/**
* returns:
* - CLAIM_FIRST : if we initialized the state
* - CLAIM_FOUND : if the state is LIVE and we have visited its SCC before
* - CLAIM_SUCCESS : if the state is LIVE and we have not yet visited its SCC
* - CLAIM_DEAD : if the state is part of a completed SCC
*/
char
uf_make_claim (const uf_t *uf, ref_t state, size_t worker)
{
HREassert (worker < WORKER_BITS);
sz_w w_id = 1ULL << worker;
ref_t f = uf_find (uf, state);
sz_w orig_pset;
// is the state dead?
if (atomic_read (&uf->array[f].uf_status) == UF_DEAD)
return CLAIM_DEAD;
// did we previously explore a state in this SCC?
if ( (atomic_read (&uf->array[f].p_set) & w_id ) != 0) {
return CLAIM_FOUND;
// NB: cycle is possibly missed (in case f got updated)
// - however, next iteration should detect this
}
// Add our worker ID to the set, and ensure it is the UF representative
orig_pset = fetch_or (&uf->array[f].p_set, w_id);
while ( atomic_read (&uf->array[f].parent) != 0 ) {
f = uf_find (uf, f);
fetch_or (&uf->array[f].p_set, w_id);
}
if (orig_pset == 0ULL)
return CLAIM_FIRST;
else
return CLAIM_SUCCESS;
}
/** Function update_uf()
* Given fragment IDs of the same cluster, update the union find
* structure [uf_clust] to reflect this information
*/
void update_uf (ivec_t& uf_clst, const ivec_t& clusters) {
int sz = clusters.size ();
for (int i = 0; i < sz - 1; ++ i) {
for (int j = i + 1; j < sz; ++ j) {
int fragID_i = clusters[i],
fragID_j = clusters[j];
int root_i = uf_find (fragID_i, uf_clst),
root_j = uf_find (fragID_j, uf_clst);
uf_clst[root_j] = root_i;
}
}
} // update_uf
/**
* @brief Unites two components.
* @details Unites the compoments the nodes `u` and `v` belong to.
* @param uf Pointer to initialized uf data structure.
* @param u Node that belongs to the first component.
* @param v Node that belongs to the second component.
*/
void uf_union(uf_t *uf, uf_node_t u, uf_node_t v)
{
if(uf == NULL)
{
fprintf(stderr, "Error: null pointer in uf_union\n");
exit(0);
}
u = uf_find(uf, u);
v = uf_find(uf, v);
if(u != v)
uf->parents[u] = v;
}
/*合并包含两元素p和q的树集合*/
void uf_union(uf_t *t,int p,int q){
int r1=uf_find(t,p);
int r2=uf_find(t,q); //返回的是索引下标，而不是id值
if(r1==r2) return; //已在同一集合内，无需再合并
/*id值作为负数时，它的相反数表示该树中结点的个数*/
if(t->id[r1] > t->id[r2]){ //r2作为根
t->id[r2] += t->id[r1];
t->id[r1]=r2;
} else {
t->id[r1] += t->id[r2];
t->id[r2]=r1;
}
t->count--;
}
void uf_union(int a, int b, uf &in)
{
a = uf_find(a, in);
b = uf_find(b, in);
if (a == b)
return;
if (in[a].second < in[b].second)
in[a].first = b;
else if (in[a].second > in[b].second)
in[b].first = a;
else
{
in[a].first = b;
in[b].second++;
}
}
int uf_find(int loc, uf &in)
{
if (in[loc].first == loc)
return loc;
in[loc].first = uf_find(in[loc].first, in);
return in[loc].first;
}
graph kruskal(graph G, float (*pesoArco )(void *)) {
int nNodes = graphCountNodes(G);
graph GF = graphInit(nNodes, GRAPH_IS_NOT_ORIENTED); // e gli orientati??
uf_handler uf = uf_init(graphGetMaxNodes(G));
archInfo arco;
coda allArcs=graphGetAllArchs(G);
heap archHeap=heapInit(nNodes, pesoArco, HEAP_GET_MIN);
while ((arco=codaGet(allArcs))!=NULL) {
heapInsert(archHeap, arco);
}
int from, to;
while ((arco= heapExtract(archHeap))!=NULL) {
from=arco->fromNode;
to= arco->toNode;
if (uf_find(uf,from , to)) {
uf_unionFind(uf, from, to);
graphAddNode(GF, from, arco->fromInfo);
graphAddNode(GF, to, arco->toInfo);
graphAddArch(GF, from, to, arco->archInfo);
}
}
return GF;
}
/**
* returns whether or not a and b reside in the same UF set
*/
bool
uf_sameset (const uf_t *uf, ref_t a, ref_t b)
{
// TODO: try to improve performance (if necessary)
ref_t a_r = uf_find (uf, a);
ref_t b_r = uf_find (uf, b);
// return true if the representatives are equal
if (a_r == b_r)
return 1;
// return false if the parent for a has not been updated
if (atomic_read (&uf->array[a_r].parent) == 0)
return 0;
// otherwise retry
else
return uf_sameset (uf, a_r, b_r);
}
// Returns the new leader (uf_name)
// Stupid question: Is there any problems that arise
// when uf_union is called multiple times on the same objects?
// I don't think so, right?
uf_name uf_union(uf_object *obj1, uf_object *obj2) {
uf_name class1 = uf_find(obj1);
uf_name class2 = uf_find(obj2);
// Union-by-rank:
// If class1 == class2, then obj1 and obj2 are already
// in the same set so don't do anything! (Is this correct?)
if (class1 == class2) {
return class1;
}
if(class1->rank < class2->rank) {
class1->parent = class2;
return class2;
}
else {
class2->parent = class1;
if(class1->rank == class2->rank) {
(class1->rank)++;
}
return class1;
}
}
/**
* set the UF status for the representative of state to DEAD
*/
bool
uf_mark_dead (const uf_t *uf, ref_t state)
{
bool result = false;
ref_t f = uf_find (uf, state);
uf_status status = atomic_read (&uf->array[f].uf_status);
while ( status != UF_DEAD ) {
if (status == UF_LIVE)
result = cas (&uf->array[f].uf_status, UF_LIVE, UF_DEAD);
status = atomic_read (&uf->array[f].uf_status);
}
HREassert (atomic_read (&uf->array[f].parent) == 0,
"the parent of a DEAD representative should not change");
HREassert (uf_is_dead (uf, state), "state should be dead");
return result;
}
/**
* returns the representative for the UF set
*/
ref_t
uf_find (const uf_t *uf, ref_t state)
{
//HREassert (state != 0);
// recursively find and update the parent (path compression)
ref_t parent = atomic_read (&uf->array[state].parent);
ref_t root;
if (parent == 0)
return state;
root = uf_find (uf, parent);
if (root != parent)
atomic_write (&uf->array[state].parent, root);
return root;
}
/**
* unites the acceptance set of the uf representative with acc (via logical OR)
* returns the new acceptance set for the uf representative
*/
uint32_t
uf_add_acc (const uf_t *uf, ref_t state, uint32_t acc)
{
// just return the acceptance set if nothing is added
if (acc == 0)
return uf_get_acc (uf, state);
ref_t r;
uint32_t r_acc;
do {
r = uf_find (uf, state);
r_acc = atomic_read (&uf->array[r].acc_set);
// only unite if it updates the acceptance set
if ( (r_acc | acc) == r_acc) return r_acc;
// update!
r_acc = or_fetch (&uf->array[r].acc_set, acc);
} while (atomic_read (&uf->array[r].parent) != 0);
return r_acc;
}
uint32_t
uf_get_acc (const uf_t *uf, ref_t state)
{
ref_t r = uf_find (uf, state);
return atomic_read (&uf->array[r].acc_set);
}
/**
* (return == 1) ==> ensures DEAD (we cannot ensure a non-DEAD state)
*/
bool
uf_is_dead (const uf_t *uf, ref_t state)
{
ref_t f = uf_find (uf, state);
return ( atomic_read (&uf->array[f].uf_status) == UF_DEAD );
}
/**
* unites two sets and ensures that their cyclic lists are combined to one list
*/
bool
uf_union (const uf_t *uf, ref_t a, ref_t b)
{
ref_t a_r, b_r, a_l, b_l, a_n, b_n, r, q;
sz_w q_w, r_w;
while ( 1 ) {
a_r = uf_find (uf, a);
b_r = uf_find (uf, b);
// find the representatives
if (a_r == b_r) {
return 0;
}
// decide on the new root (deterministically)
// take the highest index as root
r = a_r;
q = b_r;
if (a_r < b_r) {
r = b_r;
q = a_r;
}
// lock the non-root
if ( !uf_lock_uf (uf, q) )
continue;
break;
}
// lock the list entries
if ( !uf_lock_list (uf, a, &a_l) ) {
// HREassert ( uf_is_dead(uf, a) && uf_sameset(uf, a, b) );
return 0;
}
if ( !uf_lock_list (uf, b, &b_l) ) {
// HREassert ( uf_is_dead(uf, b) && uf_sameset(uf, a, b) );
uf_unlock_list (uf, a_l);
return 0;
}
// swap the list entries
a_n = atomic_read (&uf->array[a_l].list_next);
b_n = atomic_read (&uf->array[b_l].list_next);
if (a_n == 0) // singleton
a_n = a_l;
if (b_n == 0) // singleton
b_n = b_l;
atomic_write (&uf->array[a_l].list_next, b_n);
atomic_write (&uf->array[b_l].list_next, a_n);
// update parent
atomic_write (&uf->array[q].parent, r);
// only update worker set for r if q adds workers
q_w = atomic_read (&uf->array[q].p_set);
r_w = atomic_read (&uf->array[r].p_set);
if ( (q_w | r_w) != r_w) {
// update!
fetch_or (&uf->array[r].p_set, q_w);
while (atomic_read (&uf->array[r].parent) != 0) {
r = uf_find (uf, r);
fetch_or (&uf->array[r].p_set, q_w);
}
}
// unlock
uf_unlock_list (uf, a_l);
uf_unlock_list (uf, b_l);
uf_unlock_uf (uf, q);
return 1;
}
/** Function make_cluster()
*
* Given a list of fragments denoted by seeds, make pairwise comparison
* and clustering conforming max_mismatch criteria
*
* Output: clusters in 2d vector format, where each row of the vector
* stores the clustered fragment IDs.
*/
void make_cluster (iivec_t& clusters, const ii64vec_t& list_seeds,
const ivec_t& init_cluster, int max_mismatch, const ivec_t& uf_clst) {
if (list_seeds.size() == 0) {
abording ("DuplRm.cpp -- make_cluster(): SC failed");
}
//--------- union find: (1) initialize the cluster ---------
int sz = init_cluster.size();
bvec_t visited (sz, false);
ivec_t clst (sz);
for (int i = 0; i < sz; ++ i) clst[i] = i;
//--------- pairwise comparison ---------
for (int i = 0; i < sz - 1; ++ i) {
if (visited[i]) continue; // to speed up
int idx_i = init_cluster[i];
for (int j = i + 1; j < sz; ++ j) {
if (visited[j]) continue; // to speed up, avoid of comparison
// if this is already clustered
int idx_j = init_cluster[j];
// check global uf structure according to fragID
int root_uf_i = uf_clsfind ((int) list_seeds[idx_i].back(), uf_clst),
root_uf_j = uf_clsfind ((int) list_seeds[idx_j].back(), uf_clst);
if (root_uf_i != root_uf_j) {
int root_i = uf_find (i, clst),
root_j = uf_find (j, clst);
if (root_i != root_j) {
if (is_similar (list_seeds[idx_i], list_seeds[idx_j],
max_mismatch)) {
clst[root_j] = root_i;
visited[j] = true;
}
}
} // if
} // for (int j = i + 1
} // for (int i = 0
//----- generate final cluster { clusterID --> fragment IDs } ------
std::map<int, ivec_t> clstID_fragIDs;
std::map<int, ivec_t>::iterator it;
for (int i = 0; i < sz; ++ i) {
int idx_i = init_cluster[i];
int fragID = list_seeds[idx_i].back();
int root_i = uf_clsfind (i, clst);
it = clstID_fragIDs.find (root_i);
if (it != clstID_fragIDs.end()) it->second.push_back(fragID);
else clstID_fragIDs[root_i] = ivec_t (1, fragID);
} // for (int i = 0
// go through the map and produce clusters in sorted vector format
for (it = clstID_fragIDs.begin(); it != clstID_fragIDs.end(); ++ it) {
if (it->second.size() > 1) {
std::sort (it->second.begin(), it->second.end());
clusters.push_back(it->second);
}
} // for (it
} // make_cluster
/*返回并查集中包含p元素的集合大小*/
int uf_set_size(uf_t *t,int p){
int root=uf_find(t,p);
return -t->id[root];
}
bool uf_connected(int a, int b, uf &in)
{
int aComp = uf_find(a, in);
int bComp = uf_find(b, in);
return aComp == bComp;
}