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 = "GT_WU" != "
GT_WU" = expected size",
gt_str_get(sfxmappedrange->filename), (GtUword) mappedsize,
(GtUword) gt_Sfxmappedrange_size_entire(sfxmappedrange));
gt_fa_xmunmap(sfxmappedrange->entire);
sfxmappedrange->entire = NULL;
return NULL;
}
gt_log_log("map %s completely ("GT_WU" units of size %u)",
gt_str_get(sfxmappedrange->tablename),
(GtUword) sfxmappedrange->numofunits,
(unsigned int) sfxmappedrange->sizeofunit);
return sfxmappedrange->entire;
}
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);
}
void *genericmaponlytable(const GtStr *indexname,const char *suffix,
size_t *numofbytes,GtError *err)
{
GtStr *tmpfilename;
void *ptr;
bool haserr = false;
gt_error_check(err);
tmpfilename = gt_str_clone(indexname);
gt_str_append_cstr(tmpfilename,suffix);
ptr = gt_fa_mmap_read(gt_str_get(tmpfilename),numofbytes);
if (ptr == NULL)
{
gt_error_set(err,"cannot map file \"%s\": %s",gt_str_get(tmpfilename),
strerror(errno));
haserr = true;
}
gt_str_delete(tmpfilename);
return haserr ? NULL : ptr;
}
int gt_mapspec_read(GtMapspecSetupFunc setup, void *data,
const char *filename, GtUword expectedsize,
void **mapped, GtError *err)
{
void *mapptr;
uint64_t expectedaccordingtomapspec;
GtUword byteoffset = 0;
size_t numofbytes;
GtMapspec *ms = gt_malloc(sizeof (GtMapspec));
GtMapspecification *mapspecptr;
int had_err = 0;
GtUword totalpadunits = 0;
gt_error_check(err);
GT_INITARRAY(&ms->mapspectable, GtMapspecification);
setup(ms, data, false);
mapptr = gt_fa_mmap_read(filename, &numofbytes, err);
if (mapptr == NULL)
{
had_err = -1;
}
*mapped = mapptr;
if (!had_err)
{
if (assigncorrecttype(ms->mapspectable.spaceGtMapspecification,
mapptr,0,err) != 0)
{
had_err = -1;
}
}
if (!had_err)
{
expectedaccordingtomapspec =
detexpectedaccordingtomapspec(&ms->mapspectable);
if (expectedaccordingtomapspec != (uint64_t) numofbytes)
{
gt_error_set(err, GT_WU " bytes read from %s, but " Formatuint64_t
" expected",
(GtUword) numofbytes,
filename,
PRINTuint64_tcast(expectedaccordingtomapspec));
had_err = -1;
}
}
if (!had_err)
{
mapspecptr = ms->mapspectable.spaceGtMapspecification;
gt_assert(mapspecptr != NULL);
byteoffset = CALLCASTFUNC(uint64_t,unsigned_long,
(uint64_t) (mapspecptr->sizeofunit *
mapspecptr->numofunits));
if (byteoffset % (GtUword) GT_WORDSIZE_INBYTES > 0)
{
size_t padunits
= GT_WORDSIZE_INBYTES - (byteoffset % GT_WORDSIZE_INBYTES);
byteoffset += (GtUword) padunits;
totalpadunits += (GtUword) padunits;
}
for (mapspecptr++;
mapspecptr < ms->mapspectable.spaceGtMapspecification +
ms->mapspectable.nextfreeGtMapspecification; mapspecptr++)
{
if (assigncorrecttype(mapspecptr,mapptr,byteoffset,err) != 0)
{
had_err = -1;
break;
}
byteoffset = CALLCASTFUNC(uint64_t,unsigned_long,
(uint64_t) (byteoffset +
mapspecptr->sizeofunit *
mapspecptr->numofunits));
if (byteoffset % (GtUword) GT_WORDSIZE_INBYTES > 0)
{
size_t padunits
= GT_WORDSIZE_INBYTES - (byteoffset % GT_WORDSIZE_INBYTES);
byteoffset += (GtUword) padunits;
totalpadunits += (GtUword) padunits;
}
}
}
if (!had_err)
{
if (expectedsize + totalpadunits != byteoffset)
{
gt_error_set(err,"mapping: expected file size is "GT_WU" bytes, "
"but file has "GT_WU" bytes",
expectedsize,byteoffset);
had_err = -1;
}
}
GT_FREEARRAY(&ms->mapspectable,GtMapspecification);
gt_free(ms);
return had_err;
}
