static GtRadixsortinfo *gt_radixsort_new(bool pairs,GtUword maxlen)
{
GtRadixsortinfo *radixsortinfo = gt_malloc(sizeof (*radixsortinfo));
radixsortinfo->size = sizeof (*radixsortinfo);
radixsortinfo->rbuf = gt_radixbuffer_new(pairs);
radixsortinfo->size += gt_radixbuffer_size(radixsortinfo->rbuf);
radixsortinfo->pairs = pairs;
radixsortinfo->maxlen = maxlen;
if (maxlen > 0)
{
if (pairs)
{
radixsortinfo->sortspace.ulongpairptr
= gt_malloc(sizeof (*radixsortinfo->sortspace.ulongpairptr) * maxlen);
radixsortinfo->size += sizeof (*radixsortinfo->sortspace.ulongpairptr)
* maxlen;
} else
{
radixsortinfo->sortspace.ulongptr
= gt_malloc(sizeof (*radixsortinfo->sortspace.ulongptr) * maxlen);
radixsortinfo->size += sizeof (*radixsortinfo->sortspace.ulongptr)
* maxlen;
}
}
GT_STACK_INIT(&radixsortinfo->stack,32UL);
radixsortinfo->size += sizeof (radixsortinfo->stack);
#ifdef GT_THREADS_ENABLED
{
const unsigned int threads = GT_THREADS_JOBS;
if (threads > 1U)
{
unsigned int t;
radixsortinfo->lentab
= gt_malloc(sizeof (*radixsortinfo->lentab) * (UINT8_MAX+1));
radixsortinfo->size += sizeof (*radixsortinfo->lentab) * (UINT8_MAX+1);
radixsortinfo->endindexes
= gt_malloc(sizeof (*radixsortinfo->endindexes) * threads);
radixsortinfo->size += sizeof (*radixsortinfo->endindexes) * threads;
radixsortinfo->threadinfo
= gt_malloc(sizeof (*radixsortinfo->threadinfo) * threads);
radixsortinfo->size += sizeof (*radixsortinfo->threadinfo) * threads;
for (t = 0; t < threads; t++)
{
GT_STACK_INIT(&radixsortinfo->threadinfo[t].stack,32UL);
radixsortinfo->size += sizeof (radixsortinfo->threadinfo[t].stack);
radixsortinfo->threadinfo[t].rbuf = gt_radixbuffer_new(pairs);
radixsortinfo->size
+= gt_radixbuffer_size(radixsortinfo->threadinfo[t].rbuf);
}
}
}
#endif
return radixsortinfo;
}
void gt_pck_count_nodes_dfs(const FMindex *index,
GtUword totallength,
unsigned int numofchars)
{
GtStackNodecount stack;
Nodecount root;
Nodecount *current;
Mbtab *tmpmbtab;
GtUword *rangeOccs;
GtUword resize = 128UL; /* TODO DW make this user definable, or dependable
on input data */
GT_STACK_INIT(&stack, resize);
rangeOccs = gt_malloc(sizeof (*rangeOccs) * GT_MULT2(numofchars));
tmpmbtab = gt_malloc(sizeof (*tmpmbtab) * numofchars);
root.lower = 0UL;
root.upper = totallength + 1;
root.leaves = 0UL;
root.branching = 1UL;
root.parentOffset = 0U;
root.visited = false;
root.on_branch = false;
GT_STACK_PUSH(&stack, root);
while (!GT_STACK_ISEMPTY(&stack))
{
current = &(stack.space[stack.nextfree -1]);
if (current->visited)
{
current = &(GT_STACK_POP(&stack));
if GT_STACK_ISEMPTY(&stack)
{
/* TODO DW change to gt_loger_log */
gt_log_log("on root:\n "GT_WU" branching nodes\n "GT_WU" leaves\n",
current->branching, current->leaves);
}
else
{
process_count_node(&stack, current);
}
}
static GtRadixsortinfo *gt_radixsort_new(GtRadixelemtype elemtype,
GtUword maxlen)
{
GtRadixsortinfo *radixsortinfo = gt_malloc(sizeof *radixsortinfo);
radixsortinfo->size = sizeof *radixsortinfo;
radixsortinfo->rbuf = gt_radixbuffer_new(elemtype);
radixsortinfo->size += gt_radixbuffer_size(radixsortinfo->rbuf);
radixsortinfo->elemtype = elemtype;
radixsortinfo->maxlen = maxlen;
if (maxlen > 0)
{
if (elemtype == GtRadixelemtypeGtUwordPair)
{
radixsortinfo->sortspace.ulongpairptr
= gt_malloc(sizeof *radixsortinfo->sortspace.ulongpairptr * maxlen);
radixsortinfo->size += sizeof *radixsortinfo->sortspace.ulongpairptr
* maxlen;
} else
{
if (elemtype == GtRadixelemtypeGtUword)
{
radixsortinfo->sortspace.ulongptr
= gt_malloc(sizeof *radixsortinfo->sortspace.ulongptr * maxlen);
radixsortinfo->size += sizeof *radixsortinfo->sortspace.ulongptr
* maxlen;
} else
{
radixsortinfo->sortspace.uint64keypairptr
= gt_malloc(sizeof *radixsortinfo->sortspace.uint64keypairptr
* maxlen);
radixsortinfo->size
+= sizeof *radixsortinfo->sortspace.uint64keypairptr * maxlen;
}
}
}
GT_STACK_INIT(&radixsortinfo->stack,32UL);
radixsortinfo->size += sizeof radixsortinfo->stack;
#ifdef GT_THREADS_ENABLED
{
const unsigned int threads = GT_THREADS_JOBS;
if (threads > 1U)
{
unsigned int t;
radixsortinfo->lentab
= gt_malloc(sizeof *radixsortinfo->lentab * (UINT8_MAX+1));
radixsortinfo->size += sizeof *radixsortinfo->lentab * (UINT8_MAX+1);
radixsortinfo->endindexes
= gt_malloc(sizeof *radixsortinfo->endindexes * threads);
radixsortinfo->size += sizeof *radixsortinfo->endindexes * threads;
radixsortinfo->threadinfo
= gt_malloc(sizeof *radixsortinfo->threadinfo * threads);
radixsortinfo->size += sizeof *radixsortinfo->threadinfo * threads;
for (t = 0; t < threads; t++)
{
GT_STACK_INIT(&radixsortinfo->threadinfo[t].stack,32UL);
radixsortinfo->size += sizeof (radixsortinfo->threadinfo[t].stack);
radixsortinfo->threadinfo[t].rbuf = gt_radixbuffer_new(elemtype);
radixsortinfo->size
+= gt_radixbuffer_size(radixsortinfo->threadinfo[t].rbuf);
}
}
}
#endif
return radixsortinfo;
}
