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mpi_tree.h
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#include "exODT.h"
#include <boost/mpi.hpp>
class mpi_tree
{
public:
exODT_model * model;//del-loc
boost::mpi::communicator world;
int server,rank,size;
std::vector<approx_posterior*> ale_pointers;//del-loc
std::vector<std::string> client_fnames;
scalar_type N_ales;
std::vector<std::pair<std::string,scalar_type> > MLRec_res;//del-loc
std::vector<std::string> Ttokens;//del-loc
std::map<std::string,scalar_type> scalar_parameter;
std::map<std::string,std::string> string_parameter;
void set_parameter(std::string name, scalar_type value)
{
scalar_parameter[name]=value;
};
void set_parameter(std::string name, std::string value)
{
string_parameter[name]=value;
};
scalar_type delta_avg,tau_avg,lambda_avg;
scalar_type delta_norm,tau_norm,lambda_norm;
std::vector<scalar_type> delta_branch_avg,tau_branch_avg,lambda_branch_avg;//del-loc
std::vector<scalar_type> delta_branch_norm,tau_branch_norm,lambda_branch_norm;//del-loc
mpi_tree(std::string Sstring,const boost::mpi::communicator mpi_world,std::map<std::string,scalar_type> set_parameters=std::map<std::string,scalar_type>())
{
set_parameter("use_mpp_trees",0);
set_parameter("min_delta",1e-6);
set_parameter("min_tau",1e-6);
set_parameter("min_lambda",1e-6);
set_parameter("inital_delta",0.01);
set_parameter("inital_tau",0.01);
set_parameter("inital_lambda",0.02);
model=new exODT_model();
model->set_model_parameter("D",1);
model->set_model_parameter("event_node",1);
model->set_model_parameter("DD",20);
for (std::map<std::string,scalar_type>::iterator it=set_parameters.begin();it!=set_parameters.end();it++)
model->set_model_parameter((*it).first,(*it).second);
model->construct(Sstring);//del-loc
scalar_type N=1e6;
model->set_model_parameter("N",1e6);//we can almost scale out N assuming height from coalescent..
model->set_model_parameter("Delta_bar",N*2.);
model->set_model_parameter("Lambda_bar",N*2.);
model->set_model_parameter("delta",scalar_parameter["inital_delta"]);
model->set_model_parameter("tau",scalar_parameter["inital_tau"]);
model->set_model_parameter("lambda",scalar_parameter["inital_lambda"]);
model->calculate_EG();//with default parameters
world = mpi_world;
server=0;
rank = world.rank();
size = world.size();
};
~mpi_tree()
{
for (std::vector<approx_posterior*>::iterator it=ale_pointers.begin();it!=ale_pointers.end();it++)
delete (*it);
ale_pointers.clear();
MLRec_res.clear();
client_fnames.clear();
delta_branch_avg.clear(),tau_branch_avg.clear(),lambda_branch_avg.clear();//del-loc
delta_branch_norm.clear(),tau_branch_norm.clear(),lambda_branch_norm.clear();//del-loc
delete model;
};
//implimented in mpi_tree.cpp
void distribute_ales(std::vector<std::string>,bool list_of_trees=false);
void gather_counts();
void clear_counts();
std::string branch_counts_string();
void show_branch_counts();
void print_branch_counts();
scalar_type calculate_MLRecs(bool estimate=false,bool branchwise=false);
scalar_type calculate_p();
//implimented in rae_estimate.cpp
std::vector<scalar_type> dtl_estimate(int branch,scalar_type N_ales_norm);
scalar_type estimate_rates(std::string mode="uniform");
void set_rates(bool branchwise=false);
void register_rates();
void clear_rate_register();
void show_rates();
private:
;
};