Pckbuckettable *gt_pckbuckettable_map(const char *indexname,
unsigned int numofchars,
GtError *err)
{
size_t numofbytes;
void *mapptr;
unsigned int maxdepth;
Pckbuckettable *pckbt;
gt_error_check(err);
mapptr = gt_fa_mmap_read_with_suffix(indexname,PCKBUCKETTABLE,
&numofbytes,err);
if (mapptr == NULL)
{
return NULL;
}
maxdepth = (unsigned int) ((unsigned long *) mapptr)[0];
pckbt = pckbuckettable_allocandinittable(numofchars,maxdepth,false);
pckbt->mapptr = mapptr;
pckbt->mbtab[0] = (Mbtab *) (((unsigned long *) mapptr) + 1);
pckbuckettable_settaboffsets(pckbt);
gt_assert(numofbytes ==
sizeof (unsigned long) + sizeof (Mbtab) * pckbt->maxnumofvalues);
return pckbt;
}
Tyrcountinfo *gt_tyrcountinfo_new(const Tyrindex *tyrindex,
const char *tyrindexname,
GtError *err)
{
size_t numofbytes;
void *tmp;
bool haserr = false;
Tyrcountinfo *tyrcountinfo;
gt_error_check(err);
tyrcountinfo = gt_malloc(sizeof *tyrcountinfo);
tyrcountinfo->indexfilename = tyrindexname;
tyrcountinfo->mappedmctfileptr
= gt_fa_mmap_read_with_suffix(tyrindexname,COUNTSSUFFIX,&numofbytes,err);
if (tyrcountinfo->mappedmctfileptr == NULL)
{
tyrcountinfo->smallcounts = NULL;
haserr = true;
} else
{
tyrcountinfo->smallcounts
= (GtUchar *) tyrcountinfo->mappedmctfileptr;
tmp = &tyrcountinfo->smallcounts[tyrindex->numofmers];
tyrcountinfo->largecounts = (Largecount *) tmp;
if (numofbytes < tyrindex->numofmers)
{
gt_error_set(err,"size of file \"%s.%s\" is smaller than minimum size "
""GT_WU"",tyrindexname,COUNTSSUFFIX,
(GtUword) tyrindex->numofmers);
haserr = true;
}
}
if (!haserr && (numofbytes - tyrindex->numofmers) % sizeof (Largecount) != 0)
{
gt_error_set(err,"(numofbytes - numofmers) = "GT_WU
" must be a multiple of "GT_WU,
(GtUword) (numofbytes - tyrindex->numofmers),
(GtUword) sizeof (Largecount));
haserr = true;
}
if (!haserr)
{
tyrcountinfo->numoflargecounts
= (GtUword) (numofbytes - tyrindex->numofmers)/
(GtUword) sizeof (Largecount);
}
if (haserr)
{
if (tyrcountinfo->mappedmctfileptr != NULL)
{
gt_fa_xmunmap(tyrcountinfo->mappedmctfileptr);
tyrcountinfo->mappedmctfileptr = NULL;
}
gt_free(tyrcountinfo);
}
return haserr ? NULL : tyrcountinfo;
}
Tyrindex *gt_tyrindex_new(const char *tyrindexname,GtError *err)
{
bool haserr = false;
size_t numofbytes, rest;
Tyrindex *tyrindex;
gt_error_check(err);
tyrindex = gt_malloc(sizeof *tyrindex);
tyrindex->indexfilename = tyrindexname;
tyrindex->mappedfileptr = gt_fa_mmap_read_with_suffix(tyrindexname,MERSUFFIX,
&numofbytes,err);
if (tyrindex->mappedfileptr == NULL)
{
haserr = true;
}
if (!haserr)
{
tyrindex->mertable = (GtUchar *) tyrindex->mappedfileptr;
rest = sizeof (GtUword) * EXTRAINTEGERS;
if (rest > numofbytes)
{
gt_error_set(err,"index must contain at least "GT_WU" bytes",
(GtUword) rest);
haserr = true;
}
}
if (!haserr)
{
gt_assert(tyrindex->mertable != NULL);
tyrindex->mersize
= gt_decodesingleinteger(tyrindex->mertable + numofbytes - rest);
tyrindex->alphasize
= (unsigned int) gt_decodesingleinteger(tyrindex->mertable +
numofbytes - rest +
sizeof (GtUword));
tyrindex->merbytes = MERBYTES(tyrindex->mersize);
if ((numofbytes - rest) % tyrindex->merbytes != 0)
{
gt_error_set(err,"size of index is "GT_WU
" which is not a multiple of "GT_WU,
(GtUword) (numofbytes - rest),
tyrindex->merbytes);
haserr = true;
}
}
if (!haserr)
{
tyrindex->numofmers = (numofbytes - rest) / tyrindex->merbytes;
gt_assert(tyrindex->mertable != NULL);
if (tyrindex->numofmers == 0)
{
tyrindex->lastmer = tyrindex->mertable - 1;
} else
{
tyrindex->lastmer
= tyrindex->mertable + numofbytes - rest - tyrindex->merbytes;
}
}
if (haserr)
{
if (tyrindex->mappedfileptr != NULL)
{
gt_fa_xmunmap(tyrindex->mappedfileptr);
tyrindex->mappedfileptr = NULL;
}
gt_free(tyrindex);
}
return haserr ? NULL : tyrindex;
}
