void print(const dynamic_bitset<>& items, ostream& out) {
out << "{ ";
for(dynamic_bitset<>::size_type i = items.find_first(); i != items.npos; i = items.find_next(i)){
out << i << " ";
}
out << "} -- " << items.count() << endl;
}
static
std::string dumpStates(const dynamic_bitset<> &s) {
std::ostringstream oss;
for (size_t i = s.find_first(); i != s.npos; i = s.find_next(i)) {
oss << i << " ";
}
return oss.str();
}
static
flat_set<NFAVertex> getVertices(const dynamic_bitset<> &in,
const vector<StateInfo> &info) {
flat_set<NFAVertex> out;
for (size_t i = in.find_first(); i != in.npos; i = in.find_next(i)) {
out.insert(info[i].vertex);
}
return out;
}
static
void step(const NGHolder &g, const vector<StateInfo> &info,
const dynamic_bitset<> &in, dynamic_bitset<> *out) {
out->reset();
for (size_t i = in.find_first(); i != in.npos; i = in.find_next(i)) {
NFAVertex u = info[i].vertex;
for (auto v : adjacent_vertices_range(u, g)) {
out->set(g[v].index);
}
}
}
vector<pair<partition,unsigned> >
get_Ml_partitions_and_counts(const tree_sample& sample,double l,const dynamic_bitset<>& mask)
{
// find the first bit
int first = mask.find_first();
assert(first >= 0);
if (l <= 0.0)
throw myexception()<<"Consensus level must be > 0.0";
if (l > 1.0)
throw myexception()<<"Consensus level must be <= 1.0";
// use a sorted list of <partition,count>, sorted by partition.
typedef map<dynamic_bitset<>,p_count> container_t;
container_t counts;
// use a linked list of pointers to <partition,count> records.
list<container_t::iterator> majority;
vector<string> names = sample.names();
unsigned count = 0;
for(int i=0;i<sample.trees.size();i++)
{
const vector<dynamic_bitset<> >& T = sample.trees[i].partitions;
unsigned min_old = std::min(1+(unsigned)(l*count),count);
count ++;
unsigned min_new = std::min(1+(unsigned)(l*count),count);
// for each partition in the next tree
dynamic_bitset<> partition(names.size());
for(int b=0;b<T.size();b++)
{
partition = T[b];
if (not partition[first])
partition.flip();
partition &= mask;
// Look up record for this partition
container_t::iterator record = counts.find(partition);
if (record == counts.end()) {
counts.insert(container_t::value_type(partition,p_count()));
record = counts.find(partition);
assert(record != counts.end());
}
// FIXME - we are doing the lookup twice
p_count& pc = record->second;
int& C2 = pc.count;
int C1 = C2;
if (pc.last_tree != i) {
pc.last_tree=i;
C2 ++;
}
// add the partition if it wasn't good before, but is now
if ((C1==0 or C1<min_old) and C2 >= min_new)
majority.push_back(record);
}
// for partition in the majority tree
typedef list<container_t::iterator>::iterator iterator_t;
for(iterator_t p = majority.begin();p != majority.end();) {
if ((*p)->second.count < min_new) {
iterator_t old = p;
p++;
majority.erase(old);
}
else
p++;
}
}
vector<pair<partition,unsigned> > partitions;
partitions.reserve( 2*names.size() );
for(auto p : majority)
{
partition pi(p->first, mask);
unsigned p_count = p->second.count;
if (valid(pi))
partitions.push_back(pair<partition,unsigned>(pi,p_count));
}
return partitions;
}
