pass chromosome to ParamLoader::load in a list of strings

Allows for chromosome to be optional (list is empty by default)
as well as multiple chromosomes (coming soon)

src/aevol_create.cpp

@@ -41,6 +41,7 @@ const char* DEFAULT_PARAM_FILE_NAME = "param.in";
 #include <getopt.h>
 
 #include <fstream>
+#include <list>
 #include <sstream>
 #include <string>
 
@@ -73,7 +74,7 @@ int main(int argc, char* argv[]) {
   exp_manager = new ExpManager();
 
   // Initialize the simulation from the parameter file
-  std::string chromosome;
+  std::list<std::string> chromosomes;
 
   if (chromosome_file_name != nullptr) {
     std::ifstream chromosome_file(chromosome_file_name);
@@ -81,19 +82,21 @@ int main(int argc, char* argv[]) {
       Utils::ExitWithUsrMsg(std::string("failed to open source chromosome file ") + chromosome_file_name);
     }
 
+    std::string chromosome;
     std::getline(chromosome_file, chromosome);
     if (not chromosome_file or chromosome.length() == 0) {
       Utils::ExitWithUsrMsg(std::string("failed to read from chromosome file ") + chromosome_file_name);
     }
+    chromosomes.push_back(std::move(chromosome));
 
-    std::cout << "Loading chromosome from text file " << chromosome_file_name << " (" << chromosome.length()
+    std::cout << "Loading chromosome from text file " << chromosome_file_name << " (" << chromosomes.front().length()
               << " base pairs)" << std::endl;
     delete [] chromosome_file_name;
   }
 
   if(param_file_name != nullptr) {
-    if (chromosome.length() != 0) {
-      ParamLoader::load(param_values, exp_manager, true, chromosome.c_str(), chromosome.length());
+    if (chromosomes.size() != 0) {
+      ParamLoader::load(param_values, exp_manager, chromosomes, true);
     } else {
       ParamLoader::load(param_values, exp_manager, true);
     }

src/libaevol/io/parameters/ParamLoader.cpp

@@ -45,9 +45,14 @@ namespace aevol {
 
 void ParamLoader::load(const ParamValues& param_values,
                        ExpManager* exp_m,
-                       bool verbose,
-                       const char* chromosome,
-                       int32_t lchromosome) {
+                       bool verbose) {
+  load(param_values, exp_m, std::list<std::string>(), verbose);
+}
+
+void ParamLoader::load(const ParamValues& param_values,
+                       ExpManager* exp_m,
+                       const std::list<std::string>& chromosomes,
+                       bool verbose) {
   // Initialize master prng
   // Will be used to create the initial genome(s) and to generate seeds for the other prngs
   auto prng = std::make_shared<JumpingMT>(param_values.seed_);
@@ -247,8 +252,7 @@ void ParamLoader::load(const ParamValues& param_values,
   Individual * indiv = NULL;
   int32_t id_new_indiv = 0;
 
-  if (chromosome != NULL)
-  {
+  if (not chromosomes.empty()) {
     printf("Option -c is used: chromosome will be loaded from a text file\n");
 #ifndef __REGUL
     Individual * indiv = new Individual(exp_m,
@@ -276,9 +280,11 @@ void ParamLoader::load(const ParamValues& param_values,
 #endif
 
     // Make a copy of the provided chromosome and transfer ownership to the genetic unit we create with it
-    char* chromosome_copy = new char[lchromosome + 1];
-    strncpy(chromosome_copy, chromosome, lchromosome + 1);
-    indiv->add_GU(chromosome_copy, lchromosome);
+    assert(chromosomes.size() == 1);
+    auto& chromosome = chromosomes.front();
+    char* chromosome_copy = new char[chromosome.length() + 1];
+    strncpy(chromosome_copy, chromosome.c_str(), chromosome.length() + 1);
+    indiv->add_GU(chromosome_copy, chromosome.length());
     chromosome_copy = nullptr;
 
     indiv->genetic_unit_nonconst(0).set_min_gu_length(param_values.chromosome_minimal_length_);

src/libaevol/io/parameters/ParamLoader.h

@@ -31,6 +31,8 @@
 //                              Includes
 // =================================================================
 #include <cinttypes>
+#include <list>
+#include <string>
 
 #include "legacy/ExpManager.h"
 #include "ParamValues.h"
@@ -58,9 +60,11 @@ class ParamLoader {
   // =========================================================================
   static void load(const ParamValues& param_values,
                    ExpManager* exp_m,
-                   bool verbose = false,
-                   const char* chromosome = nullptr,
-                   int32_t lchromosome = 0);
+                   bool verbose = false);
+  static void load(const ParamValues& param_values,
+                   ExpManager* exp_m,
+                   const std::list<std::string>& chromosomes,
+                   bool verbose = false);
 
  protected:
 };