/*
  Copyright (c) 2007 Stefan Kurtz <kurtz@zbh.uni-hamburg.de>
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include <stdlib.h>
#include <stdio.h>
#include "core/assert_api.h"
#include "core/codetype.h"
#include "core/encseq.h"
#include "sfx-enumcodes.h"
#include "initbasepower.h"

struct Enumcodeatposition
{
  GtRange previousrange;
  GtSpecialrangeiterator *sri;
  bool moveforward;
  GtUword totallength;
  bool exhausted;
  const GtEncseq *encseq;
  GtReadmode readmode;
  unsigned int prefixlength;
  GtCodetype **multimappower, *filltable;
};

Enumcodeatposition *gt_Enumcodeatposition_new(const GtEncseq *encseq,
                                              GtReadmode readmode,
                                              unsigned int prefixlength,
                                              unsigned int numofchars)
{
  Enumcodeatposition *ecp;

  ecp = gt_malloc(sizeof *ecp);
  ecp->encseq = encseq;
  ecp->readmode = readmode;
  ecp->multimappower = gt_initmultimappower(numofchars,prefixlength);
  ecp->filltable = gt_initfilltable(numofchars,prefixlength);
  ecp->prefixlength = prefixlength;
  ecp->moveforward = GT_ISDIRREVERSE(readmode) ? true : false;
  ecp->totallength = gt_encseq_total_length(encseq);
  if (ecp->moveforward)
  {
    ecp->previousrange.start = ecp->previousrange.end = 0;
  } else
  {
    ecp->previousrange.start = ecp->previousrange.end = ecp->totallength;
  }
  ecp->exhausted = false;
  if (gt_encseq_has_specialranges(encseq))
  {
    ecp->sri = gt_specialrangeiterator_new(encseq,ecp->moveforward);
  } else
  {
    ecp->sri = NULL;
  }
  return ecp;
}

static bool newcodelistelem(Specialcontext *specialcontext,
                            GtUword smallerval,
                            GtUword largerval,
                            const Enumcodeatposition *ecp)
{
  if (smallerval < largerval)
  {
    GtUword distance = largerval - smallerval;

    if (distance > (GtUword) (ecp->prefixlength-1))
    {
      distance = (GtUword) (ecp->prefixlength-1);
    }
    specialcontext->maxprefixindex = (unsigned int) distance;
    if (ecp->moveforward)
    {
      specialcontext->position = ecp->totallength - smallerval;
    } else
    {
      specialcontext->position = largerval;
    }
    gt_assert(specialcontext->position >=
              (GtUword) specialcontext->maxprefixindex);
    return true;
  }
  return false;
}

bool gt_Enumcodeatposition_next(Specialcontext *specialcontext,
                                Enumcodeatposition *ecp)
{
  GtRange currentrange;
  bool done;

  if (ecp->exhausted)
  {
    return false;
  }
  while (ecp->sri != NULL)
  {
    if (!gt_specialrangeiterator_next(ecp->sri,&currentrange))
    {
      gt_specialrangeiterator_delete(ecp->sri);
      ecp->sri = NULL;
      break;
    }
    if (ecp->moveforward)
    {
      if (newcodelistelem(specialcontext,
                          ecp->previousrange.end,
                          currentrange.start,
                          ecp))
      {
        ecp->previousrange = currentrange;
        return true;
      }
    } else
    {
      if (newcodelistelem(specialcontext,
                          currentrange.end,
                          ecp->previousrange.start,
                          ecp))
      {
        ecp->previousrange = currentrange;
        return true;
      }
    }
    ecp->previousrange = currentrange;
  }
  ecp->exhausted = true;
  if (ecp->moveforward)
  {
    done = newcodelistelem(specialcontext,
                           ecp->previousrange.end,
                           ecp->totallength,
                           ecp);
  } else
  {
    done = newcodelistelem(specialcontext,
                           0,
                           ecp->previousrange.start,
                           ecp);
  }
  return done;
}

void gt_Enumcodeatposition_delete(Enumcodeatposition *ecp)
{
  if (ecp != NULL)
  {
    gt_free(ecp->filltable);
    gt_multimappower_delete(ecp->multimappower);
    gt_free(ecp);
  }
}

GtCodetype gt_Enumcodeatposition_filledqgramcode(const Enumcodeatposition *ecp,
                                                 unsigned int prefixindex,
                                                 GtUword pos)
{
  GtCodetype code;
  unsigned int idx;
  GtUchar cc;

  gt_assert(prefixindex > 0 && prefixindex < ecp->prefixlength);
  code = ecp->filltable[prefixindex];
  for (idx=0; idx<prefixindex; idx++)
  {
    gt_assert((GtUword) (pos + idx) < ecp->totallength);
    cc = gt_encseq_get_encoded_char_nospecial(ecp->encseq,
                                              pos + idx,
                                              ecp->readmode);
    gt_assert(GT_ISNOTSPECIAL(cc));
    code += ecp->multimappower[idx][cc];
  }
  return code;
}

bool gt_Enumcodeatposition_filledqgramcodestopatmax(
                                        GtCodetype *code,
                                        const Enumcodeatposition *ecp,
                                        unsigned int prefixindex,
                                        GtUword pos,
                                        GtCodetype stopcode)
{
  GtCodetype tmpcode;
  unsigned int idx;
  GtUchar cc;

  gt_assert(prefixindex > 0 && prefixindex < ecp->prefixlength);
  tmpcode = ecp->filltable[prefixindex];
  if (tmpcode > stopcode)
  {
    return false;
  }
  for (idx=0; idx<prefixindex; idx++)
  {
    gt_assert((GtUword) (pos + idx) < ecp->totallength);
    cc = gt_encseq_get_encoded_char_nospecial(ecp->encseq,
                                              pos + idx,
                                              ecp->readmode);
    gt_assert(GT_ISNOTSPECIAL(cc));
    tmpcode += ecp->multimappower[idx][cc];
    if (tmpcode > stopcode)
    {
      return false;
    }
  }
  *code = tmpcode;
  return true;
}
