void ProteinsAnchorsSamplingSpace::show(std::ostream &s) const {
for (std::map<std::string, IntsList>::const_iterator it = paths_map_.begin();
it != paths_map_.end(); it++) {
IntsList inds = it->second;
s << it->first << " " << inds.size() << std::endl;
for (unsigned j = 0; j < inds.size(); j++) {
s << inds[j] << std::endl;
}
}
}
IntsList
DensitySegmentationByCommunities::calculate_communities(int num_clusters) {
//calculate the connected components
std::vector<int> component(num_vertices(g_));
int num = boost::connected_components(g_, &component[0]);
//get the largest connected components
compatibility::map<int,int> max_comp_list;
for(int i=0;i<num;i++){
max_comp_list[i]=0;}
for(int i=0;i<num;i++){
max_comp_list[component[i]]+=1;}
int max_comp=0;
for(int i=0;i<num;i++){
if (max_comp_list[i]>max_comp_list[max_comp]){max_comp=i;}
}
//remove all nodes not path of the first component
Ints not_first_comp_indexes;
for(int i=0;i<(int)component.size();i++) {
if (component[i] != max_comp) not_first_comp_indexes.push_back(i);
}
IMP_LOG(VERBOSE,"removing vertices, starting with "
<<boost::num_vertices(g_)<<std::endl);
boost::graph_traits<DensityGraph>::vertex_iterator vi, vi_end, next;
boost::tie(vi, vi_end) = boost::vertices(g_);
std::pair<boost::graph_traits<DensityGraph>::out_edge_iterator,
boost::graph_traits<DensityGraph>::out_edge_iterator> ei;
int rank0_nodes=0;
int index=0;
for(;vi!=vi_end;vi++) {
if (not_first_comp_indexes[index] != (int)*vi) continue;
++index;
++rank0_nodes;
for(ei=boost::out_edges(*vi,g_);
ei.first!=ei.second;ei.first++) {
boost::remove_edge(ei.first,g_);
}
}
IMP_LOG(VERBOSE,"rank0 nodes:"<<rank0_nodes
<<" not in first cc:"<<not_first_comp_indexes.size()<<std::endl);
boost::property_map<DensityGraph, boost::edge_centrality_t>::type m
= boost::get(boost::edge_centrality, g_);
unsigned int n=boost::num_vertices(g_);
boost::betweenness_centrality_clustering(
g_, Done(num_clusters+rank0_nodes, n),
m);//we add all the new rank0 nodes
IMP_LOG(TERSE,"preparing output"<<std::endl);
std::vector<int> rank(n), parent(n);
DS ds(&rank[0], &parent[0]);
boost::initialize_incremental_components(g_, ds);
boost::incremental_components(g_, ds);
compatibility::map<int, Ints> sets;
//voxel indexes correspoding to node indexes for each cluster
for (unsigned int i=0; i< boost::num_vertices(g_); ++i) {
int s= ds.find_set(i);
sets[s].push_back(node2voxel_ind_[node_index_[i]]);
}
IntsList clusters;
for (compatibility::map<int, Ints>::const_iterator it
= sets.begin(); it != sets.end(); ++it) {
clusters.push_back(it->second);
}
return clusters;
}
IntsList _pass_ints_list(const IntsList &in) {
std::cout << "IntsList of length " << in.size();
return in;
}