/*
  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 <string.h>
#include <inttypes.h>
#include "core/fa_api.h"
#include "core/alphabet.h"
#include "core/chardef_api.h"
#include "core/divmodmul_api.h"
#include "core/encseq_metadata.h"
#include "core/error_api.h"
#include "core/str_api.h"
#include "core/xansi_api.h"
#include "core/ma_api.h"

#include "emimergeesa.h"
#include "esa-fileend.h"
#include "fmindex.h"
#include "esa-map.h"

#include "encseq2offset.h"
#include "fmi-keyval.h"
#include "fmi-mapspec.h"
#include "fmi-sufbwtstream.h"

static int copytheindexfile(const char *destindex,
                            const char *sourceindex,
                            const char *suffix,
                            uint64_t maxlength,
                            GtError *err)
{
  FILE *fpdest = NULL, *fpsource = NULL;
  int cc;
  bool haserr = false;

  gt_error_check(err);
  fpdest = gt_fa_fopen_with_suffix(destindex,suffix,"wb",err);
  if (fpdest == NULL)
  {
    haserr = true;
  }
  if (!haserr)
  {
    fpsource = gt_fa_fopen_with_suffix(sourceindex,suffix,"rb",err);
    if (fpsource == NULL)
    {
      haserr = true;
    }
  }
  printf("# cp %s%s %s%s\n",sourceindex,suffix,destindex,suffix);
  if (!haserr)
  {
    if (maxlength == 0)
    {
      while ((cc = fgetc(fpsource)) != EOF)
      {
        (void) putc(cc,fpdest);
      }
    } else
    {
      uint64_t pos;

      for (pos = 0; pos < maxlength; pos++)
      {
        if ((cc = fgetc(fpsource)) == EOF)
        {
          break;
        }
        (void) putc(cc,fpdest);
      }
    }
  }
  gt_fa_xfclose(fpdest);
  gt_fa_xfclose(fpsource);
  return haserr ? -1 : 0;
}

static void allocatefmtables(Fmindex *fm,
                             const GtSpecialcharinfo *specialcharinfo,
                             bool storeindexpos)
{
  fm->tfreq = gt_malloc(sizeof *fm->tfreq * TFREQSIZE(fm->mapsize));
  fm->superbfreq = gt_malloc(sizeof *fm->superbfreq
                             * SUPERBFREQSIZE(fm->mapsize,fm->nofsuperblocks));
  if (storeindexpos)
  {
    fm->markpostable = gt_malloc(sizeof *fm->markpostable
                                 * MARKPOSTABLELENGTH(fm->bwtlength,
                                                      fm->markdist));
    fm->specpos.nextfreeGtPairBwtidx = 0;
    fm->specpos.allocatedGtPairBwtidx
      = (GtUword) gt_determinenumberofspecialstostore(specialcharinfo);
    printf("# "GT_WU" wildcards in the last "GT_WU" characters (%.2f)\n",
           (GtUword) specialcharinfo->specialcharacters -
                           fm->specpos.allocatedGtPairBwtidx,
           specialcharinfo->specialcharacters,
            (double) (specialcharinfo->specialcharacters -
                      fm->specpos.allocatedGtPairBwtidx)/
                     specialcharinfo->specialcharacters);
    fm->specpos.spaceGtPairBwtidx
      = gt_malloc(sizeof *fm->specpos.spaceGtPairBwtidx
                  * fm->specpos.allocatedGtPairBwtidx);
  } else
  {
    GT_INITARRAY(&fm->specpos,GtPairBwtidx);
    fm->markpostable = NULL;
  }
  fm->bfreq = gt_malloc(sizeof *fm->bfreq
                        * BFREQSIZE(fm->mapsize,fm->nofblocks));
}

static void set0frequencies(Fmindex *fm)
{
  GtUword i;

  for (i = 0; i < (GtUword) TFREQSIZE(fm->mapsize); i++)
  {
    fm->tfreq[i] = 0;
  }
  for (i = 0; i < (GtUword) BFREQSIZE(fm->mapsize,fm->nofblocks); i++)
  {
    fm->bfreq[i] = 0;
  }
  for (i = 0;
       i < (GtUword) SUPERBFREQSIZE(fm->mapsize,fm->nofsuperblocks);
       i++)
  {
    fm->superbfreq[i] = 0;
  }
}

static void finalizefmfrequencies(Fmindex *fm)
{
  unsigned int j;
  GtUword i, *freqptr;

  for (j = 2U; j <= fm->mapsize; j++)
  {
    fm->tfreq[j] += fm->tfreq[j - 1];
  }
  freqptr = fm->superbfreq;
  for (j = 0; j < fm->mapsize; j++)
  {
    for (i = (GtUword) 2; i < fm->nofsuperblocks; i++)
    {
      freqptr[i] += freqptr[i-1];
    }
    freqptr += fm->nofsuperblocks;
  }
}

static void showconstructionmessage(const char *indexname,
                                    GtUword totallength,
                                    GtUword fmsize,
                                    unsigned int log2bsize,
                                    unsigned int log2markdist,
                                    unsigned int numofchars)
{
  printf("# construct fmindex \"%s\" for bsize="GT_WU", superbsize="GT_WU",",
          indexname,
          (GtUword) GT_POW2(log2bsize),
          (GtUword) GT_POW2(log2markdist));
  printf(" len="GT_WU", alphasize=%u: size ",
          totallength,
          numofchars);
  printf(""GT_WU" bytes, space overhead %.2f\n",
          fmsize,
          (double) fmsize/(double) (totallength+1));
}

static int nextesamergedsufbwttabvalues(Definedunsignedlong *longest,
                                       GtUchar *bwtvalue,
                                       GtUword *suftabvalue,
                                       Emissionmergedesa *emmesa,
                                       const GtUword *sequenceoffsettable,
                                       GtUword bwtpos,
                                       GtError *err)
{
  Indexedsuffix indexedsuffix;

  gt_error_check(err);
  if (emmesa->buf.nextaccessidx >= emmesa->buf.nextstoreidx)
  {
    if (emmesa->numofentries == 0)
    {
      return 0;
    }
    if (gt_emissionmergedesa_stepdeleteandinsertothersuffixes(emmesa,err) != 0)
    {
      return -1;
    }
    if (emmesa->buf.nextstoreidx == 0)
    {
      return 0;
    }
    emmesa->buf.nextaccessidx = 0;
  }
  indexedsuffix = emmesa->buf.suftabstore[emmesa->buf.nextaccessidx];
  *suftabvalue = sequenceoffsettable[indexedsuffix.idx] +
                 indexedsuffix.startpos;
  if (indexedsuffix.startpos == 0)
  {
    if (indexedsuffix.idx == 0)
    {
      if (longest->defined)
      {
        gt_error_set(err,"longest is already defined as "GT_WU"",
                      longest->valueunsignedlong);
        return -2;
      }
      longest->defined = true;
      longest->valueunsignedlong = bwtpos;
      *bwtvalue = (GtUchar) GT_UNDEFBWTCHAR;
    } else
    {
      *bwtvalue = (GtUchar) GT_SEPARATOR;
    }
  } else
  {
    *bwtvalue
      = gt_encseq_get_encoded_char( /* Random access */
           emmesa->suffixarraytable[indexedsuffix.idx].encseq,
           indexedsuffix.startpos-1,
           emmesa->suffixarraytable[indexedsuffix.idx].readmode);
  }
  emmesa->buf.nextaccessidx++;
  return 1;
}

int gt_sufbwt2fmindex(Fmindex *fmindex,
                   GtSpecialcharinfo *specialcharinfo,
                   unsigned int log2bsize,
                   unsigned int log2markdist,
                   const char *outfmindex,
                   const GtStrArray *indexnametab,
                   bool storeindexpos,
                   GtLogger *logger,
                   GtError *err)
{
  Suffixarray suffixarray;
  Emissionmergedesa emmesa;
  GtUchar cc;
  GtUword bwtpos,
         totallength = 0,
         suftabvalue = 0,
         *sequenceoffsettable = NULL,
         firstignorespecial = 0,
         nextmark,
         *markptr,
         nextprogress,
         tmpsuftabvalue,
         stepprogress;
  unsigned int numofchars = 0,
               suffixlength = 0,
               numofindexes;
  int retval;
  Definedunsignedlong longest = { false, 0 };
  GtPairBwtidx *pairptr;
  FILE *outbwt = NULL;
  GtStr *tmpfilename = NULL;
  bool haserr = false;

  gt_error_check(err);
  longest.defined = false;
  longest.valueunsignedlong = 0;
  numofindexes = (unsigned int) gt_str_array_size(indexnametab);
  if (numofindexes == 1U)
  {
    const char *indexname = gt_str_array_get(indexnametab,0);

    if (streamsuffixarray(&suffixarray,
                          SARR_BWTTAB | (storeindexpos ? SARR_SUFTAB : 0),
                          indexname,
                          logger,
                          err) != 0)
    {
      haserr = true;
    } else
    {
      totallength = gt_encseq_total_length(suffixarray.encseq);
    }
    if (!haserr && gt_specialcharinfo_read(specialcharinfo,indexname,err) != 0)
    {
      haserr = true;
    }
    if (!haserr)
    {
      numofchars = gt_alphabet_num_of_chars(
                               gt_encseq_alphabet(suffixarray.encseq));
      firstignorespecial = totallength - specialcharinfo->specialcharacters;
      if (gt_alphabet_to_file(gt_encseq_alphabet(suffixarray.encseq),
                              outfmindex, err) != 0)
      {
        haserr = true;
      }
    }
    if (!haserr)
    {
      if (copytheindexfile(outfmindex,
                            indexname,
                            GT_BWTTABSUFFIX,
                            (uint64_t) firstignorespecial,
                            err) != 0)
      {
        haserr = true;
      }
    }
  } else
  {
    GtEncseqMetadata *emd = NULL;
    if (gt_emissionmergedesa_init(&emmesa,
                               indexnametab,
                               SARR_ESQTAB | SARR_SUFTAB | SARR_LCPTAB,
                               logger,
                               err) != 0)
    {
      haserr = true;
    }
    if (!haserr)
    {
      const char *indexname = NULL;
      indexname = gt_str_array_get(indexnametab,0);
      emd = gt_encseq_metadata_new(indexname, err);
      if (emd == NULL) {
        haserr = true;
      }
    }
    if (!haserr) {
      suffixlength = 0;
      if (gt_alphabet_to_file(gt_encseq_metadata_alphabet(emd),
                              outfmindex, err) != 0)
      {
        haserr = true;
      }
    }
    gt_encseq_metadata_delete(emd);
    if (!haserr)
    {
      sequenceoffsettable = gt_encseqtable2sequenceoffsets(&totallength,
                                                        specialcharinfo,
                                                        emmesa.suffixarraytable,
                                                        numofindexes);
      if (sequenceoffsettable == NULL)
      {
        haserr = true;
      }
    }
    if (!haserr)
    {
      longest.defined = false;
      longest.valueunsignedlong = 0;
      outbwt = gt_fa_fopen_with_suffix(outfmindex,GT_BWTTABSUFFIX,"wb",err);
      if (outbwt == NULL)
      {
        haserr = true;
      }
    }
    if (!haserr)
    {
      numofchars = emmesa.numofchars;
      firstignorespecial = totallength - specialcharinfo->specialcharacters;
    }
  }
  if (!haserr)
  {
    printf("# firstignorespecial="GT_WU"\n",
              firstignorespecial);
    gt_computefmkeyvalues (fmindex,
                        specialcharinfo,
                        totallength+1,
                        log2bsize,
                        log2markdist,
                        numofchars,
                        suffixlength,
                        storeindexpos);
    showconstructionmessage(outfmindex,
                            totallength,
                            fmindex->sizeofindex,
                            log2bsize,
                            log2markdist,
                            numofchars);
    allocatefmtables(fmindex,specialcharinfo,storeindexpos);
    set0frequencies(fmindex);
    if (storeindexpos)
    {
      markptr = fmindex->markpostable;
    } else
    {
      markptr = NULL;
    }
    nextprogress = stepprogress = totallength/78;
    for (bwtpos = 0, nextmark = 0; ; bwtpos++)
    {
      if (numofindexes == 1U)
      {
        if (storeindexpos)
        {
          retval = gt_readnextfromstream_GtUword(&tmpsuftabvalue,
                                            &suffixarray.suftabstream_GtUword);
          if (retval == 0)
          {
            break;
          }
          suftabvalue = (GtUword) tmpsuftabvalue;
        }
        retval = gt_readnextfromstream_GtUchar(&cc,&suffixarray.bwttabstream);
        if (retval == 0)
        {
          break;
        }
      } else
      {
        retval = nextesamergedsufbwttabvalues(&longest,
                                              &cc,
                                              &suftabvalue,
                                              &emmesa,
                                              sequenceoffsettable,
                                              bwtpos,
                                              err);
        if (retval < 0)
        {
          haserr = true;
          break;
        }
        if (retval == 0)
        {
          break;
        }
        gt_xfwrite(&cc, sizeof (GtUchar), (size_t) 1, outbwt);
      }
      if (bwtpos == nextprogress)
      {
        if (bwtpos == stepprogress)
        {
          (void) putchar('#');
        }
        (void) putchar('.');
        (void) fflush(stdout);
        nextprogress += stepprogress;
      }
      if (storeindexpos && bwtpos == nextmark)
      {
        *markptr++ = suftabvalue;
        nextmark += fmindex->markdist;
      }
      if (GT_ISBWTSPECIAL(cc))
      {
        if (storeindexpos && bwtpos < firstignorespecial)
        {
          pairptr = fmindex->specpos.spaceGtPairBwtidx +
                    fmindex->specpos.nextfreeGtPairBwtidx++;
          if (pairptr >= fmindex->specpos.spaceGtPairBwtidx +
                         fmindex->specpos.allocatedGtPairBwtidx)
          {
            gt_error_set(err,"program error: not enough space for specpos");
            haserr = true;
            break;
          }
          pairptr->bwtpos = bwtpos;
          pairptr->suftabvalue = suftabvalue;
        }
      } else
      {
        fmindex->tfreq[cc+1]++;
        fmindex->bfreq[(cc * fmindex->nofblocks) +
                       (bwtpos >> fmindex->log2bsize)]++;
        fmindex->superbfreq[(cc * fmindex->nofsuperblocks) +
                       (bwtpos >> fmindex->log2superbsize) + 1]++;
      }
    }
  }
  if (!haserr)
  {
    if (storeindexpos &&
        fmindex->specpos.allocatedGtPairBwtidx !=
        fmindex->specpos.nextfreeGtPairBwtidx)
    {
      gt_error_set(err,"program error: too much space for specpos: "
                    "allocated = "GT_WU" != "GT_WU" = used",
                    fmindex->specpos.allocatedGtPairBwtidx,
                    fmindex->specpos.nextfreeGtPairBwtidx);
      haserr = true;
    }
  }
  if (!haserr)
  {
    (void) putchar('\n');
    finalizefmfrequencies(fmindex);
    if (fmindex->suffixlength > 0)
    {
      fmindex->boundarray = gt_malloc(sizeof *fmindex->boundarray
                                      * fmindex->numofcodes);
    }
    if (numofindexes == 1U)
    {
      fmindex->longestsuffixpos = suffixarray.longest.valueunsignedlong;
      gt_freesuffixarray(&suffixarray);
    } else
    {
      if (!longest.defined)
      {
        gt_error_set(err,"longest is not defined after merging");
        haserr = true;
      }
      if (!haserr)
      {
        fmindex->longestsuffixpos = longest.valueunsignedlong;
      }
      gt_fa_xfclose(outbwt);
      gt_emissionmergedesa_wrap(&emmesa);
    }
  }
  gt_free(sequenceoffsettable);
  gt_free(tmpfilename);
  return haserr ? -1 : 0;
}
