package uk.ac.vamsas.objects.utils;

import java.util.Vector;


import uk.ac.vamsas.objects.core.RangeType;
import uk.ac.vamsas.objects.core.Seg;

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;
  }
}