attempt on makeing R package

modify .gitignore to untrack files

simulation core part was not called

update gitignore file

move around finalize function to public, now it can be called from hybridLambda build

.gitignore

@@ -87,6 +87,8 @@ tests/caterpillar_test/*gt*
 # unittest
 unit_tests
 unit_tests.trs
+test-driver
+compile
 
 # gcov
 *gcov

src/node.hpp

@@ -30,14 +30,14 @@
 
 using namespace std;
 
-//Unless compiled with options NDEBUG, we will produce a debug output using 
-//'dout' instead of cout and execute (expensive) assert statements.
-#ifndef NDEBUG
-#define dout std::cout
-#else
-#pragma GCC diagnostic ignored "-Wunused-value"
-#define dout 0 && std::cout
-#endif
+////Unless compiled with options NDEBUG, we will produce a debug output using 
+////'dout' instead of cout and execute (expensive) assert statements.
+//#ifndef NDEBUG
+//#define dout std::cout
+//#else
+//#pragma GCC diagnostic ignored "-Wunused-value"
+//#define dout 0 && std::cout
+//#endif
 
 #ifndef NODE
 #define NODE

src/sim_gt.cpp

@@ -67,13 +67,8 @@ void SimulationParameters::finalize(){
 	my_para_net = new Net (para_string);
 }
 
-
-simTree::simTree ( SimulationParameters* sim_param, action_board* simulation_jobs, ofstream &Si_table): parameters_(sim_param), simulation_jobs_ (simulation_jobs) {
-    this->init();
-	dout<<"	Starting simulating gene tree from "<<  this->parameters_->sp_string_coal_unit<<endl;
-    this->Si_table_ = &Si_table;
-
-	sim_num_gener_bool_ = this->simulation_jobs_->sim_num_gener_bool;	
+void simTree::core (){
+    sim_num_gener_bool_ = this->simulation_jobs_->sim_num_gener_bool;
     if ( this->simulation_jobs_->sim_mut_unit_bool ||  this->simulation_jobs_->sim_num_mut_bool) sim_num_gener_bool_ = true;
 
 	this->initialize_remaining_sp_node ( this->parameters_->my_Net );
@@ -134,6 +129,21 @@ simTree::simTree ( SimulationParameters* sim_param, action_board* simulation_job
     this->finalize( this->parameters_->my_Net->tax_name.size() );
 }
 
+
+simTree::simTree ( SimulationParameters* sim_param, action_board* simulation_jobs ): parameters_(sim_param), simulation_jobs_ (simulation_jobs) {
+    this->init();
+    dout<<"	Starting simulating gene tree from "<<  this->parameters_->sp_string_coal_unit<<endl;
+    this->core();
+}
+
+
+simTree::simTree ( SimulationParameters* sim_param, action_board* simulation_jobs, ofstream &Si_table): parameters_(sim_param), simulation_jobs_ (simulation_jobs) {
+    this->init();
+    dout<<"	Starting simulating gene tree from "<<  this->parameters_->sp_string_coal_unit<<endl;
+    this->Si_table_ = &Si_table;
+    this->core();
+}
+
 void simTree::remove_unused_nodes(){
     for ( size_t node_i = 0; node_i < this->NodeContainer.size(); ){
 		if ( this->NodeContainer[node_i].num_descndnt == 0 ){

src/sim_gt.hpp

@@ -49,13 +49,18 @@ class SimulationParameters{
     bool num_gener_bool;
     bool sp_coal_unit_bool;
 
-    string net_str;
     vector < int > sample_size;
 
     Net * my_Net;
 	Net * my_pop_net;
 	Net * my_para_net;
 
+    string write_sp_string_in_coal_unit( string &sp_num_gener_string, string &pop_size_string );
+    string rewrite_pop_string_by_para_string( string para_string,string pop_size_string );
+
+    public:
+    string net_str;
+    void finalize();
     SimulationParameters(){
         this->mutation_rate=0.00005;
         this->pop_bool=false;
@@ -74,10 +79,6 @@ class SimulationParameters{
         if ( my_pop_net )  delete my_pop_net;
         if ( my_para_net ) delete my_para_net;
         };
-    string write_sp_string_in_coal_unit( string &sp_num_gener_string, string &pop_size_string );
-    string rewrite_pop_string_by_para_string( string para_string,string pop_size_string );
-
-    void finalize();
 };
 
 
@@ -103,6 +104,7 @@ class action_board {
     bool mono_bool;
     bool Si_num_bool;
 
+    public:
     action_board(){
         this->sim_mut_unit_bool  = false;
         this->sim_num_gener_bool = false;
@@ -123,7 +125,6 @@ class simTree : public Tree {
 
     action_board* simulation_jobs_;
     SimulationParameters* parameters_;
-    string gt_string_coal_unit;
     string gt_string_mut_num;
     string gt_string_mut_unit;
     string gt_string_gener_num;
@@ -137,8 +138,6 @@ class simTree : public Tree {
     bool sim_num_gener_bool_;
 
     simTree(){ this->parameters_ = NULL; this->simulation_jobs_ = NULL; };
-    simTree( SimulationParameters* sim_param, action_board *simulation_jobs, std::ofstream &Si_table );    
-    ~simTree(){};		
 
     void init(){ this->sim_num_gener_bool_ = false;}
     void initialize_gt_tip_nodes( Net * my_Net );
@@ -210,6 +209,12 @@ class simTree : public Tree {
         return k;
     }
 
+    void core();
+    public:
+        string gt_string_coal_unit;
+        simTree( SimulationParameters* sim_param, action_board *simulation_jobs, std::ofstream &Si_table );
+        simTree( SimulationParameters* sim_param, action_board *simulation_jobs);
+        ~simTree(){};
 };
 
 string write_para_into_tree(string sp_string, double para);