diff --git a/src/aevol_create.cpp b/src/aevol_create.cpp
index 605385d092b765c250b70c9e7f3420b2f439af01..35c127f1b1872568157ae12a367958742d4e7099 100644
--- a/src/aevol_create.cpp
+++ b/src/aevol_create.cpp
@@ -24,15 +24,6 @@
//
// ****************************************************************************
-/** \class
- * \brief
- */
-
-const char* DEFAULT_PARAM_FILE_NAME = "param.in";
-
-// ============================================================================
-// Includes
-// ============================================================================
#include <cstdlib>
#include <cstdio>
#include <cstring>
@@ -40,7 +31,11 @@ const char* DEFAULT_PARAM_FILE_NAME = "param.in";
#include <getopt.h>
+#include <fstream>
+#include <list>
#include <sstream>
+#include <string>
+#include <tuple>
#include "legacy/ExpManager.h"
#include "aevol_version.h"
@@ -51,81 +46,38 @@ using namespace aevol;
// Helper functions
void print_help(char* prog_path);
-void interpret_cmd_line_options(int argc, char* argv[]);
-
-// Command-line option variables
-static char* param_file_name = nullptr;
-static char* chromosome_file_name = nullptr;
+auto interpret_cmd_line_options(int argc, char* argv[]) -> std::tuple<std::string, std::string>;
+auto read_sequence_file(const std::string& chromosome_file_name) -> std::list<std::string>;
int main(int argc, char* argv[]) {
- interpret_cmd_line_options(argc, argv);
+ const auto [param_file_name, chromosome_file_name] = interpret_cmd_line_options(argc, argv);
// Print the hash and date of the commit used to compile this executable
printf("Running aevol version %s\n", version_string);
- assert(param_file_name != nullptr);
// Read the parameter file
- ParamValues param_values = ParamReader::read_file(param_file_name);
+ ParamValues param_values = ParamReader::read_file(param_file_name.c_str());
// Initialize the experiment manager
exp_manager = new ExpManager();
-
- // Initialize the simulation from the parameter file
- int32_t lchromosome = -1;
- char* chromosome = nullptr;
-
- if (chromosome_file_name != nullptr) {
- const int max_input_chrom_size = 1000000;
- char raw_chromosome[max_input_chrom_size];
- FILE* chromosome_file = fopen(chromosome_file_name, "r");
- if (chromosome_file == nullptr) {
- printf("ERROR: failed to open source chromosome file %s\n",
- chromosome_file_name);
- exit(EXIT_FAILURE);
- }
- if (fgets(raw_chromosome, max_input_chrom_size, chromosome_file) == nullptr)
- {
- printf("ERROR: failed to read from chromosome file %s\n",
- chromosome_file_name);
- exit(EXIT_FAILURE);
- }
- lchromosome = strlen(raw_chromosome) - 1;
- chromosome = new char[lchromosome]; // Warning: will become the DNA of the
- // first individual created -> do not
- // delete, will be freed in Dna
- strncpy(chromosome, raw_chromosome, lchromosome);
- printf("Loading chromosome from text file %s (%" PRId32 " base pairs) \n",
- chromosome_file_name, lchromosome);
- fclose(chromosome_file);
+ // Initialize the simulation from the parameter file (and the provided sequences if any)
+ if (chromosome_file_name.length() != 0) {
+ 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);
}
-
- if(param_file_name != nullptr) {
- if (lchromosome > -1) {
- ParamLoader::load(param_values, exp_manager, true, chromosome, lchromosome);
- } else {
- ParamLoader::load(param_values, exp_manager, true);
- }
+ else {
+ ParamLoader::load(param_values, exp_manager, true);
}
- // 8) Save the experiment
- if(exp_manager->indivs().front()==nullptr){printf("null\n");}
+ // Save the experiment
exp_manager->Save(true);
delete exp_manager;
- delete[] param_file_name;
}
-
-
-
-
-
-
-/*!
- \brief
-
-*/
void print_help(char* prog_path) {
// Get the program file-name in prog_name (strip prog_path of the path)
char* prog_name; // No new, it will point to somewhere inside prog_path
@@ -163,7 +115,11 @@ void print_help(char* prog_path) {
printf("\tload chromosome from given text file instead of generating it\n");
}
-void interpret_cmd_line_options(int argc, char* argv[]) {
+auto interpret_cmd_line_options(int argc, char* argv[]) -> std::tuple<std::string, std::string> {
+ // Command-line option variables
+ std::string param_file_name = "param.in";
+ std::string chromosome_file_name;
+
// Define allowed options
const char* options_list = "hVf:C:r:";
static struct option long_options_list[] = {
@@ -188,13 +144,11 @@ void interpret_cmd_line_options(int argc, char* argv[]) {
exit(EXIT_SUCCESS);
}
case 'f' : {
- param_file_name = new char[strlen(optarg) + 1];
- strcpy(param_file_name, optarg);
+ param_file_name = optarg;
break;
}
case 'C': {
- chromosome_file_name = new char[strlen(optarg) + 1];
- strcpy(chromosome_file_name, optarg);
+ chromosome_file_name = optarg;
break;
}
default : {
@@ -205,9 +159,31 @@ void interpret_cmd_line_options(int argc, char* argv[]) {
}
}
- // Set undefined command line parameters to default values
- if (param_file_name == nullptr) {
- param_file_name = new char[strlen(DEFAULT_PARAM_FILE_NAME) + 1];
- strcpy(param_file_name, DEFAULT_PARAM_FILE_NAME);
+ return std::make_tuple(param_file_name, chromosome_file_name);
+}
+
+auto read_sequence(std::ifstream& chromosome_file, const std::string& 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);
+ }
+
+ return chromosome;
+}
+
+auto read_sequence_file(const std::string& chromosome_file_name) -> std::list<std::string> {
+ 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);
}
+
+ chromosomes.push_back(read_sequence(chromosome_file, chromosome_file_name));
+
+ return chromosomes;
}
diff --git a/src/libaevol/io/parameters/ParamLoader.cpp b/src/libaevol/io/parameters/ParamLoader.cpp
index 4c9397f1a0127b69fbf65d7e8cc9d0e82b9c8495..f75cfee647a42e5170c6505f3a2a8cc348f0c815 100644
--- a/src/libaevol/io/parameters/ParamLoader.cpp
+++ b/src/libaevol/io/parameters/ParamLoader.cpp
@@ -45,9 +45,14 @@ namespace aevol {
void ParamLoader::load(const ParamValues& param_values,
ExpManager* exp_m,
- bool verbose,
- 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,
@@ -275,7 +279,14 @@ void ParamLoader::load(const ParamValues& param_values,
#endif
- indiv->add_GU(chromosome, lchromosome);
+ // Make a copy of the provided chromosome and transfer ownership to the genetic unit we create with it
+ 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_);
indiv->genetic_unit_nonconst(0).set_max_gu_length(param_values.chromosome_maximal_length_);
diff --git a/src/libaevol/io/parameters/ParamLoader.h b/src/libaevol/io/parameters/ParamLoader.h
index de423c1f10f5840f2892b60fb6aca920617be86f..51cbac6b53a1024dda78097081fd3a801f2c58a5 100644
--- a/src/libaevol/io/parameters/ParamLoader.h
+++ b/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,
- 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:
};