static void reheap (c_heap_t *h, size_t root, enum reheap_direction dir)
{
size_t left;
size_t right;
size_t min;
int status;
/* Calculate the positions of the children */
left = (2 * root) + 1;
if (left >= h->list_len)
left = 0;
right = (2 * root) + 2;
if (right >= h->list_len)
right = 0;
/* Check which one of the children is smaller. */
if ((left == 0) && (right == 0))
return;
else if (left == 0)
min = right;
else if (right == 0)
min = left;
else
{
status = h->compare (h->list[left], h->list[right]);
if (status > 0)
min = right;
else
min = left;
}
status = h->compare (h->list[root], h->list[min]);
if (status <= 0)
{
/* We didn't need to change anything, so the rest of the tree should be
* okay now. */
return;
}
else /* if (status > 0) */
{
void *tmp;
tmp = h->list[root];
h->list[root] = h->list[min];
h->list[min] = tmp;
}
if ((dir == DIR_UP) && (root == 0))
return;
if (dir == DIR_UP)
reheap (h, (root - 1) / 2, dir);
else if (dir == DIR_DOWN)
reheap (h, min, dir);
} /* void reheap */
byte * MultipleIndexIterator::getNextListCompressed(int *length, int *size, byte *buffer) {
#if SUPPORT_APPEND_TAIT
*length = currentChunkLength;
*size = currentChunkSize;
byte *result;
if (buffer == NULL)
buffer = currentChunkCompressed;
else {
memcpy(buffer, currentChunkCompressed, currentChunkSize);
free(currentChunkCompressed);
}
currentChunkCompressed = NULL;
prepareNextChunk();
return buffer;
#else
int top = iteratorHeap[0];
if (!iterators[top].hasMoreData) {
*length = 0;
*size = 0;
return NULL;
}
buffer = iterators[top].iterator->getNextListCompressed(length, size, buffer);
listPos++;
reheap();
return buffer;
#endif
} // end of getNextListCompressed(int*, int*, byte*)
int c_heap_insert(c_heap_t *h, void *ptr) {
size_t index;
if ((h == NULL) || (ptr == NULL))
return (-EINVAL);
pthread_mutex_lock(&h->lock);
assert(h->list_len <= h->list_size);
if (h->list_len == h->list_size) {
void **tmp;
tmp = realloc(h->list, (h->list_size + 16) * sizeof(*h->list));
if (tmp == NULL) {
pthread_mutex_unlock(&h->lock);
return (-ENOMEM);
}
h->list = tmp;
h->list_size += 16;
}
/* Insert the new node as a leaf. */
index = h->list_len;
h->list[index] = ptr;
h->list_len++;
/* Reorganize the heap from bottom up. */
reheap(h, /* parent of this node = */ (index - 1) / 2, DIR_UP);
pthread_mutex_unlock(&h->lock);
return (0);
} /* int c_heap_insert */
void heap<T>::modified(T data, bool (*eqCb)(const T&, const T&))
{
signed i = treeArr.indexOf(data, eqCb);
if (i > 0) // assert that i < currSize
{
reheap(i);
}
}
void deheap (void const * heap [], size_t size, int comp (void const *, void const *), void swap (void const *[], size_t, size_t))
{
while (size > 1)
{
swap (heap, 0, --size);
reheap (heap, size, comp, swap);
}
return;
}
size_t saveheap (char * heap [], size_t heapsize, FILE * ofp)
{
while ((heapsize > 0) && (fputs (heap [0], ofp) != EOF))
{
swap ((void *) (heap), 0, -- heapsize);
reheap ((void *) (heap), heapsize, (int (*)(void const *, void const *)) (comp), swap);
free (heap [heapsize]);
}
return (heapsize);
}
T heap<T>::extract()
{
if (0 == currSize)
{
throw std::runtime_error("removing from empty heap");
}
T data = treeArr[0];
swap(treeArr, 0, currSize-1);
g_delete(treeArr[--currSize]);
reheap(0);
return data;
}
bool heap<T>::remove(T data, bool (*eqCb)(const T&, const T&))
{
bool dataRemoved = false;
signed i = treeArr.indexOf(data, eqCb);
if (i > 0) // assert that i < currSize
{
dataRemoved = true;
swap(treeArr, i, currSize);
g_delete(treeArr[--currSize]);
reheap(i);
}
return dataRemoved;
}
void *c_heap_get_root (c_heap_t *h)
{
void *ret = NULL;
if (h == NULL)
return (NULL);
pthread_mutex_lock (&h->lock);
if (h->list_len == 0)
{
pthread_mutex_unlock (&h->lock);
return (NULL);
}
else if (h->list_len == 1)
{
ret = h->list[0];
h->list[0] = NULL;
h->list_len = 0;
}
else /* if (h->list_len > 1) */
{
ret = h->list[0];
h->list[0] = h->list[h->list_len - 1];
h->list[h->list_len - 1] = NULL;
h->list_len--;
reheap (h, /* root = */ 0, DIR_DOWN);
}
/* free some memory */
if ((h->list_len + 32) < h->list_size)
{
void **tmp;
tmp = realloc (h->list, (h->list_len + 16) * sizeof (*h->list));
if (tmp != NULL)
{
h->list = tmp;
h->list_size = h->list_len + 16;
}
}
pthread_mutex_unlock (&h->lock);
return (ret);
} /* void *c_heap_get_root */
offset * MultipleIndexIterator::getNextListUncompressed(int *length, offset *buffer) {
#if SUPPORT_APPEND_TAIT
*length = currentChunkLength;
if (buffer == NULL)
buffer = typed_malloc(offset, currentChunkLength);
memcpy(buffer, currentChunk, currentChunkLength * sizeof(offset));
free(currentChunkCompressed);
currentChunkCompressed = NULL;
prepareNextChunk();
return buffer;
#else
int top = iteratorHeap[0];
if (!iterators[top].hasMoreData) {
*length = 0;
return NULL;
}
offset *result = iterators[top].iterator->getNextListUncompressed(length, buffer);
listPos++;
reheap();
return result;
#endif
} // end of getNextListUncompressed(int*, offset*)
/*
* merge --
* Merge sort a group of files to 'outfile'.
*/
void merge(FILE *infile[], int nfiles, FILE *outfile)
{
char *lineptr[MERGEORDER];
char linebuf[MERGETEXT];
int lbp = 0, nf = 0;
int i, inf;
for (i = 0; i < nfiles; i++) {
if (fgets(&linebuf[lbp], MAXLINE, infile[i]) != NULL) {
lineptr[nf++] = &linebuf[lbp];
lbp += MAXLINE;
}
}
qsort(lineptr, nf, sizeof(lineptr[0]), qcmpstr);
while (nf > 0) {
fputs(lineptr[0], outfile);
inf = (lineptr[0] - linebuf) / MAXLINE;
if (fgets(lineptr[0], MAXLINE, infile[inf]) == NULL) {
lineptr[0] = lineptr[nf-1];
nf--;
}
reheap(lineptr, nf, linebuf);
}
}
static DAZZ_TRACK *merge_tracks(DAZZ_DB *block, int mtop, int64 nsize)
{ DAZZ_TRACK *ntrack;
Event ev[mtop+1];
Event *heap[mtop+2];
int r, mhalf;
int64 *anno;
int *data;
ntrack = (DAZZ_TRACK *) Malloc(sizeof(DAZZ_TRACK),"Allocating merged track");
if (ntrack == NULL)
Clean_Exit(1);
ntrack->name = Strdup("merge","Allocating merged track");
ntrack->anno = anno = (int64 *) Malloc(sizeof(int64)*(block->nreads+1),"Allocating merged track");
ntrack->data = data = (int *) Malloc(sizeof(int)*nsize,"Allocating merged track");
ntrack->size = sizeof(int);
ntrack->next = NULL;
if (anno == NULL || data == NULL || ntrack->name == NULL)
Clean_Exit(1);
{ DAZZ_TRACK *track;
int i;
track = block->tracks;
for (i = 0; i < mtop; i++)
{ ev[i].ano = ((int *) (track->data)) + ((int64 *) (track->anno))[0];
ev[i].out = 1;
heap[i+1] = ev+i;
track = track->next;
}
ev[mtop].idx = INT32_MAX;
heap[mtop+1] = ev+mtop;
}
mhalf = mtop/2;
nsize = 0;
for (r = 0; r < block->nreads; r++)
{ int i, level, hsize;
DAZZ_TRACK *track;
anno[r] = nsize;
track = block->tracks;
for (i = 0; i < mtop; i++)
{ ev[i].end = ((int *) (track->data)) + ((int64 *) (track->anno))[r+1];
if (ev[i].ano < ev[i].end)
ev[i].idx = *(ev[i].ano);
else
ev[i].idx = INT32_MAX;
track = track->next;
}
hsize = mtop;
for (i = mhalf; i > 1; i--)
reheap(i,heap,hsize);
level = 0;
while (1)
{ Event *p;
reheap(1,heap,hsize);
p = heap[1];
if (p->idx == INT32_MAX) break;
p->out = 1-p->out;
if (p->out)
{ level -= 1;
if (level == 0)
data[nsize++] = p->idx;
}
else
{ if (level == 0)
data[nsize++] = p->idx;
level += 1;
}
p->ano += 1;
if (p->ano >= p->end)
p->idx = INT32_MAX;
else
p->idx = *(p->ano);
}
}
anno[r] = nsize;
return (ntrack);
}
static int64 merge_size(DAZZ_DB *block, int mtop)
{ Event ev[mtop+1];
Event *heap[mtop+2];
int r, mhalf;
int64 nsize;
{ DAZZ_TRACK *track;
int i;
track = block->tracks;
for (i = 0; i < mtop; i++)
{ ev[i].ano = ((int *) (track->data)) + ((int64 *) (track->anno))[0];
ev[i].out = 1;
heap[i+1] = ev+i;
track = track->next;
}
ev[mtop].idx = INT32_MAX;
heap[mtop+1] = ev+mtop;
}
mhalf = mtop/2;
nsize = 0;
for (r = 0; r < block->nreads; r++)
{ int i, level, hsize;
DAZZ_TRACK *track;
track = block->tracks;
for (i = 0; i < mtop; i++)
{ ev[i].end = ((int *) (track->data)) + ((int64 *) (track->anno))[r+1];
if (ev[i].ano < ev[i].end)
ev[i].idx = *(ev[i].ano);
else
ev[i].idx = INT32_MAX;
track = track->next;
}
hsize = mtop;
for (i = mhalf; i > 1; i--)
reheap(i,heap,hsize);
level = 0;
while (1)
{ Event *p;
reheap(1,heap,hsize);
p = heap[1];
if (p->idx == INT32_MAX) break;
p->out = 1-p->out;
if (p->out)
{ level -= 1;
if (level == 0)
nsize += 1;
}
else
{ if (level == 0)
nsize += 1;
level += 1;
}
p->ano += 1;
if (p->ano >= p->end)
p->idx = INT32_MAX;
else
p->idx = *(p->ano);
}
}
return (nsize);
}
void heap<T>::insert(T data)
{
T buffer;
treeArr[currSize++] = data;
reheap(currSize-1);
}