddenColumns.get(index);
        hiddenCount += region[1] - region[0] + 1;
        index++;
      }
    }
    else
    {
      while ((index > 0)
              && (hiddenColumns.get(index - 1)[1] >= column + hiddenCount))
      {
        index--;
        int[] region = hiddenColumns.get(index);
        hiddenCount -= region[1] - region[0] + 1;
      }

    }

    HiddenCursorPosition newpos = new HiddenCursorPosition(index,
            hiddenCount);
    cursorPos.compareAndSet(oldpos, newpos);
    return newpos;
  }
}