text: /*
    Copyright (c) 2011 Stefan Kurtz <kurtz@zbh.uni-hamburg.de>
    Copyright (c) 2011 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>
  #ifndef S_SPLINT_S
  #include <unistd.h>
  #endif
  #include "core/xposix.h"
  #include "core/xansi_api.h"
  #include "core/fa.h"
  #include "core/intbits.h"
  #include "core/log.h"
  #include "sfx-maprange.h"
  
  static unsigned long gt_multipleofpagesize(unsigned long code,
                                             bool smaller,
                                             size_t sizeofbasetype,
                                             unsigned long pagesize)
  {
    if ((code * sizeofbasetype) % pagesize == 0)
    {
      return code * sizeofbasetype;
    }
    if (smaller)
    {
      return ((code * sizeofbasetype)/pagesize) * pagesize;
    }
    return ((code * sizeofbasetype)/pagesize) * pagesize + pagesize;
  }
  
  typedef struct
  {
    unsigned long mapoffset, mapend;
  } GtMappedrange;
  
  static void gt_Sfxmapped_offset_end(GtMappedrange *range,
                                      size_t sizeofbasetype,
                                      unsigned long pagesize,
                                      unsigned long minindex,
                                      unsigned long maxindex)
  {
    range->mapoffset = gt_multipleofpagesize(minindex,true,sizeofbasetype,
                                             pagesize);
    range->mapend = gt_multipleofpagesize(maxindex,false,sizeofbasetype,pagesize);
  }
  
  struct GtSfxmappedrange
  {
    void *ptr, *entire, **usedptrptr;
    GtStr *filename, *tablename;
    unsigned long pagesize;
    size_t numofunits, sizeofunit;
    GtSfxmappedrangetype type;
    unsigned long currentminindex, currentmaxindex;
    bool indexrange_defined;
    GtSfxmappedrangetransformfunc transformfunc;
    const void *transformfunc_data;
    bool writable;
  };
  
  size_t gt_Sfxmappedrange_size_entire(const GtSfxmappedrange *sfxmappedrange)
  {
    gt_assert(sfxmappedrange != NULL);
    return sfxmappedrange->sizeofunit * sfxmappedrange->numofunits;
  }
  
  void *gt_Sfxmappedrange_map_entire(GtSfxmappedrange *sfxmappedrange,
                                     GtError *err)
  {
    size_t mappedsize;
  
    gt_assert(sfxmappedrange != NULL);
    sfxmappedrange->entire = gt_fa_mmap_read(gt_str_get(sfxmappedrange->filename),
                                             &mappedsize,err);
    if (sfxmappedrange->entire == NULL)
    {
      return NULL;
    }
    if (mappedsize != gt_Sfxmappedrange_size_entire(sfxmappedrange))
    {
      gt_error_set(err,"map file %s: mapped size = %lu != %lu = expected size",
                       gt_str_get(sfxmappedrange->filename),
                       (unsigned long) mappedsize,
                       (unsigned long) gt_Sfxmappedrange_size_entire(
                                                        sfxmappedrange));
      gt_fa_xmunmap(sfxmappedrange->entire);
      sfxmappedrange->entire = NULL;
      return NULL;
    }
    gt_log_log("map %s completely (%lu units of size %u)",
                gt_str_get(sfxmappedrange->tablename),
                (unsigned long) sfxmappedrange->numofunits,
                (unsigned int) sfxmappedrange->sizeofunit);
    return sfxmappedrange->entire;
  }
  
  GtSfxmappedrange *gt_Sfxmappedrange_new(const char *tablename,
                                          unsigned long numofentries,
                                          GtSfxmappedrangetype type,
                                          GtSfxmappedrangetransformfunc
                                            transformfunc,
                                          const void *transformfunc_data)
  {
    GtSfxmappedrange *sfxmappedrange;
  
    sfxmappedrange = gt_malloc(sizeof (*sfxmappedrange));
    sfxmappedrange->ptr = NULL;
    sfxmappedrange->pagesize = (unsigned long) sysconf((int) _SC_PAGESIZE);
    sfxmappedrange->usedptrptr = NULL;
    sfxmappedrange->filename = NULL;
    sfxmappedrange->writable = false;
    sfxmappedrange->entire = NULL;
    sfxmappedrange->transformfunc = transformfunc;
    sfxmappedrange->transformfunc_data = transformfunc_data;
    sfxmappedrange->type = type;
    sfxmappedrange->tablename = gt_str_new_cstr(tablename);
    sfxmappedrange->currentminindex = sfxmappedrange->currentmaxindex = 0;
    sfxmappedrange->indexrange_defined = false;
    switch (type)
    {
      case GtSfxGtBitsequence:
        sfxmappedrange->sizeofunit = sizeof (GtBitsequence);
        sfxmappedrange->numofunits = GT_NUMOFINTSFORBITS(numofentries);
        break;
      case GtSfxuint32_t:
        sfxmappedrange->sizeofunit = sizeof (uint32_t);
        sfxmappedrange->numofunits = (size_t) numofentries;
        break;
      case GtSfxunsignedlong:
        sfxmappedrange->sizeofunit = sizeof (unsigned long);
        sfxmappedrange->numofunits = (size_t) numofentries;
        break;
      default:
        gt_assert(false);
        break;
    }
    return sfxmappedrange;
  }
  
  typedef union {
    GtBitsequence **bs;
    unsigned long **ulong;
    uint32_t **uint32;
  } GtSfxStoretype;
  
  static void gt_Sfxmappedrange_storetmp(GtSfxmappedrange *sfxmappedrange,
                                         GtSfxStoretype usedptrptr,
                                         GtSfxmappedrangetype type,
                                         bool writable)
  {
    FILE *outfp;
  
    gt_assert(sfxmappedrange != NULL);
    sfxmappedrange->ptr = NULL;
    sfxmappedrange->filename = gt_str_new();
    sfxmappedrange->writable = writable;
    outfp = gt_xtmpfp(sfxmappedrange->filename);
    gt_assert(outfp != NULL);
    gt_log_log("write %s to file %s (%lu units of %lu bytes)",
               gt_str_get(sfxmappedrange->tablename),
               gt_str_get(sfxmappedrange->filename),
               (unsigned long) sfxmappedrange->numofunits,
               (unsigned long) sfxmappedrange->sizeofunit);
    switch (type) {
      case GtSfxGtBitsequence:
        gt_xfwrite(*(usedptrptr.bs),sfxmappedrange->sizeofunit,
                   sfxmappedrange->numofunits,outfp);
        sfxmappedrange->usedptrptr = (void**) usedptrptr.bs;
        gt_free(*(usedptrptr.bs));
        *(usedptrptr.bs) = NULL;
        break;
      case GtSfxunsignedlong:
        gt_xfwrite(*(usedptrptr.ulong),sfxmappedrange->sizeofunit,
                   sfxmappedrange->numofunits,outfp);
        sfxmappedrange->usedptrptr = (void**) usedptrptr.ulong;
        gt_free(*(usedptrptr.ulong));
        *(usedptrptr.ulong) = NULL;
        break;
      case GtSfxuint32_t:
        gt_xfwrite(*(usedptrptr.uint32),sfxmappedrange->sizeofunit,
                   sfxmappedrange->numofunits,outfp);
        sfxmappedrange->usedptrptr = (void**) usedptrptr.uint32;
        gt_free(*(usedptrptr.uint32));
        *(usedptrptr.uint32) = NULL;
        break;
     }
     gt_fa_fclose(outfp);
  }
  
  void gt_Sfxmappedrange_storetmp_ulong(GtSfxmappedrange *sfxmappedrange,
                                        unsigned long **usedptrptr,
                                        bool writable)
  {
    GtSfxStoretype st;
    gt_assert(usedptrptr != NULL);
  
    st.ulong = usedptrptr;
    gt_Sfxmappedrange_storetmp(sfxmappedrange, st, GtSfxunsignedlong, writable);
  }
  
  void gt_Sfxmappedrange_storetmp_uint32(GtSfxmappedrange *sfxmappedrange,
                                         uint32_t **usedptrptr,
                                         bool writable)
  {
    GtSfxStoretype st;
    gt_assert(usedptrptr != NULL);
  
    st.uint32 = usedptrptr;
    gt_Sfxmappedrange_storetmp(sfxmappedrange, st, GtSfxuint32_t, writable);
  }
  
  void gt_Sfxmappedrange_storetmp_bitsequence(GtSfxmappedrange *sfxmappedrange,
                                              GtBitsequence **usedptrptr,
                                              bool writable)
  {
    GtSfxStoretype st;
    gt_assert(usedptrptr != NULL);
  
    st.bs = usedptrptr;
    gt_Sfxmappedrange_storetmp(sfxmappedrange, st, GtSfxGtBitsequence, writable);
  }
  
  void gt_Sfxmappedrange_usetmp(GtSfxmappedrange *sfxmappedrange,
                                const GtStr *tmpfilename,
                                void **usedptrptr,
                                unsigned long numofentries,
                                bool writable)
  {
    gt_assert(sfxmappedrange != NULL);
    sfxmappedrange->ptr = NULL;
    /*gt_assert(usedptrptr != NULL && *usedptrptr == NULL);*/
    sfxmappedrange->usedptrptr = usedptrptr;
    sfxmappedrange->filename = gt_str_clone(tmpfilename);
    sfxmappedrange->writable = writable;
    if (sfxmappedrange->type == GtSfxGtBitsequence)
    {
      sfxmappedrange->numofunits = GT_NUMOFINTSFORBITS(numofentries);
    } else
    {
      sfxmappedrange->numofunits = (size_t) numofentries;
    }
    gt_log_log("use file %s for table %s (%lu units of %lu bytes)",
               gt_str_get(sfxmappedrange->filename),
               gt_str_get(sfxmappedrange->tablename),
               (unsigned long) sfxmappedrange->numofunits,
               (unsigned long) sfxmappedrange->sizeofunit);
    gt_free(*sfxmappedrange->usedptrptr);
    *sfxmappedrange->usedptrptr = NULL;
  }
  
  unsigned long gt_Sfxmappedrange_size_mapped(const GtSfxmappedrange
                                                        *sfxmappedrange,
                                              unsigned long minindex,
                                              unsigned long maxindex)
  {
    gt_assert(sfxmappedrange != NULL);
    if (sfxmappedrange->transformfunc != NULL)
    {
      sfxmappedrange->transformfunc(&minindex,&maxindex,
                                    sfxmappedrange->transformfunc_data);
    }
    if (minindex <= maxindex)
    {
      GtMappedrange lbrange;
  
      gt_Sfxmapped_offset_end(&lbrange,
                              sfxmappedrange->sizeofunit,
                              sfxmappedrange->pagesize,
                              minindex,
                              maxindex);
      return lbrange.mapend - lbrange.mapoffset + 1;
    }
    return 0;
  }
  
  void gt_Sfxmappedrange_unmap(GtSfxmappedrange *sfxmappedrange)
  {
    gt_assert(sfxmappedrange != NULL);
    if (sfxmappedrange->ptr != NULL)
    {
      gt_fa_xmunmap(sfxmappedrange->ptr);
    }
    sfxmappedrange->ptr = 0;
  }
  
  void *gt_Sfxmappedrange_map(GtSfxmappedrange *sfxmappedrange,
                              unsigned long minindex,
                              unsigned long maxindex)
  {
    gt_assert(sfxmappedrange != NULL);
    if (sfxmappedrange->ptr != NULL)
    {
      gt_fa_xmunmap(sfxmappedrange->ptr);
    }
    if (sfxmappedrange->transformfunc != NULL)
    {
      sfxmappedrange->transformfunc(&minindex,&maxindex,
                                    sfxmappedrange->transformfunc_data);
    }
    if (minindex <= maxindex)
    {
      GtMappedrange lbrange;
      unsigned long unitoffset;
      size_t sizeoftable;
  
      gt_Sfxmapped_offset_end(&lbrange,
                              sfxmappedrange->sizeofunit,
                              sfxmappedrange->pagesize,
                              minindex,
                              maxindex);
      sizeoftable = gt_Sfxmappedrange_size_entire(sfxmappedrange);
      gt_log_log("mapped %s[%lu..%lu] for %s (%.1f%% of all)",
                 gt_str_get(sfxmappedrange->tablename),
                 lbrange.mapoffset,
                 lbrange.mapend,
                 sfxmappedrange->writable ? "writing" : "reading",
                 (lbrange.mapend - lbrange.mapoffset + 1
                   >= (unsigned long) sizeoftable)
                      ? 100.0
                      : 100.0 * (lbrange.mapend - lbrange.mapoffset + 1)/
                                 sizeoftable);
      gt_assert(lbrange.mapoffset <= lbrange.mapend);
      gt_assert(lbrange.mapoffset <= minindex * sfxmappedrange->sizeofunit);
      gt_assert(maxindex * sfxmappedrange->sizeofunit <= lbrange.mapend);
      gt_assert(lbrange.mapoffset % sfxmappedrange->pagesize == 0);
      if (sfxmappedrange->writable)
      {
        sfxmappedrange->ptr
          = gt_fa_xmmap_write_range(gt_str_get(sfxmappedrange->filename),
                                    (size_t) (lbrange.mapend-lbrange.mapoffset+1),
                                    (size_t) lbrange.mapoffset);
      } else
      {
        sfxmappedrange->ptr
          = gt_fa_xmmap_read_range (gt_str_get(sfxmappedrange->filename),
                                    (size_t) (lbrange.mapend-lbrange.mapoffset+1),
                                    (size_t) lbrange.mapoffset);
      }
      sfxmappedrange->indexrange_defined = true;
      sfxmappedrange->currentmaxindex = maxindex;
      sfxmappedrange->currentminindex = minindex;
      unitoffset = lbrange.mapoffset / sfxmappedrange->sizeofunit;
      switch (sfxmappedrange->type)
      {
        case GtSfxGtBitsequence:
          return ((GtBitsequence *) sfxmappedrange->ptr) - unitoffset;
        case GtSfxuint32_t:
          return ((uint32_t *) sfxmappedrange->ptr) - unitoffset;
        case GtSfxunsignedlong:
          return ((unsigned long *) sfxmappedrange->ptr) - unitoffset;
        default:
          gt_assert(false);
          break;
      }
      gt_assert(false);
    }
    sfxmappedrange->ptr = NULL;
    sfxmappedrange->indexrange_defined = true;
    sfxmappedrange->currentmaxindex = maxindex;
    sfxmappedrange->currentminindex = minindex;
    return NULL;
  }
  
  void gt_Sfxmappedrange_checkindex(const GtSfxmappedrange *sfxmappedrange,
                                    GT_UNUSED unsigned long idx)
  {
    if (sfxmappedrange->indexrange_defined)
    {
      gt_assert(sfxmappedrange->currentminindex <= idx);
      gt_assert(idx <= sfxmappedrange->currentminindex);
    }
  }
  
  void gt_Sfxmappedrange_delete(GtSfxmappedrange *sfxmappedrange)
  {
    if (sfxmappedrange == NULL)
    {
      return;
    }
    gt_log_log("delete table %s",gt_str_get(sfxmappedrange->tablename));
    gt_fa_xmunmap(sfxmappedrange->ptr);
    sfxmappedrange->ptr = NULL;
    gt_fa_xmunmap(sfxmappedrange->entire);
    sfxmappedrange->entire = NULL;
    if (sfxmappedrange->usedptrptr != NULL)
    {
      *sfxmappedrange->usedptrptr = NULL;
    }
    if (sfxmappedrange->filename != NULL)
    {
      gt_log_log("remove \"%s\"",gt_str_get(sfxmappedrange->filename));
      gt_xunlink(gt_str_get(sfxmappedrange->filename));
    }
    gt_str_delete(sfxmappedrange->tablename);
    gt_str_delete(sfxmappedrange->filename);
    gt_free(sfxmappedrange);
  }
  
  struct GtSfxmappedrangelist
  {
    GtSfxmappedrange **arr;
    unsigned long nextfree, allocated;
  };
  
  GtSfxmappedrangelist *gt_Sfxmappedrangelist_new(void)
  {
    GtSfxmappedrangelist *sfxmrlist = gt_malloc(sizeof (*sfxmrlist));
  
    sfxmrlist->arr = NULL;
    sfxmrlist->nextfree = sfxmrlist->allocated = 0;
    return sfxmrlist;
  }
  
  void gt_Sfxmappedrangelist_add(GtSfxmappedrangelist *sfxmrlist,
                                 GtSfxmappedrange *sfxmappedrange)
  {
    gt_assert(sfxmrlist != NULL);
  
    if (sfxmrlist->nextfree >= sfxmrlist->allocated)
    {
      sfxmrlist->allocated += 4UL;
      sfxmrlist->arr = gt_realloc(sfxmrlist->arr,sizeof (*sfxmrlist->arr) *
                                                 sfxmrlist->allocated);
    }
    sfxmrlist->arr[sfxmrlist->nextfree++] = sfxmappedrange;
  }
  
  unsigned long gt_Sfxmappedrangelist_size_mapped(
                                           const GtSfxmappedrangelist *sfxmrlist,
                                           unsigned long minindex,
                                           unsigned long maxindex)
  {
    if (sfxmrlist == NULL)
    {
      gt_assert(maxindex >= minindex);
      return maxindex - minindex + 1;
    } else
    {
      unsigned long idx, sumsize = 0;
  
      for (idx = 0; idx < sfxmrlist->nextfree; idx++)
      {
        GtSfxmappedrange *sfxmappedrange = sfxmrlist->arr[idx];
        if (sfxmappedrange != NULL)
        {
          /*printf("size_mapped %s %lu %lu => %lu\n",
                      gt_str_get(sfxmappedrange->tablename),
                      minindex,maxindex,
                      gt_Sfxmappedrange_size_mapped(sfxmappedrange,minindex,
                                                    maxindex));*/
          sumsize += gt_Sfxmappedrange_size_mapped(sfxmappedrange,
                                                   minindex,
                                                   maxindex);
        }
      }
      return sumsize;
    }
  }
  
  unsigned long gt_Sfxmappedrangelist_size_entire(
                                           const GtSfxmappedrangelist *sfxmrlist)
  {
    if (sfxmrlist == NULL)
    {
      return 0;
    } else
    {
      unsigned long idx, sumsize = 0;
  
      for (idx = 0; idx < sfxmrlist->nextfree; idx++)
      {
        GtSfxmappedrange *sfxmappedrange = sfxmrlist->arr[idx];
        if (sfxmappedrange != NULL)
        {
          sumsize += gt_Sfxmappedrange_size_entire(sfxmappedrange);
        }
      }
      return sumsize;
    }
  }
  
  void gt_Sfxmappedrangelist_delete(GtSfxmappedrangelist *sfxmrlist)
  {
    if (sfxmrlist != NULL)
    {
      gt_free(sfxmrlist->arr);
      gt_free(sfxmrlist);
    }
  }
  