/*
  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 <errno.h>
#include <string.h>
#include <stdbool.h>
#include "core/fa_api.h"
#include "core/types_api.h"
#include "core/unused_api.h"
#include "core/ma_api.h"
#include "test-pairwise.h"
#include "greedyedist.h"
#include "squarededist.h"

void gt_runcheckfunctionontwofiles(Checkcmppairfuntype checkfunction,
                                   const char *file1,
                                   const char *file2)
{
  const GtUchar *useq = NULL, *vseq = NULL;
  size_t ulen, vlen;
  bool forward = true;
  GtError *err;

  err = gt_error_new();
  useq = (const GtUchar *) gt_fa_mmap_read(file1,&ulen,err);
  if (useq == NULL)
  {
    fprintf(stderr, "error: %s\n", gt_error_get(err));
    exit(GT_EXIT_PROGRAMMING_ERROR);
  }
  vseq = (const GtUchar *) gt_fa_mmap_read(file2,&vlen,err);
  if (vseq == NULL)
  {
    fprintf(stderr, "error: %s\n", gt_error_get(err));
    exit(GT_EXIT_PROGRAMMING_ERROR);
  }
  gt_error_delete(err);
  while (true)
  {
    checkfunction(forward,useq,(GtUword) ulen,
                          vseq,(GtUword) vlen);
    if (!forward)
    {
      break;
    }
    forward = false;
  }
  gt_fa_xmunmap((void *) useq);
  gt_fa_xmunmap((void *) vseq);
}

GtUword gt_runcheckfunctionontext(Checkcmppairfuntype checkfunction,
                                     const char *text)
{
  GtUword i, len;

  len = (GtUword) strlen(text);
  for (i=1UL; i<=len/2; i++)
  {
    checkfunction(true,
                  (const GtUchar *) text,
                  i,
                  (const GtUchar *) (text+i),
                  len-i);
  }
  return len/2;
}

GtUword gt_applycheckfunctiontotext(const GtUchar *text,
                                       GtUword textlen,
                                       void *info)
{
  GtUword i;
  Checkcmppairfuntype checkfunction = (Checkcmppairfuntype) info;

#ifdef SKDEBUG
  printf("%s\n",(char *) text);
#endif
  for (i=0; i<=textlen/2; i++)
  {
    checkfunction(true,text,i,text+i,textlen-i);
  }
  return textlen/2+1;
}

static GtUword applyall(const char *alpha,
                              GtUword textlen,void *info,
                              GtUword (*apply)(const GtUchar *,
                                                     GtUword,
                                                     void *))
{
  GtUword i, *w, z = textlen-1,
                testcases = 0,
                asize = (GtUword) strlen(alpha);
  GtUchar *text;
  bool stop = false;

  w = gt_malloc(sizeof *w * (textlen+1));
  text = gt_malloc(sizeof *text * (textlen+1));
  for (i=0; i<=textlen; i++)
  {
    w[i] = 0;
  }
  text[textlen] = (GtUchar) '\0';
  while (!stop)
  {
    for (i = 0; i<textlen; i++)
    {
      text[i] = (GtUchar) alpha[w[i]];
    }
    testcases += apply(text,textlen,info);
    while (true)
    {
      w[z]++;
      if (w[z] == asize)
      {
        w[z] = 0;
        if (z == 0)
        {
          stop = true;
          break;
        }
        z--;
      } else
      {
        z = textlen-1;
        /*@innerbreak@*/ break;
      }
    }
  }
  gt_free(w);
  gt_free(text);
  return testcases;
}

GtUword gt_runcheckfunctiononalphalen(Checkcmppairfuntype checkfunction,
                                         const char *charlist,
                                         GtUword len)
{
  return applyall(charlist,
                  len,
                  (void *) checkfunction,
                  gt_applycheckfunctiontotext);
}

GtUword gt_computegreedyunitedist(const GtUchar *useq,
                                        GtUword ulen,
                                        const GtUchar *vseq,
                                        GtUword vlen)
{
  GtUword edist;
  bool rightextension = true;
  GtFrontResource *frontresource = gt_frontresource_new(10UL);
  GtSeqabstract *greedyedistuseq, *greedyedistvseq;

  greedyedistuseq
    = gt_seqabstract_new_gtuchar(rightextension,GT_READMODE_FORWARD,
                                 useq,ulen,0,ulen);
  greedyedistvseq
    = gt_seqabstract_new_gtuchar(rightextension,GT_READMODE_FORWARD,
                                 vseq,vlen,0,vlen);
  edist = greedyunitedist(frontresource,greedyedistuseq,greedyedistvseq);
  gt_seqabstract_delete(greedyedistuseq);
  gt_seqabstract_delete(greedyedistvseq);
  gt_frontresource_delete(frontresource);
  return edist;
}

void gt_checkgreedyunitedist(GT_UNUSED bool forward,
                             const GtUchar *useq,
                             GtUword ulen,
                             const GtUchar *vseq,
                             GtUword vlen)
{
  GtUword edist1, edist2;
  GtFrontResource *frontresource = gt_frontresource_new(10UL);
  bool rightextension = true;
  GtSeqabstract *greedyedistuseq, *greedyedistvseq;

  greedyedistuseq
    = gt_seqabstract_new_gtuchar(rightextension,GT_READMODE_FORWARD,
                                 useq,ulen,0,ulen);
  greedyedistvseq
    = gt_seqabstract_new_gtuchar(rightextension,GT_READMODE_FORWARD,
                                 vseq,vlen,0,vlen);
  edist1 = greedyunitedist(frontresource,greedyedistuseq,greedyedistvseq);
  edist2 = gt_squarededistunit (useq,ulen,vseq,vlen);
#ifdef SKDEBUG
  printf("edist = " GT_WU "\n",edist1);
#endif
  if (edist1 != edist2)
  {
    fprintf(stderr,"greedyunitedist = "GT_WU" != "GT_WU
            " = gt_squarededistunit\n", edist1,edist2);
    exit(GT_EXIT_PROGRAMMING_ERROR);
  }
  gt_seqabstract_delete(greedyedistuseq);
  gt_seqabstract_delete(greedyedistvseq);
  gt_frontresource_delete(frontresource);
}
