package uk.ac.vamsas.objects.utils;

import java.util.Vector;

import uk.ac.vamsas.objects.core.Local;
import uk.ac.vamsas.objects.core.MapType;
import uk.ac.vamsas.objects.core.Mapped;
import uk.ac.vamsas.objects.core.RangeType;
import uk.ac.vamsas.objects.core.Seg;

/**
 * Utilities for working with RangeType and MapType objects.
 * Derived from bitter experience.
 * @author JimP
 *
 */
public class Range {

  /**
   * get start<end range of segment, adjusting for inclusivity flag and
   * polarity.
   *
   * @param visSeg
   * @param ensureDirection when true - always ensure start is less than end.
   * @return int[] { start, end, direction} where direction==1 for range running from end to start.
   */
  public static int[] getSegRange(Seg visSeg, boolean ensureDirection)
  {
    boolean incl = visSeg.getInclusive();
    // adjust for inclusive flag.
    int pol = (visSeg.getStart() <= visSeg.getEnd()) ? 1 : -1; // polarity of
    // region.
    int start = visSeg.getStart() + (incl ? 0 : pol);
    int end = visSeg.getEnd() + (incl ? 0 : -pol);
    if (ensureDirection && pol == -1)
    {
      // jalview doesn't deal with inverted ranges, yet.
      int t = end;
      end = start;
      start = t;
    }
    return new int[]
        {
        start, end, pol < 0 ? 1 : 0};
  }

  /**
   * get real bounds of a RangeType's specification. start and end are an
   * inclusive range within which all segments and positions lie.
   * TODO: refactor to vamsas utils
   * @param dseta
   * @return int[] { start, end}
   */
  public static int[] getBounds(RangeType dseta)
  {
    if (dseta != null)
    {
      int[] se = null;
      if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
      {
        throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
      }
      if (dseta.getSegCount() > 0)
      {
        se = getSegRange(dseta.getSeg(0), true);
        for (int s = 1, sSize = dseta.getSegCount(); s < sSize; s++)
        {
          int nse[] = getSegRange(dseta.getSeg(s), true);
          if (se[0] > nse[0])
          {
            se[0] = nse[0];
          }
          if (se[1] < nse[1])
          {
            se[1] = nse[1];
          }
        }
      }
      if (dseta.getPosCount() > 0)
      {
        // could do a polarity for pos range too. and pass back indication of discontinuities.
        int pos = dseta.getPos(0).getI();
        se = new int[]
            {
            pos, pos};
        for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
        {
          pos = dseta.getPos(p).getI();
          if (se[0] > pos)
          {
            se[0] = pos;
          }
          if (se[1] < pos)
          {
            se[1] = pos;
          }
        }
      }
      return se;
    }
    return null;
  }

  /**
   * map from a rangeType's internal frame to the referenced object's coordinate frame.
   * @param dseta
   * @return int [] { ref(pos)...} for all pos in rangeType's frame.
   */
  public static int[] getMapping(RangeType dseta)
  {
    Vector posList = new Vector();
    if (dseta != null)
    {
      int[] se = null;
      if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
      {
        throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
      }
      if (dseta.getSegCount() > 0)
      {
        for (int s = 0, sSize = dseta.getSegCount(); s < sSize; s++)
        {
          se = getSegRange(dseta.getSeg(s), false);
          int se_end = se[1 - se[2]] + (se[2] == 0 ? 1 : -1);
          for (int p = se[se[2]]; p != se_end; p += se[2] == 0 ? 1 : -1)
          {
            posList.add(new Integer(p));
          }
        }
      }
      else if (dseta.getPosCount() > 0)
      {
        int pos = dseta.getPos(0).getI();

        for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
        {
          pos = dseta.getPos(p).getI();
          posList.add(new Integer(pos));
        }
      }
    }
    if (posList != null && posList.size() > 0)
    {
      int[] range = new int[posList.size()];
      for (int i = 0; i < range.length; i++)
      {
        range[i] = ( (Integer) posList.elementAt(i)).intValue();
      }
      posList.clear();
      return range;
    }
    return null;
  }

  public static int[] getIntervals(RangeType range)
  {
    int[] intervals=null;
    Vector posList = new Vector();
    if (range != null)
    {
      int[] se = null;
      if (range.getSegCount() > 0 && range.getPosCount() > 0)
      {
        throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
}
      if (range.getSegCount() > 0)
      {
        for (int s = 0, sSize = range.getSegCount(); s < sSize; s++)
        {
          se = getSegRange(range.getSeg(s), false);
          posList.addElement(new Integer(se[0]));
          posList.addElement(new Integer(se[1]));
        }
      }
      else if (range.getPosCount() > 0)
      {
        int pos = range.getPos(0).getI();
        for (int p = 0, pSize = range.getPosCount(); p < pSize; p++)
        {
          pos = range.getPos(p).getI();
          posList.add(new Integer(pos));
          posList.add(new Integer(pos));
        }
      }
    }
    if (posList != null && posList.size() > 0)
    {
      intervals=new int[posList.size()];
      java.util.Enumeration e = posList.elements();
      int i=0;
      while (e.hasMoreElements())
      {
        intervals[i++] = ((Integer)e.nextElement()).intValue();
      }
    }
    return intervals;
  }
  /**
   * initialise a range type object from a set of start/end inclusive intervals
   * @param mrt
   * @param range
   */
  public static void initRangeType(RangeType mrt, int[] range)
  {
    for (int i=0; i<range.length; i+=2)
    {
      Seg vSeg = new Seg();
      vSeg.setStart(range[i]);
      vSeg.setEnd(range[i+1]);
      vSeg.setInclusive(true);
      mrt.addSeg(vSeg);
    }
  }

  /**
   * 
   * @param maprange where the from range is the local mapped range, and the to range is the 'mapped' range in the MapRangeType
   * @param default unit for local
   * @param default unit for mapped
   * @return MapList
   */
  public static MapList parsemapType(MapType maprange, int localu, int mappedu)
  {
    MapList ml = null;
    int[] localRange = getIntervals(maprange.getLocal());
    int[] mappedRange = getIntervals(maprange.getMapped());
    long lu = maprange.getLocal().hasUnit() ? maprange.getLocal().getUnit() : localu;
    long mu = maprange.getMapped().hasUnit() ? maprange.getMapped().getUnit() : mappedu;
    ml = new MapList(localRange, mappedRange, (int)lu, (int)mu);
    return ml;
  }
  /**
   * Parse map with default units of 1,1
   * @param map
   * @return MapList representing map
   */
  public static MapList parsemapType(MapType map)
  {
    return parsemapType(map, 1, 1); 
  }

  /**
   * initialise a MapType object from a MapList object.
   * @param maprange
   * @param ml
   * @param setUnits
   */
  public static void initMapType(MapType maprange, MapList ml, boolean setUnits)
  {
    initMapType(maprange, ml, setUnits, false);
  }
  /**
   * 
   * @param maprange
   * @param ml
   * @param setUnits
   * @param reverse - reverse MapList mapping for Local and Mapped ranges and units 
   */
  public static void initMapType(MapType maprange, MapList ml, boolean setUnits, boolean reverse)
  {
    maprange.setLocal(new Local());
    maprange.setMapped(new Mapped());
    if (!reverse)
      {
      initRangeType(maprange.getLocal(), ml.getFromRanges());
      initRangeType(maprange.getMapped(), ml.getToRanges());
      } else {
        initRangeType(maprange.getLocal(), ml.getToRanges());
        initRangeType(maprange.getMapped(), ml.getFromRanges());
      }
    if (setUnits)
    {
      if (!reverse)
      { 
        maprange.getLocal().setUnit(ml.getFromRatio());
        maprange.getMapped().setUnit(ml.getToRatio());
      } else {
        maprange.getLocal().setUnit(ml.getToRatio());
        maprange.getMapped().setUnit(ml.getFromRatio());
      }
    }
  }

}