modernize aevol_create

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;
 }

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_);
 

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:
 };