int del(int i) // delete node i
{
if (i == na) return i;
int x, y, l, r;
l = tr[i].l;
r = tr[i].r;
y = tr[i].f;
tr[i].l = tr[i].r = tr[i].f = na;
tr[x = merge(l, r)].f = y;
if (y != na && tr[y].l == i) tr[y].l = x;
if (y != na && tr[y].r == i) tr[y].r = x;
for ( ; y != na; x = y, y = tr[y].f)
{
if (tr[tr[y].l].dist < tr[tr[y].r].dist)
swap(tr[y].l, tr[y].r);
if (tr[tr[y].r].dist + 1 == tr[y].dist) break;
tr[y].dist = tr[tr[y].r].dist + 1;
}
if (x != na) return iroot(x); // return new root
else return iroot(y);
}
CMPICascade::CMPICascade(int nodes_per_level, MPI_Comm comm)
{
int remaining_levels;
MPI_Comm intraComm;
int l = 0; // current level
do {
level.push_back(comm);
remaining_levels = ilog(nodes_per_level /*base*/, level[l].size /*arg*/) + 1;
level[l].group_size = iroot(remaining_levels, level[l].size); // group_size^remaining_levels <= size
level[l].p_grp_size = level[l].size/level[l].group_size;
MPI_Comm_split(comm, level[l].colour(), level[l].key(), &intraComm);
MPI_Comm_split(comm, level[l].p_colour(), level[l].p_key(), &(level[l].pg_comm));
comm = intraComm;
l++;
} while (--remaining_levels);
num_levels = l;
}
// build root file
void EXOnator::makeTables(string bed_file,string conf_file)
{
string files[] = {"T_dup.txt","N_dup.txt"};
char buffer[5000];
string chrom,gene,sid;
int start,end;
double vals[1000];
for (int i = 0;i < 2;i++) {
TFile iroot(_root_file.c_str(),"update");
TTree tree(files[i].substr(0,5).c_str(),files[i].substr(0,5).c_str());
tree.Branch("chrom",&chrom);
tree.Branch("start",&start,"start/I");
tree.Branch("end", &end, "end/I");
tree.Branch("gene", &gene);
ifstream fin(files[i].c_str());
fin.getline(buffer,5000);
istringstream line0(buffer);
line0>>sid>>sid>>sid>>sid;
double *address = vals;
while (line0>>sid)
tree.Branch(sid.c_str(),address++,(sid + "/D").c_str());
while (fin.good()) {
fin.getline(buffer,5000);
istringstream line(buffer);
line>>chrom>>start>>end>>gene;
address = vals;
while (line>>(*address)) address++;
tree.Fill();
}
fin.close();
tree.Write("",TObject::kOverwrite);
iroot.Close();
}
}
