extract fn read_sequence_file

src/aevol_create.cpp

@@ -48,6 +48,7 @@ using namespace aevol;
 // Helper functions
 void print_help(char* prog_path);
 void interpret_cmd_line_options(int argc, char* argv[]);
+std::list<std::string> read_sequence_file(const std::string& chromosome_file_name);
 
 // Command-line option variables
 static std::string param_file_name;
@@ -65,27 +66,16 @@ int main(int argc, char* argv[]) {
   // Initialize the experiment manager
   exp_manager = new ExpManager();
 
-  // Initialize the simulation from the parameter file
-  std::list<std::string> chromosomes;
-
+  // Initialize the simulation from the parameter file (and the provided sequences if any)
   if (chromosome_file_name.length() != 0) {
-    std::ifstream chromosome_file(chromosome_file_name);
-    if (not chromosome_file) {
-      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));
-
+    auto chromosomes = read_sequence_file(chromosome_file_name);
     std::cout << "Loading chromosome from text file " << chromosome_file_name << " (" << chromosomes.front().length()
               << " base pairs)" << std::endl;
+    ParamLoader::load(param_values, exp_manager, chromosomes, true);
+  }
+  else {
+    ParamLoader::load(param_values, exp_manager, true);
   }
-
-  ParamLoader::load(param_values, exp_manager, chromosomes, true);
 
   // 8) Save the experiment
   exp_manager->Save(true);
@@ -185,3 +175,23 @@ void interpret_cmd_line_options(int argc, char* argv[]) {
     param_file_name = DEFAULT_PARAM_FILE_NAME;
   }
 }
+
+std::list<std::string> read_sequence_file(const std::string& chromosome_file_name) {
+  assert(chromosome_file_name.length() != 0);
+
+  std::list<std::string> chromosomes;
+
+  std::ifstream chromosome_file(chromosome_file_name);
+  if (not chromosome_file) {
+    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));
+
+  return chromosomes;
+}