static GtUword determinefmindexsize (const Fmindex *fm,
const GtSpecialcharinfo
*specialcharinfo,
unsigned int suffixlength,
bool storeindexpos)
{
uint64_t sumsize = 0;
sumsize +=
(uint64_t) sizeof (GtUword) * (uint64_t) TFREQSIZE(fm->mapsize);
sumsize += (uint64_t) sizeof (GtUword) *
(uint64_t) SUPERBFREQSIZE(fm->mapsize,fm->nofsuperblocks);
if (storeindexpos)
{
sumsize += (uint64_t) sizeof (GtUword) *
(uint64_t) MARKPOSTABLELENGTH(fm->bwtlength,fm->markdist);
}
if (suffixlength > 0)
{
sumsize += (uint64_t) sizeof (GtUlongBound) * (uint64_t) fm->numofcodes;
}
if (storeindexpos)
{
sumsize += (uint64_t) sizeof (GtPairBwtidx) *
(uint64_t) gt_determinenumberofspecialstostore(specialcharinfo);
}
sumsize += (uint64_t) sizeof (GtUchar) *
(uint64_t) BFREQSIZE(fm->mapsize,fm->nofblocks);
return CALLCASTFUNC(uint64_t,unsigned_long,sumsize);
}
int gt_mapfmindex (Fmindex *fmindex,const char *indexname,
GtLogger *logger,GtError *err)
{
FILE *fpin = NULL;
bool haserr = false, storeindexpos = true;
GtSpecialcharinfo specialcharinfo;
gt_error_check(err);
fmindex->mappedptr = NULL;
fmindex->bwtformatching = NULL;
fmindex->alphabet = NULL;
fpin = gt_fa_fopen_with_suffix(indexname,FMASCIIFILESUFFIX,"rb",err);
if (fpin == NULL)
{
haserr = true;
}
if (!haserr)
{
if (scanfmafileviafileptr(fmindex,
&specialcharinfo,
&storeindexpos,
indexname,
fpin,
logger,
err) != 0)
{
haserr = true;
}
}
gt_fa_xfclose(fpin);
if (!haserr)
{
fmindex->bwtformatching = mapbwtencoding(indexname,logger,err);
if (fmindex->bwtformatching == NULL)
{
haserr = true;
}
}
if (!haserr)
{
fmindex->specpos.nextfreeGtPairBwtidx
= (unsigned long) gt_determinenumberofspecialstostore(&specialcharinfo);
fmindex->specpos.spaceGtPairBwtidx = NULL;
fmindex->specpos.allocatedGtPairBwtidx = 0;
fmindex->alphabet = gt_alphabet_ref(
gt_encseq_alphabet(fmindex->bwtformatching));
if (fmindex->alphabet == NULL)
{
haserr = true;
}
}
if (!haserr)
{
GtStr *tmpfilename;
gt_computefmkeyvalues (fmindex,
&specialcharinfo,
fmindex->bwtlength,
fmindex->log2bsize,
fmindex->log2markdist,
gt_alphabet_num_of_chars(fmindex->alphabet),
fmindex->suffixlength,
storeindexpos);
tmpfilename = gt_str_new_cstr(indexname);
gt_str_append_cstr(tmpfilename,FMDATAFILESUFFIX);
if (gt_fillfmmapspecstartptr(fmindex,storeindexpos,tmpfilename,err) != 0)
{
haserr = true;
}
gt_str_delete(tmpfilename);
}
if (haserr)
{
gt_freefmindex(fmindex);
}
return haserr ? -1 : 0;
}
