/*
 * 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
 */
package jalview.util;

import java.util.*;

/**
 * MapList
 * Simple way of bijectively mapping a non-contiguous linear range to another non-contiguous linear range
 * Use at your own risk!
 * TODO: efficient implementation of private posMap method
 * TODO: test/ensure that sense of from and to ratio start position is conserved (codon start position recovery)
 * TODO: optimize to use int[][] arrays rather than vectors.
 */
public class MapList
{
  public Vector fromShifts;
  public Vector toShifts;
  int fromRatio; // number of steps in fromShifts to one toRatio unit
  int toRatio; // number of steps in toShifts to one fromRatio
  public MapList(int from[], int to[], int fromRatio, int toRatio)
  {
    fromShifts = new Vector();
    for (int i = 0; i < from.length; i += 2)
    {
      fromShifts.add(new int[]
                     {from[i], from[i + 1]});
    }
    toShifts = new Vector();
    for (int i = 0; i < to.length; i += 2)
    {
      toShifts.add(new int[]
                   {to[i], to[i + 1]});
    }
    this.fromRatio = fromRatio;
    this.toRatio = toRatio;
  }

  /**
   * get all mapped positions from 'from' to 'to'
   * @return int[][] { int[] { fromStart, fromFinish, toStart, toFinish }, int [fromFinish-fromStart+2] { toStart..toFinish mappings}}
   */
  public int[][] makeFromMap()
  {
    return posMap(fromShifts, fromRatio, toShifts, toRatio);
  }

  /**
   * get all mapped positions from 'to' to 'from'
   * @return int[to position]=position mapped in from
   */
  public int[][] makeToMap()
  {
    return posMap(toShifts, toRatio, fromShifts, fromRatio);
  }

  /**
   * construct an int map for intervals in intVals
   * @param intVals
   * @return int[] { from, to pos in range }, int[range.to-range.from+1] returning mapped position
   */
  private int[][] posMap(Vector intVals, int ratio, Vector toIntVals,
                         int toRatio)
  {
    Iterator iv = intVals.iterator();
    if (!iv.hasNext())
    {
      return null;
    }
    int[] intv = (int[]) iv.next();
    int from = intv[0], to = intv[1];
    if (from > to)
    {
      from = intv[1];
      to = intv[0];
    }
    while (iv.hasNext())
    {
      intv = (int[]) iv.next();
      if (intv[0] < from)
      {
        from = intv[0];
      }
      if (intv[1] < from)
      {
        from = intv[1];
      }
      if (intv[0] > to)
      {
        to = intv[0];
      }
      if (intv[1] > to)
      {
        to = intv[1];
      }
    }
    int tF = 0, tT = 0;
    int mp[][] = new int[to - from + 2][];
    for (int i = 0; i < mp.length; i++)
    {
      int[] m = shift(i + from, intVals, ratio, toIntVals, toRatio);
      if (m != null)
      {
        if (i == 0)
        {
          tF = tT = m[0];
        }
        else
        {
          if (m[0] < tF)
          {
            tF = m[0];
          }
          if (m[0] > tT)
          {
            tT = m[0];
          }
        }
      }
      mp[i] = m;
    }
    int[][] map = new int[][]
        {
        new int[]
        {
        from, to, tF, tT}, new int[to - from + 2]};

    map[0][2] = tF;
    map[0][3] = tT;

    for (int i = 0; i < mp.length; i++)
    {
      if (mp[i] != null)
      {
        map[1][i] = mp[i][0] - tF;
      }
      else
      {
        map[1][i] = -1; // indicates an out of range mapping
      }
    }
    return map;
  }

  /**
   * 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 from pos to To(pos)
   *
   * @param pos int
   * @return int shifted position in To, frameshift in From
   */
  public int[] shiftFrom(int pos)
  {
    return shift(pos, fromShifts, fromRatio, toShifts, toRatio);
  }

  /**
   * inverse of shiftFrom - maps pos in To to a position in From
   * @param pos (in To)
   * @return shifted position in From, frameshift in To
   */
  public int[] shiftTo(int pos)
  {
    return shift(pos, toShifts, toRatio, fromShifts, fromRatio);
  }

  /**
   *
   * @param fromShifts
   * @param fromRatio
   * @param toShifts
   * @param toRatio
   * @return
   */
  private int[] shift(int pos, Vector fromShifts, int fromRatio,
                      Vector toShifts, int toRatio)
  {
    int[] fromCount = countPos(fromShifts.iterator(), pos);
    if (fromCount == null)
    {
      return null;
    }
    int fromRemainder = (fromCount[0] - 1) % fromRatio;
    int toCount = 1 + ( ( (fromCount[0] - 1) / fromRatio) * toRatio);
    int[] toPos = countToPos(toShifts.iterator(), toCount);
    if (toPos == null)
    {
      return null; // throw new Error("Bad Mapping!");
    }
    //System.out.println(fromCount[0]+" "+fromCount[1]+" "+toCount);
    return new int[]
        {
        toPos[0], fromRemainder};
  }

  /**
   * count how many positions pos is along the series of intervals.
   * @param intVals
   * @param pos
   * @return number of positions or null if pos is not within intervals
   */
  private int[] countPos(Iterator intVals, int pos)
  {
    int count = 0, intv[];
    while (intVals.hasNext())
    {
      intv = (int[]) intVals.next();
      if (intv[0] <= intv[1])
      {
        if (pos >= intv[0] && pos <= intv[1])
        {
          return new int[]
              {
              count + pos - intv[0] + 1, +1};
        }
        else
        {
          count += intv[1] - intv[0] + 1;
        }
      }
      else
      {
        if (pos >= intv[1] && pos <= intv[0])
        {
          return new int[]
              {
              count + intv[0] - pos + 1, -1};
        }
        else
        {
          count += intv[0] - intv[1] + 1;
        }
      }
    }
    return null;
  }

  /**
   * count out pos positions into a series of intervals and return the position
   * @param intVals
   * @param pos
   * @return position pos in interval set
   */
  private int[] countToPos(Iterator intVals, int pos)
  {
    int count = 0, diff = 0, intv[] =
        {
        0, 0};
    while (intVals.hasNext())
    {
      intv = (int[]) intVals.next();
      diff = intv[1] - intv[0];
      if (diff >= 0)
      {
        if (pos <= count + 1 + diff)
        {
          return new int[]
              {
              pos - count - 1 + intv[0], +1};
        }
        else
        {
          count += 1 + diff;
        }
      }
      else
      {
        if (pos <= count + 1 - diff)
        {
          return new int[]
              {
              intv[0] - (pos - count - 1), -1};
        }
        else
        {
          count += 1 - diff;
        }
      }
    }
    return null; //(diff<0) ? (intv[1]-1) : (intv[0]+1);
  }

  public static void testMap(MapList ml, int fromS, int fromE)
  {
    for (int from = 1; from <= 25; from++)
    {
      int[] too = ml.shiftFrom(from);
      System.out.print("ShiftFrom(" + from + ")==");
      if (too == null)
      {
        System.out.print("NaN\n");
      }
      else
      {
        System.out.print(too[0] + " % " + too[1]);
        System.out.print("\t+--+\t");
        int[] toofrom = ml.shiftTo(too[0]);
        if (toofrom != null)
        {
          if (toofrom[0] != from)
          {
            System.err.println("Mapping not reflexive:" + from + " " + too[0] +
                               "->" + toofrom[0]);
          }
          System.out.println("ShiftTo(" + too[0] + ")==" + toofrom[0] + " % " +
                             toofrom[1]);
        }
        else
        {
          System.out.println("ShiftTo(" + too[0] + ")==" +
                             "NaN! - not Bijective Mapping!");
        }
      }
    }
    int mmap[][] = ml.makeFromMap();
    System.out.println("FromMap : (" + mmap[0][0] + " " + mmap[0][1] + " " +
                       mmap[0][2] + " " + mmap[0][3] + " ");
    for (int i = 1; i <= mmap[1].length; i++)
    {
      if (mmap[1][i - 1] == -1)
      {
        System.out.print(i + "=XXX");

      }
      else
      {
        System.out.print(i + "=" + (mmap[0][2] + mmap[1][i - 1]));
      }
      if (i % 20 == 0)
      {
        System.out.print("\n");
      }
      else
      {
        System.out.print(",");
      }
    }
    System.out.print("\n");
  }

  public static void main(String argv[])
  {
    MapList ml = new MapList(new int[]
                             {1, 5, 10, 15, 25, 20},
                             new int[]
                             {51, 1}, 1, 3);
    MapList ml1 = new MapList(new int[]
                              {1, 3, 17, 4},
                              new int[]
                              {51, 1}, 1, 3);

    // test internal consistency
    int to[] = new int[51];
    MapList.testMap(ml, 1, 25);
    /*
           for (int from=1; from<=51; from++) {
        int[] too=ml.shiftTo(from);
        int[] toofrom=ml.shiftFrom(too[0]);
        System.out.println("ShiftFrom("+from+")=="+too[0]+" % "+too[1]+"\t+-+\tShiftTo("+too[0]+")=="+toofrom[0]+" % "+toofrom[1]);
           }*/
    System.out.print("Success?\n"); // if we get here - something must be working!
  }
}