static void seekCoreMultiplexer(Multiplexer * multi, const char * chrom, int start, int finish) {
int i;
multi->done = false;
for (i=0; i<multi->count; i++)
seek(multi->iters[i], chrom, start, finish);
fh_deleteheap(multi->starts);
fh_deleteheap(multi->finishes);
multi->starts = fh_makeheap();
multi->finishes = fh_makeheap();
multi->inplay_count = 0;
popMultiplexer(multi);
}
void GRAPHpfs(Tree T, int s, int *st, double *wt){
int v, w;
link t;
struct fibheap *pq;
pq = fh_makeheap();
fh_setcmp(pq, wt_cmp);
/* PQinit(); */
/* priority = wt; */
for (v = 0; v < G->V; v++) {
st[v] = -1;
wt[v] = Inf;
PQinsert(v);
}
wt[s] = 0.0;
PQdec(s);
while (!PQempty())
if (wt[v = PQdelmin()] != maxWT)
for (t = G->adj[v]; t != NULL; t = t->next)
if (P < wt[w = t->v]){
wt[w] = P;
PQdec(w);
st[w] = v;
}
}
void make_graph (const char* fn)
{
FILE *fw = mustOpen(fn, "w");
int i, j, cnt;
int rec_num = 0;
if (po->COL_WIDTH == 2) po->COL_WIDTH = MAX(cols/20, 2);
/* edge_ptr describe edges */
AllocArray(edge_list, HEAP_SIZE);
/* Allocating heap structure */
struct fibheap *heap;
heap = fh_makeheap();
fh_setcmp(heap, edge_cmpr);
/* Generating seed list and push into heap */
progress("Generating seed list (minimum weight %d)", po->COL_WIDTH);
Edge __cur_min = {0, 0, po->COL_WIDTH};
Edge *_cur_min = &__cur_min;
Edge **cur_min = & _cur_min;
/* iterate over all genes to retrieve all edges */
for (i = 0; i < rows; i++)
{
for (j = i+1; j < rows; j++)
{
cnt = str_intersect_r(arr_c[i], arr_c[j]);
if (cnt < (*cur_min)->score) continue;
AllocVar(edge_ptr);
edge_ptr -> gene_one = i;
edge_ptr -> gene_two = j;
edge_ptr -> score = cnt;
fh_insert_fixed(heap, edge_ptr, cur_min);
rec_num++;
}
}
/*rec_num = heap->fh_n;*/
if (rec_num == 0)
errAbort("Not enough overlap between genes");
/* sort the seeds */
uglyTime("%d seeds generated", rec_num);
ReAllocArray(edge_list, rec_num);
fh_dump(heap, edge_list);
/* bi-clustering */
int n_blocks = 0;
progress("Clustering started");
n_blocks = cluster(fw, edge_list, rec_num);
uglyTime("%d clusters are written to %s", n_blocks, fn);
/* clean up */
for (i=0; i<rec_num; i++)
free(edge_list[i]);
free(edge_list);
}
void perform_front_propagation_2d(T_callback_intert_node callback_insert_node)
{
// create the Fibonacci heap
struct fibheap* open_heap = fh_makeheap();
fh_setcmp(open_heap, compare_points);
double h = 1.0/n;
// initialize points
for( int i=0; i<n; ++i )
for( int j=0; j<p; ++j )
{
D_(i,j) = GW_INFINITE;
S_(i,j) = kFar;
Q_(i,j) = -1;
}
// record all the points
heap_pool = new fibheap_el*[n*p];
memset( heap_pool, NULL, n*p*sizeof(fibheap_el*) );
// inialize open list
point_list existing_points;
for( int k=0; k<nb_start_points; ++k )
{
int i = (int) start_points_(0,k);
int j = (int) start_points_(1,k);
if( D_( i,j )==0 )
ERROR_MSG("start_points should not contain duplicates.");
point* pt = new point( i,j );
existing_points.push_back( pt ); // for deleting at the end
heap_pool_(i,j) = fh_insert( open_heap, pt ); // add to heap
if( values==NULL )
D_( i,j ) = 0;
else
D_( i,j ) = values[k];
S_( i,j ) = kOpen;
Q_(i,j) = k;
}
// perform the front propagation
int num_iter = 0;
bool stop_iteration = GW_False;
while( !fh_isempty(open_heap) && num_iter<nb_iter_max && !stop_iteration )
{
num_iter++;
// current point
point& cur_point = * ((point*) fh_extractmin( open_heap ));
int i = cur_point.i;
int j = cur_point.j;
heap_pool_(i,j) = NULL;
S_(i,j) = kDead;
stop_iteration = end_points_reached(i,j);
/*
char msg[200];
sprintf(msg, "Cool %f", Q_(i,j) );
WARN_MSG( msg );
*/
CHECK_HEAP;
// recurse on each neighbor
int nei_i[4] = {i+1,i,i-1,i};
int nei_j[4] = {j,j+1,j,j-1};
for( int k=0; k<4; ++k )
{
int ii = nei_i[k];
int jj = nei_j[k];
bool bInsert = true;
if( callback_insert_node!=NULL )
bInsert = callback_insert_node(i,j,ii,jj);
// check that the contraint distance map is ok
if( ii>=0 && jj>=0 && ii<n && jj<p && bInsert )
{
double P = h/W_(ii,jj);
// compute its neighboring values
double a1 = GW_INFINITE;
int k1 = -1;
if( ii<n-1 )
{
bool bParticipate = true;
if( callback_insert_node!=NULL )
bParticipate = callback_insert_node(ii,jj,ii+1,jj);
if( bParticipate )
{
a1 = D_(ii+1,jj);
k1 = Q_(ii+1,jj);
}
}
if( ii>0 )
{
bool bParticipate = true;
if( callback_insert_node!=NULL )
bParticipate = callback_insert_node(ii,jj,ii-1,jj);
if( bParticipate )
{
if( D_(ii-1,jj)<a1 )
k1 = Q_(ii-1,jj);
a1 = GW_MIN( a1, D_(ii-1,jj) );
}
}
double a2 = GW_INFINITE;
int k2 = -1;
if( jj<p-1 )
{
bool bParticipate = true;
if( callback_insert_node!=NULL )
bParticipate = callback_insert_node(ii,jj,ii,jj+1);
if( bParticipate )
{
a2 = D_(ii,jj+1);
k2 = Q_(ii,jj+1);
}
}
if( jj>0 )
{
bool bParticipate = true;
if( callback_insert_node!=NULL )
bParticipate = callback_insert_node(ii,jj,ii,jj-1);
if( bParticipate )
{
if( D_(ii,jj-1)<a2 )
k2 = Q_(ii,jj-1);
a2 = GW_MIN( a2, D_(ii,jj-1) );
}
}
if( a1>a2 ) // swap so that a1<a2
{
double tmp = a1; a1 = a2; a2 = tmp;
int tmpi = k1; k1 = k2; k2 = tmpi;
}
// update its distance
// now the equation is (a-a1)^2+(a-a2)^2 = P, with a >= a2 >= a1.
double A1 = 0;
if( P*P > (a2-a1)*(a2-a1) )
{
double delta = 2*P*P-(a2-a1)*(a2-a1);
A1 = (a1+a2+sqrt(delta))/2.0;
}
else
A1 = a1 + P;
if( ((int) S_(ii,jj)) == kDead )
{
// check if action has change. Should not happen for FM
// if( A1<D_(ii,jj) )
// WARN_MSG("The update is not monotone");
#if 1
if( A1<D_(ii,jj) ) // should not happen for FM
{
D_(ii,jj) = A1;
// update the value of the closest starting point
//if( GW_ABS(a1-A1)<GW_ABS(a2-A1) && k1>=0 )
Q_(ii,jj) = k1;
//else
// Q_(ii,jj) = k2;
//Q_(ii,jj) = Q_(i,j);
}
#endif
}
else if( ((int) S_(ii,jj)) == kOpen )
{
// check if action has change.
if( A1<D_(ii,jj) )
{
D_(ii,jj) = A1;
// update the value of the closest starting point
//if( GW_ABS(a1-A1)<GW_ABS(a2-A1) && k1>=0 )
Q_(ii,jj) = k1;
//else
// Q_(ii,jj) = k2;
//Q_(ii,jj) = Q_(i,j);
// Modify the value in the heap
fibheap_el* cur_el = heap_pool_(ii,jj);
if( cur_el!=NULL )
fh_replacedata( open_heap, cur_el, cur_el->fhe_data ); // use same data for update
else
ERROR_MSG("Error in heap pool allocation.");
}
}
else if( ((int) S_(ii,jj)) == kFar )
{
if( D_(ii,jj)!=GW_INFINITE )
ERROR_MSG("Distance must be initialized to Inf");
if( L==NULL || A1<=L_(ii,jj) )
{
S_(ii,jj) = kOpen;
// distance must have change.
D_(ii,jj) = A1;
// update the value of the closest starting point
//if( GW_ABS(a1-A1)<GW_ABS(a2-A1) && k1>=0 )
Q_(ii,jj) = k1;
//else
// Q_(ii,jj) = k2;
//Q_(ii,jj) = Q_(i,j);
// add to open list
point* pt = new point(ii,jj);
existing_points.push_back( pt );
heap_pool_(ii,jj) = fh_insert( open_heap, pt ); // add to heap
}
}
else
ERROR_MSG("Unkwnown state.");
} // end switch
} // end for
} // end while
// char msg[200];
// sprintf(msg, "Cool %f", Q_(100,100) );
// WARN_MSG( msg );
// free heap
fh_deleteheap(open_heap);
// free point pool
for( point_list::iterator it = existing_points.begin(); it!=existing_points.end(); ++it )
GW_DELETE( *it );
// free fibheap pool
GW_DELETEARRAY(heap_pool);
}
int
main(void)
{
#if !TESTCASE
struct fibheap_el *w;
#else
int e, j, k;
#endif
struct fibheap *a;
int i, x;
a = fh_makeheap();
fh_setcmp(a, cmp);
srandom(time(NULL));
#if TESTCASE
#if VERBOSE
printf("inserting: ");
#endif
e = 0;
for (i = 0; i < COUNT; i++) {
#if VERBOSE
if (i)
printf(", ");
#endif
fh_insert(a, (void *)(x = random()/10));
#if VERBOSE
printf("%d", x);
#endif
if (i - e > DIF) {
k = random() % MAXEXT;
for (j = 0; j < k; j++, e++)
printf("throwing: %d\n", (int)fh_extractmin(a));
}
}
#if VERBOSE
printf("\nremaining: %d\n", COUNT - e);
printf("extracting: ");
#endif
for (i = 0; i < COUNT - e; i++) {
#if VERBOSE
if (i)
printf(", ");
printf("%d", (int)fh_extractmin(a));
#else
fh_extractmin(a);
#endif
}
#if VERBOSE
printf("\n");
#endif
if ((int)fh_extractmin(a) == 0)
printf("heap empty!\n");
else {
printf("heap not empty! ERROR!\n");
exit(1);
}
#else
w = fh_insert(a, (void *)6);
printf("adding: %d\n", 6);
fh_insert(a, (void *)9);
printf("adding: %d\n", 9);
fh_insert(a, (void *)1);
printf("adding: %d\n", 1);
for(i = 0; i < 5; i++) {
x = random()/10000;
printf("adding: %d\n", x);
fh_insert(a, (void *)x);
}
fh_insert(a, (void *)4);
printf("adding: %d\n", 4);
fh_insert(a, (void *)8);
printf("adding: %d\n", 8);
printf("first: %d\n", (int)fh_extractmin(a));
printf("deleting: %d\n", (int)fh_delete(a, w));
printf("first: %d\n", (int)fh_extractmin(a));
printf("first: %d\n", (int)fh_extractmin(a));
printf("first: %d\n", (int)fh_extractmin(a));
printf("first: %d\n", (int)fh_extractmin(a));
printf("first: %d\n", (int)fh_extractmin(a));
for(i = 0; i < 5; i++) {
x = random()/10000;
printf("adding: %d\n", x);
fh_insert(a, (void *)x);
}
printf("first: %d\n", (int)fh_extractmin(a));
printf("first: %d\n", (int)fh_extractmin(a));
printf("first: %d\n", (int)fh_extractmin(a));
printf("first: %d\n", (int)fh_extractmin(a));
printf("first: %d\n", (int)fh_extractmin(a));
#endif
fh_deleteheap(a);
return 0;
}
void perform_dijkstra_propagation(T_callback_insert_node callback_insert_node = NULL)
{
// create the Fibonacci heap
struct fibheap* open_heap = fh_makeheap();
fh_setcmp(open_heap, compare_points);
// initialize points
for( int i=0; i<n; ++i )
{
D[i] = GW_INFINITE;
S[i] = kFar;
}
// record all the points
heap_pool = new fibheap_el*[n];
memset( heap_pool, NULL, n*sizeof(fibheap_el*) );
// inialize open list
for( int k=0; k<nb_start_points; ++k )
{
int i = (int) start_points[k];
if( D[i]==0 )
mexErrMsgTxt("start_points should not contain duplicates.");
heap_pool[i] = fh_insert( open_heap, (void*) i ); // add to heap
D[i] = 0;
S[i] = kOpen;
}
// perform the front propagation
int num_iter = 0;
bool stop_iteration = GW_False;
while( !fh_isempty(open_heap) && num_iter<nb_iter_max && !stop_iteration )
{
num_iter++;
// current point
int i = (int) fh_extractmin( open_heap );
heap_pool[i] = NULL;
S[i] = kDead;
stop_iteration = end_points_reached(i);
CHECK_HEAP;
// index in irs[jcs[k]]...irs[jcs[k+1]-1] are the node connected to node k
// values are W[jcs[k]]...W[jcs[k]-1]
// recurse on each neighbor of i
for( int k=jcs[i]; k<jcs[i+1]; ++k )
{
int ii = irs[k];
double P = W[k]; // graph weight
bool bInsert = true;
if( callback_insert_node!=NULL )
bInsert = callback_insert_node(ii,ii);
if( ii>=0 && ii<n && bInsert )
{
// compute its neighboring values
double a1 = D[i] + P;
if( ((int) S[ii]) == kDead )
{
// check if action has change. Should not happen for Dijkstra
if( a1<D[ii] )
mexWarnMsgTxt("The update is not monotone");
#if 1
if( a1<D[ii] ) // should not happen for FM
D[ii] = a1;
#endif
}
else if( ((int) S[ii]) == kOpen )
{
// check if action has change.
if( a1<D[ii] )
{
D[ii] = a1;
// Modify the value in the heap
fibheap_el* cur_el = heap_pool[ii];
if( cur_el!=NULL )
fh_replacedata( open_heap, cur_el, cur_el->fhe_data ); // use same data for update
else
mexErrMsgTxt("Error in heap pool allocation.");
}
}
else if( ((int) S[ii]) == kFar )
{
if( D[ii]!=GW_INFINITE )
mexErrMsgTxt("Distance must be initialized to Inf");
S[ii] = kOpen;
// distance must have change.
D[ii] = a1;
// add to open list
heap_pool[ii] = fh_insert( open_heap, (void*) ii ); // add to heap
}
else
mexErrMsgTxt("Unkwnown state.");
} // end switch
} // end for
} // end while
// free heap
fh_deleteheap(open_heap);
// free fibheap pool
GW_DELETEARRAY(heap_pool);
}
