/*
 * 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.util;

import jalview.datamodel.SequenceI;

import java.util.*;

/**
 * ShiftList
 * Simple way of mapping a linear series to a new linear range with new points introduced.
 * Use at your own risk!
 * Now growing to be used for interval ranges (position, offset) storing deletions/insertions
 */
public class ShiftList
{
    public Vector shifts;
  public ShiftList()
  {
    shifts = new Vector();
  }

  /**
   * addShift
   * @param pos start position for shift (in original reference frame)
   * @param shift length of shift
   */
  public void addShift(int pos, int shift)
  {
    int sidx = 0;
    int[] rshift=null;
    while (sidx<shifts.size() && (rshift=(int[]) shifts.elementAt(sidx))[0]<pos)
      sidx++;
    if (sidx==shifts.size())
      shifts.insertElementAt(new int[] { pos, shift}, sidx);
    else
      rshift[1]+=shift;
  }

  /**
   * shift
   *
   * @param pos int
   * @return int shifted position
   */
  public int shift(int pos)
  {
    if (shifts.size()==0)
      return pos;
    int shifted=pos;
    int sidx=0;
    int rshift[];
    while (sidx<shifts.size()
           &&
           (rshift=((int[]) shifts.elementAt(sidx++)))[0]<=pos) {
      shifted += rshift[1];
    }
    return shifted;
  }

  /**
   * clear all shifts
   */
  public void clear()
  {
    shifts.removeAllElements();
  }
  /**
   * invert the shifts
   * @return ShiftList with inverse shift operations
   */
  public ShiftList getInverse() {
    ShiftList inverse=new ShiftList();
    if (shifts!=null) {
      for (int i=0,j=shifts.size(); i<j; i++) {
        int[] sh=(int[]) shifts.elementAt(i);
        if (sh!=null)
          inverse.shifts.addElement(new int[] {sh[0], -sh[1]});
      }
    }
    return inverse;
  }

  /**
   * parse a 1d map of position 1<i<n to L<pos[i]<N
   * such as that returned from SequenceI.gapMap()
   * @param gapMap
   * @return shifts from map index to mapped position
   */
  public static ShiftList parseMap(int[] gapMap) {
    ShiftList shiftList = null;
    if (gapMap!=null && gapMap.length>0) {
      shiftList=new ShiftList();
      for (int i=0,p=0; i<gapMap.length; p++,i++) {
        if (p!=gapMap[i]) {
          shiftList.addShift(p, gapMap[i]-p);
          p=gapMap[i];
        }
      }
    }
    return shiftList;
  }
}