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  • rouzaudc/aevol
  • aevol/aevol
  • tgrohens/aevol
  • mfoley/aevol
  • jluisell/aevol
  • jluisell/aevol-eukaryotes
  • rouzaudc/aevol-asyncgarbage
  • elie.dumont/aevol
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with 396 additions and 857 deletions
src/libaevol/IndividualFactory.h
View file @ 7ffdc5fd
......@@ -65,8 +65,7 @@ namespace aevol {
class IndividualFactory
{
class IndividualFactory {
public :
// ==========================================================================
// Constructors
......
src/libaevol/Individual_X11.cpp
View file @ 7ffdc5fd
......@@ -135,7 +135,7 @@ void Individual_X11::display_cdss(X11Window * win)
else canvas_width = win->width();
int16_t canvas_height = win->height();
int16_t canvas_size = Utils::min(canvas_width, canvas_width);
int16_t canvas_size = Utils::min(canvas_width, canvas_height);
int16_t diam = round(canvas_size * log((double)genome_length) / 16);
// Prevent diameter from getting greater than 2/3 of the window size
......
src/libaevol/Makefile.am
View file @ 7ffdc5fd
......@@ -36,6 +36,7 @@ FuzzyFactory.h \
Gaussian.h \
GeneticUnit.h \
GridCell.h \
GzHelpers.h \
HybridFuzzy.h \
Individual.h \
IndividualFactory.h \
......@@ -51,7 +52,7 @@ Duplication.h \
Deletion.h \
Translocation.h \
Inversion.h \
HT.h \
HorizontalTransfer.h \
InsertionHT.h \
ReplacementHT.h \
Observable.h \
......
src/libaevol/OutputManager.cpp
View file @ 7ffdc5fd
......@@ -61,8 +61,7 @@ namespace aevol {
// =================================================================
// Constructors
// =================================================================
OutputManager::OutputManager(ExpManager * exp_m)
{
OutputManager::OutputManager(ExpManager * exp_m) {
exp_m_ = exp_m;
stats_ = nullptr;
tree_ = nullptr;
......@@ -71,14 +70,13 @@ OutputManager::OutputManager(ExpManager * exp_m)
record_tree_ = false;
make_dumps_ = false;
dump_step_ = 0;
logs_ = new Logging();
logs_ = new Logging();
}
// =================================================================
// Destructors
// =================================================================
OutputManager::~OutputManager()
{
OutputManager::~OutputManager() {
delete stats_;
delete tree_;
delete dump_;
......@@ -92,8 +90,7 @@ void OutputManager::InitStats() {
stats_ = new Stats(exp_m_);
}
void OutputManager::WriteSetupFile(gzFile setup_file) const
{
void OutputManager::WriteSetupFile(gzFile setup_file) const {
// Write the backup steps
gzwrite(setup_file, &backup_step_, sizeof(backup_step_));
gzwrite(setup_file, &big_backup_step_, sizeof(big_backup_step_));
......@@ -125,15 +122,13 @@ void OutputManager::CopyStats(const std::string& outdir, int64_t time) const {
stats_->MoveTmpFiles(outdir);
}
void OutputManager::load(gzFile setup_file, bool verbose, bool to_be_run)
{
void OutputManager::load(gzFile setup_file, bool verbose, bool to_be_run) {
// Write the backup steps
gzread(setup_file, &backup_step_, sizeof(backup_step_));
gzread(setup_file, &big_backup_step_, sizeof(big_backup_step_));
// Stats
if (to_be_run)
{
if (to_be_run) {
delete stats_;
stats_ = new Stats(exp_m_, AeTime::time());
}
......@@ -143,8 +138,7 @@ void OutputManager::load(gzFile setup_file, bool verbose, bool to_be_run)
int8_t record_tree;
gzread(setup_file, &record_tree, sizeof(record_tree));
record_tree_ = record_tree;
if (record_tree_)
{
if (record_tree_) {
int32_t tmp_tree_step;
gzread(setup_file, &tmp_tree_step, sizeof(tmp_tree_step));
......@@ -156,22 +150,19 @@ void OutputManager::load(gzFile setup_file, bool verbose, bool to_be_run)
gzread(setup_file, &make_dumps, sizeof(make_dumps));
make_dumps_ = make_dumps;
gzread(setup_file, &dump_step_, sizeof(dump_step_));
if(make_dumps_ == true)
{
if(make_dumps_) {
dump_ = new Dump(exp_m_);
}
// Logs
int8_t logs;
gzread(setup_file, &logs, sizeof(logs));
if (to_be_run)
{
if (to_be_run) {
logs_->load(logs, AeTime::time());
}
}
void OutputManager::write_current_generation_outputs() const
{
void OutputManager::write_current_generation_outputs() const {
// Write stats
stats_->write_current_generation_statistics();
......
src/libaevol/ParamLoader.cpp
View file @ 7ffdc5fd
......@@ -93,6 +93,9 @@ static const int8_t STRAIN_NAME_LOGIN_SIZE = 10;
#ifndef LOGIN_NAME_MAX
#define LOGIN_NAME_MAX 256
#endif
const char kTabChar = 0x09;
// =================================================================
// Constructors
// =================================================================
......@@ -278,7 +281,9 @@ ParamLoader::ParamLoader(const char* file_name)
_list_eval_step.insert(_nb_indiv_age);
_env_switch_probability = 0.1;
#endif
#endif
first_regul_ = true;
// Read parameter file
param_file_name_ = strdup(file_name);
......@@ -1351,6 +1356,16 @@ void ParamLoader::interpret_line(ParameterLine * line, int32_t cur_line)
param_file_name_, cur_line, _env_gaussians_list.size() );
exit( EXIT_FAILURE );
}
} else if (strcmp(line->words[0], "REGUL_FIRST") == 0)
{
if (strncmp(line->words[1], "true", 4) == 0)
{
first_regul_ = true;
}
else if (strncmp(line->words[1], "false", 5) == 0)
{
first_regul_ = false;
}
}
#endif
......@@ -1509,6 +1524,7 @@ void ParamLoader::load(ExpManager * exp_m, bool verbose,
exp_s->init_binding_matrix(_random_binding_matrix,_binding_zeros_percentage,prng_);
#endif
exp_s->set_first_regul(first_regul_);
if (FuzzyFactory::fuzzyFactory == NULL)
FuzzyFactory::fuzzyFactory = new FuzzyFactory(exp_s);
......@@ -1922,18 +1938,17 @@ void ParamLoader::load(ExpManager * exp_m, bool verbose,
\param line original line in char*
\param line_is_interpretable boolean with about the possible intrepretation of the line
*/
void ParamLoader::format_line(ParameterLine * formated_line, char* line, bool* line_is_interpretable)
{
void ParamLoader::format_line(ParameterLine * formated_line, char* line,
bool* line_is_interpretable) {
int16_t i = 0;
int16_t j;
// Parse line
while (line[i] != '\n' && line[i] != '\0' && line[i] != '\r')
{
while (line[i] != '\n' && line[i] != '\0' && line[i] != '\r') {
j = 0;
// Flush white spaces and tabs
while (line[i] == ' ' || line[i] == 0x09) i++; // 0x09 is the ASCII code for TAB
while (line[i] == ' ' || line[i] == kTabChar) i++;
// Check comments
if (line[i] == '#') break;
......@@ -1942,14 +1957,13 @@ void ParamLoader::format_line(ParameterLine * formated_line, char* line, bool* l
*line_is_interpretable = true;
// Parse word
while (line[i] != ' ' && line[i] != '\n' && line[i] != '\0' && line[i] != '\r')
{
while (line[i] != ' ' && line[i] != kTabChar && line[i] != '\n' &&
line[i] != '\0' && line[i] != '\r') {
formated_line->words[formated_line->nb_words][j++] = line[i++];
}
// Add '\0' at end of word if it's not empty (line ending with space or tab)
if (j != 0)
{
if (j != 0) {
formated_line->words[formated_line->nb_words++][j] = '\0';
}
}
......
src/libaevol/ParamLoader.h
View file @ 7ffdc5fd
......@@ -313,6 +313,8 @@ class ParamLoader {
std::vector<std::list<int8_t>> _env_signals_list;
std::vector<Protein_R*> _signals_models;
#endif
bool first_regul_;
};
} // namespace aevol
......
src/libaevol/Selection.cpp
View file @ 7ffdc5fd
......@@ -504,11 +504,10 @@ void Selection::compute_local_prob_reprod() {
}
}
Individual* Selection::do_replication(Individual* parent, int32_t index,
int16_t x, int16_t y) {
Individual* Selection::do_replication(Individual* parent, int32_t index) {
//Individual* new_indiv = NULL;
// ===========================================================================
// 1) Copy parent
// Copy parent
// ===========================================================================
#ifdef __NO_X
#ifndef __REGUL
......@@ -530,9 +529,6 @@ Individual* Selection::do_replication(Individual* parent, int32_t index,
notifyObservers(NEW_INDIV, msg);
}
// Set the new individual's location on the grid
exp_m_->world()->PlaceIndiv(new_indiv, x, y);
// Perform transfer, rearrangements and mutations
if (not new_indiv->allow_plasmids()) {
const GeneticUnit* chromosome = &new_indiv->genetic_unit_list().front();
......@@ -556,6 +552,16 @@ Individual* Selection::do_replication(Individual* parent, int32_t index,
}
}
return new_indiv;
}
Individual* Selection::do_replication(Individual* parent, int32_t index,
int16_t x, int16_t y) {
Individual* new_indiv = do_replication(parent, index);
// Set the new individual's location on the grid
exp_m_->world()->PlaceIndiv(new_indiv, x, y);
// Evaluate new individual
new_indiv->Evaluate();
......
src/libaevol/Selection.h
View file @ 7ffdc5fd
......@@ -108,17 +108,12 @@ class Selection : public Observable
void save(gzFile& backup_file) const;
void load(gzFile& exp_setup_file, gzFile& backup_file, bool verbose);
Individual* do_replication(Individual* parent, int32_t index = -1);
Individual* do_replication(Individual* parent,
int32_t index,
int16_t x = -1,
int16_t y = -1);
int16_t x,
int16_t y);
#ifdef __TBB
Individual* do_replication_tbb(Individual* parent,
int32_t index,
int16_t x = -1,
int16_t y = -1);
#endif
// =================================================================
// Public Attributes
// =================================================================
......
src/libaevol/StatRecord.cpp
View file @ 7ffdc5fd
......@@ -39,7 +39,7 @@
// =================================================================
#include "StatRecord.h"
#include "ExpManager.h"
#include "AeTime.h"
#include "ExpSetup.h"
#include "Individual.h"
#include "GeneticUnit.h"
......@@ -72,16 +72,7 @@ namespace aevol {
// =================================================================
// Constructors
// =================================================================
StatRecord::StatRecord(ExpManager * exp_m)
{
exp_m_ = exp_m;
initialize_data();
}
StatRecord::StatRecord(const StatRecord &model)
{
exp_m_ = model.exp_m_;
StatRecord::StatRecord(const StatRecord &model) {
pop_size_ = model.pop_size_;
metabolic_error_ = model.metabolic_error_;
......@@ -141,13 +132,11 @@ StatRecord::StatRecord(const StatRecord &model)
#endif
}
StatRecord::StatRecord(ExpManager* exp_m,
StatRecord::StatRecord(ExpSetup* exp_s,
Individual* indiv,
ReplicationReport* replic_report,
chrom_or_gen_unit chrom_or_gu,
bool compute_non_coding)
{
exp_m_ = exp_m;
initialize_data();
bool compute_non_coding) {
record_type_ = INDIV;
// ---------------
......@@ -216,16 +205,10 @@ StatRecord::StatRecord(ExpManager* exp_m,
#endif
// TODO : These conditions are not well managed!!!
if (indiv->nb_genetic_units() == 1)
{ // One single Genetic Unit
if (indiv->nb_genetic_units() == 1) {
// -------------------------------------------------
// Compute statistical data for the given individual
// -------------------------------------------------
ReplicationReport* replic_report = nullptr;
if (exp_m_->tree() != nullptr)
replic_report = exp_m_->tree()->report_by_index(AeTime::time(),
indiv->id());
if (compute_non_coding)
indiv->compute_non_coding();
......@@ -242,8 +225,7 @@ StatRecord::StatRecord(ExpManager* exp_m,
fitness_ = indiv->fitness();
// Secretion stats
if (exp_m_->with_secretion())
{
if (exp_s->with_secretion()) {
secretion_error_ = indiv->dist_to_target_by_feature(SECRETION);
secretion_fitness_ = indiv->fitness_by_feature(SECRETION);
compound_amount_ = indiv->grid_cell()->compound_amount();
......@@ -325,11 +307,6 @@ StatRecord::StatRecord(ExpManager* exp_m,
// -------------------------------------------------
// Compute statistical data for the given individual
// -------------------------------------------------
ReplicationReport* replic_report = nullptr;
if (exp_m_->tree() != nullptr)
replic_report = exp_m_->tree()->report_by_index(AeTime::time(),
indiv->id());
// Metabolic error stats
metabolic_error_ = (double) indiv->dist_to_target_by_feature(METABOLISM);
metabolic_fitness_ = (double) indiv->fitness_by_feature(METABOLISM);
......@@ -339,8 +316,7 @@ StatRecord::StatRecord(ExpManager* exp_m,
fitness_ = indiv->fitness();
// Secretion stats
if (exp_m_->with_secretion())
{
if (exp_s->with_secretion()) {
secretion_error_ = (double) indiv->dist_to_target_by_feature(SECRETION);
secretion_fitness_ = (double) indiv->fitness_by_feature(SECRETION);
compound_amount_ = (double) indiv->grid_cell()->compound_amount();
......@@ -425,11 +401,6 @@ StatRecord::StatRecord(ExpManager* exp_m,
// -------------------------------------------------
// Compute statistical data for the given individual
// -------------------------------------------------
ReplicationReport* replic_report = nullptr;
if (exp_m_->tree() != nullptr)
replic_report = exp_m_->tree()->report_by_index(AeTime::time(),
indiv->id());
// Metabolic error stats
metabolic_error_ = (double) gen_unit.dist_to_target_by_feature(METABOLISM);
metabolic_fitness_ = (double) gen_unit.fitness_by_feature(METABOLISM);
......@@ -439,8 +410,7 @@ StatRecord::StatRecord(ExpManager* exp_m,
fitness_ = indiv->fitness();
// Secretion stats
if (exp_m_->with_secretion())
{
if (exp_s->with_secretion()) {
secretion_error_ = (double) gen_unit.dist_to_target_by_feature(SECRETION);
secretion_fitness_ = (double) gen_unit.fitness_by_feature(SECRETION);
compound_amount_ = (double) indiv->grid_cell()->compound_amount();
......@@ -512,28 +482,26 @@ StatRecord::StatRecord(ExpManager* exp_m,
}
// Calculate average statistics for all the recorded values
StatRecord::StatRecord(ExpManager * exp_m,
const list<Individual *> indivs,
chrom_or_gen_unit chrom_or_gu)
{
exp_m_ = exp_m;
initialize_data();
StatRecord::StatRecord(ExpSetup* exp_s,
std::list<std::pair<Individual*,
ReplicationReport*>> annotated_indivs,
chrom_or_gen_unit chrom_or_gu) {
record_type_ = POP;
// ---------------
// Simulation data
// ---------------
pop_size_ = (double) indivs.size();
pop_size_ = static_cast<int32_t>(annotated_indivs.size());
// ------------------------------------------------------------------
// Compute statistical data for the each individual in the population
// ------------------------------------------------------------------
for (const auto& indiv: indivs)
{
StatRecord * indiv_stat_record = new StatRecord(exp_m_, indiv, chrom_or_gu, false);
this->add(indiv_stat_record, indiv->id());
delete indiv_stat_record;
for (const auto& annotated_indiv : annotated_indivs) {
StatRecord indiv_stat_record(exp_s,
annotated_indiv.first,
annotated_indiv.second,
chrom_or_gu, false);
this->add(&indiv_stat_record, annotated_indiv.first->id());
}
......@@ -544,28 +512,27 @@ StatRecord::StatRecord(ExpManager * exp_m,
}
// Calculate standard deviation for all the recorded values
StatRecord::StatRecord(ExpManager * exp_m,
const list<Individual *> indivs,
const StatRecord * means,
chrom_or_gen_unit chrom_or_gu)
{
exp_m_ = exp_m;
initialize_data();
StatRecord::StatRecord(ExpSetup* exp_s,
std::list<std::pair<Individual*,
ReplicationReport*>> annotated_indivs,
const StatRecord * means,
chrom_or_gen_unit chrom_or_gu) {
record_type_ = STDEVS;
// ---------------
// Simulation data
// ---------------
pop_size_ = indivs.size();
pop_size_ = static_cast<int32_t>(annotated_indivs.size());
// ------------------------------------------------------------------
// Compute statistical data for the each individual in the population
// ------------------------------------------------------------------
for (const auto& indiv : indivs) {
StatRecord * indiv_stat_record = new StatRecord(exp_m_, indiv, chrom_or_gu, false);
this->substract_power(means, indiv_stat_record, 2);
delete indiv_stat_record;
for (const auto& annotated_indiv : annotated_indivs) {
StatRecord indiv_stat_record(exp_s,
annotated_indiv.first,
annotated_indiv.second,
chrom_or_gu, false);
this->substract_power(means, &indiv_stat_record, 2);
}
// ---------------------------------------------------------------------------------
......@@ -575,30 +542,28 @@ StatRecord::StatRecord(ExpManager * exp_m,
}
// Calculate skewness for all the recorded values
StatRecord::StatRecord(ExpManager * exp_m,
const list<Individual *> indivs,
const StatRecord * means,
const StatRecord * stdevs,
chrom_or_gen_unit chrom_or_gu)
{
exp_m_ = exp_m;
initialize_data();
StatRecord::StatRecord(ExpSetup* exp_s,
std::list<std::pair<Individual*,
ReplicationReport*>> annotated_indivs,
const StatRecord* means,
const StatRecord* stdevs,
chrom_or_gen_unit chrom_or_gu) {
record_type_ = SKEWNESS;
// ---------------
// Simulation data
// ---------------
pop_size_ = (double) indivs.size();
pop_size_ = static_cast<int32_t>(annotated_indivs.size());
// ------------------------------------------------------------------
// Compute statistical data for the each individual in the population
// ------------------------------------------------------------------
for (const auto& indiv : indivs)
{
StatRecord * indiv_stat_record = new StatRecord(exp_m_, indiv, chrom_or_gu, false);
this->substract_power(means, indiv_stat_record, 3);
delete indiv_stat_record;
for (const auto& annotated_indiv : annotated_indivs) {
StatRecord indiv_stat_record(exp_s,
annotated_indiv.first,
annotated_indiv.second,
chrom_or_gu, false);
this->substract_power(means, &indiv_stat_record, 3);
}
this->divide(-pop_size_);
......@@ -616,238 +581,103 @@ StatRecord::~StatRecord()
// =================================================================
// Public Methods
// =================================================================
void StatRecord::initialize_data()
{
pop_size_ = 0.0;
metabolic_error_ = 0.0;
metabolic_fitness_ = 0.0;
parent_metabolic_error_ = 0.0;
secretion_error_ = 0.0;
parent_secretion_error_ = 0.0;
secretion_fitness_ = 0.0;
compound_amount_ = 0.0;
fitness_ = 0.0;
amount_of_dna_ = 0.0;
nb_coding_rnas_ = 0.0;
nb_non_coding_rnas_ = 0.0;
av_size_coding_rnas_ = 0.0;
av_size_non_coding_rnas_ = 0.0;
nb_functional_genes_ = 0.0;
nb_non_functional_genes_ = 0.0;
av_size_functional_gene_ = 0.0;
av_size_non_functional_gene_ = 0.0;
nb_mut_ = 0.0;
nb_rear_ = 0.0;
nb_switch_ = 0.0;
nb_indels_ = 0.0;
nb_dupl_ = 0.0;
nb_del_ = 0.0;
nb_trans_ = 0.0;
nb_inv_ = 0.0;
dupl_rate_ = 0.0;
del_rate_ = 0.0;
trans_rate_ = 0.0;
inv_rate_ = 0.0;
mean_align_score_ = 0.0;
nb_bases_in_0_CDS_ = 0.0;
nb_bases_in_0_functional_CDS_ = 0.0;
nb_bases_in_0_non_functional_CDS_ = 0.0;
nb_bases_in_0_RNA_ = 0.0;
nb_bases_in_0_coding_RNA_ = 0.0;
nb_bases_in_0_non_coding_RNA_ = 0.0;
nb_bases_non_essential_ = 0.0;
nb_bases_non_essential_including_nf_genes_ = 0.0;
#ifdef __REGUL
nb_influences_ = 0.0;
nb_enhancing_influences_ = 0.0;
nb_operating_influences_ = 0.0;
av_value_influences_ = 0.0;
av_value_enhancing_influences_ = 0.0;
av_value_operating_influences_ = 0.0;
#endif
}
void StatRecord::write_to_file(FILE* stat_file, stats_type stat_type_to_print) const
{
if (record_type_ == INDIV)
if (stat_type_to_print == FITNESS_STATS)
{
if (stat_type_to_print == FITNESS_STATS)
{
fprintf(stat_file,
"%" PRId64 " %" PRId32 " %e %" PRId32 " %e %e %e %e %e %e %e",
AeTime::time(),
pop_size_,
fitness_,
amount_of_dna_,
metabolic_error_,
parent_metabolic_error_,
metabolic_fitness_,
secretion_error_,
parent_secretion_error_,
secretion_fitness_,
compound_amount_);
#ifdef __REGUL
fprintf(stat_file,
"%" PRId64 " %" PRId32 " %e %" PRId32 " %e %e %e %e %e %e %e",
AeTime::time(),
pop_size_,
fitness_,
amount_of_dna_,
metabolic_error_,
parent_metabolic_error_,
metabolic_fitness_,
secretion_error_,
parent_secretion_error_,
secretion_fitness_,
compound_amount_);
#ifdef __REGUL
fprintf(stat_file,
" %" PRId32 " %" PRId32 " %" PRId32 " %f %f %f",
nb_influences_,
nb_enhancing_influences_,
nb_operating_influences_,
av_value_influences_,
av_value_enhancing_influences_,
av_value_operating_influences_);
#endif
}
if (stat_type_to_print == MUTATION_STATS)
{
fprintf(stat_file,
"%" PRId64 " %" PRId32 " %" PRId32 " %" PRId32 " %" PRId32 " %" PRId32 " %" PRId32 " %" PRId32 " %" PRId32 "",
AeTime::time(),
nb_mut_,
nb_rear_,
nb_switch_,
nb_indels_,
nb_dupl_,
nb_del_,
nb_trans_,
nb_inv_);
}
if (stat_type_to_print == GENES_STATS)
{
fprintf(stat_file,
"%" PRId64 " %" PRId32 " %" PRId32 " %f %f %" PRId32 " %" PRId32 " %f %f ",
AeTime::time(),
nb_coding_rnas_,
nb_non_coding_rnas_,
av_size_coding_rnas_,
av_size_non_coding_rnas_,
nb_functional_genes_,
nb_non_functional_genes_,
av_size_functional_gene_,
av_size_non_functional_gene_);
}
if (stat_type_to_print == BP_STATS)
{
fprintf(stat_file,
"%" PRId64 " %" PRId32 " %" PRId32 " %" PRId32 " %" PRId32 " %" PRId32 " %" PRId32 " %" PRId32 " %" PRId32 "",
AeTime::time(),
nb_bases_in_0_CDS_,
nb_bases_in_0_functional_CDS_,
nb_bases_in_0_non_functional_CDS_,
nb_bases_in_0_RNA_,
nb_bases_in_0_coding_RNA_,
nb_bases_in_0_non_coding_RNA_,
nb_bases_non_essential_,
nb_bases_non_essential_including_nf_genes_);
}
if (stat_type_to_print == REAR_STATS)
{
fprintf(stat_file,
"%" PRId64 " %e %e %e %e %f",
AeTime::time(),
dupl_rate_,
del_rate_,
trans_rate_,
inv_rate_,
mean_align_score_);
}
" %" PRId32 " %" PRId32 " %" PRId32 " %f %f %f",
nb_influences_,
nb_enhancing_influences_,
nb_operating_influences_,
av_value_influences_,
av_value_enhancing_influences_,
av_value_operating_influences_);
#endif
}
else // if record_type_ == POP
if (stat_type_to_print == MUTATION_STATS)
{
if (stat_type_to_print == FITNESS_STATS)
{
fprintf(stat_file,
"%" PRId64 " %" PRId32 " %e %" PRId32 " %e %e %e %e %e %e %e",
AeTime::time(),
pop_size_,
fitness_,
amount_of_dna_,
metabolic_error_,
parent_metabolic_error_,
metabolic_fitness_,
secretion_error_,
parent_secretion_error_,
secretion_fitness_,
compound_amount_);
#ifdef __REGUL
fprintf(stat_file,
" %" PRId32 " %" PRId32 " %" PRId32 " %f %f %f",
nb_influences_,
nb_enhancing_influences_,
nb_operating_influences_,
av_value_influences_,
av_value_enhancing_influences_,
av_value_operating_influences_);
#endif
}
if (stat_type_to_print == MUTATION_STATS)
{
fprintf(stat_file,
"%" PRId64 " %" PRId32 " %" PRId32 " %" PRId32 " %" PRId32
" %" PRId32 " %" PRId32 " %" PRId32 " %" PRId32 "",
AeTime::time(),
nb_mut_,
nb_rear_,
nb_switch_,
nb_indels_,
nb_dupl_,
nb_del_,
nb_trans_,
nb_inv_);
}
if (stat_type_to_print == GENES_STATS)
{
fprintf(stat_file,
"%" PRId64 " %" PRId32 " %" PRId32 " %" PRId32 " %" PRId32 " %" PRId32 " %" PRId32 " %" PRId32 " %" PRId32 "",
AeTime::time(),
nb_mut_,
nb_rear_,
nb_switch_,
nb_indels_,
nb_dupl_,
nb_del_,
nb_trans_,
nb_inv_);
}
if (stat_type_to_print == GENES_STATS)
{
fprintf(stat_file,
"%" PRId64 " %" PRId32 " %" PRId32 " %f %f %" PRId32 " %" PRId32 " %f %f ",
AeTime::time(),
nb_coding_rnas_,
nb_non_coding_rnas_,
av_size_coding_rnas_,
av_size_non_coding_rnas_,
nb_functional_genes_,
nb_non_functional_genes_,
av_size_functional_gene_,
av_size_non_functional_gene_);
}
if (stat_type_to_print == BP_STATS) {
if (record_type_ == INDIV) {
fprintf(stat_file,
"%" PRId64 " %" PRId32 " %" PRId32 " %f %f %" PRId32 " %" PRId32
" %f %f",
AeTime::time(),
nb_coding_rnas_,
nb_non_coding_rnas_,
av_size_coding_rnas_,
av_size_non_coding_rnas_,
nb_functional_genes_,
nb_non_functional_genes_,
av_size_functional_gene_,
av_size_non_functional_gene_);
}
if (stat_type_to_print == BP_STATS)
{
// TO DO (if needed) : base-pair stats for all individuals, not just for the best one.
//
// fprintf(stat_file, "%" PRId64 " %f %f %f %f %f %f %f %f",
// AeTime::time(),
// nb_bases_in_0_CDS_,
// nb_bases_in_0_functional_CDS_,
// nb_bases_in_0_non_functional_CDS_,
// nb_bases_in_0_RNA_,
// nb_bases_in_0_coding_RNA_,
// nb_bases_in_0_non_coding_RNA_,
// nb_bases_non_essential_,
// nb_bases_non_essential_including_nf_genes_);
"%" PRId64 " %" PRId32 " %" PRId32 " %" PRId32 " %" PRId32 " %" PRId32 " %" PRId32 " %" PRId32 " %" PRId32 "",
AeTime::time(),
nb_bases_in_0_CDS_,
nb_bases_in_0_functional_CDS_,
nb_bases_in_0_non_functional_CDS_,
nb_bases_in_0_RNA_,
nb_bases_in_0_coding_RNA_,
nb_bases_in_0_non_coding_RNA_,
nb_bases_non_essential_,
nb_bases_non_essential_including_nf_genes_);
}
if (stat_type_to_print == REAR_STATS)
else // if record_type_ == POP
{
fprintf(stat_file,
"%" PRId64 " %e %e %e %e %f",
AeTime::time(),
dupl_rate_,
del_rate_,
trans_rate_,
inv_rate_,
mean_align_score_);
// TO DO (if needed) : base-pair stats for all individuals, not just for the best one.
//
// fprintf(stat_file, "%" PRId64 " %f %f %f %f %f %f %f %f",
// AeTime::time(),
// nb_bases_in_0_CDS_,
// nb_bases_in_0_functional_CDS_,
// nb_bases_in_0_non_functional_CDS_,
// nb_bases_in_0_RNA_,
// nb_bases_in_0_coding_RNA_,
// nb_bases_in_0_non_coding_RNA_,
// nb_bases_non_essential_,
// nb_bases_non_essential_including_nf_genes_);
}
}
if (stat_type_to_print == REAR_STATS)
{
fprintf(stat_file,
"%" PRId64 " %e %e %e %e %f",
AeTime::time(),
dupl_rate_,
del_rate_,
trans_rate_,
inv_rate_,
mean_align_score_);
}
fprintf(stat_file, "\n");
}
......@@ -917,8 +747,7 @@ void StatRecord::divide(double divisor)
}
void StatRecord::divide_record(StatRecord const * to_divide, double power)
{
void StatRecord::divide_record(const StatRecord* to_divide, double power) {
// NB : pop_size is a "global" value and must not be divided.
if (to_divide->fitness_ != 0) { fitness_ /= pow(to_divide->fitness_, power); }
......
src/libaevol/StatRecord.h
View file @ 7ffdc5fd
......@@ -38,6 +38,8 @@
#include <cassert>
#include <list>
#include "ReplicationReport.h"
#include "ExpSetup.h"
......@@ -56,6 +58,7 @@ class ExpManager;
class Stats;
class Individual;
class ae_population;
class ReplicationReport;
enum indiv_or_pop
{
......@@ -107,24 +110,27 @@ class StatRecord
// Constructors
// =================================================================
StatRecord() = delete;
StatRecord(ExpManager * exp_m);
StatRecord(const StatRecord &model);
StatRecord(ExpManager * exp_m,
Individual * indiv,
chrom_or_gen_unit chrom_or_gu = CHROM,
bool compute_non_coding = true);
StatRecord(ExpManager * exp_m,
const std::list<Individual *> indivs,
chrom_or_gen_unit chrom_or_gu = CHROM);
StatRecord(ExpManager * exp_m,
const std::list<Individual *> indivs,
const StatRecord * means,
chrom_or_gen_unit chrom_or_gu = CHROM);
StatRecord(ExpManager * exp_m,
const std::list<Individual *> indivs,
const StatRecord * means,
const StatRecord * stdevs,
chrom_or_gen_unit chrom_or_gu = CHROM);
StatRecord(ExpSetup* exp_s,
Individual * indiv,
ReplicationReport* replic_report,
chrom_or_gen_unit chrom_or_gu = CHROM,
bool compute_non_coding = true);
StatRecord(ExpSetup* exp_s,
std::list<std::pair<Individual*,
ReplicationReport*>> annotated_indivs,
chrom_or_gen_unit chrom_or_gu = CHROM);
StatRecord(ExpSetup* exp_s,
std::list<std::pair<Individual*,
ReplicationReport*>> annotated_indivs,
const StatRecord * means,
chrom_or_gen_unit chrom_or_gu = CHROM);
StatRecord(ExpSetup* exp_s,
std::list<std::pair<Individual*,
ReplicationReport*>> annotated_indivs,
const StatRecord * means,
const StatRecord* stdevs,
chrom_or_gen_unit chrom_or_gu = CHROM);
// =================================================================
// Destructors
......@@ -163,68 +169,71 @@ class StatRecord
// =================================================================
// Protected Attributes
// =================================================================
ExpManager * exp_m_;
// NB : All the attributes are doubles because they will be used to
// compute averages over the population.
indiv_or_pop record_type_;
int32_t pop_size_;
double fitness_;
double metabolic_error_;
double parent_metabolic_error_;
double metabolic_fitness_;
double secretion_error_;
double parent_secretion_error_;
double secretion_fitness_;
double compound_amount_;
int32_t amount_of_dna_;
int32_t nb_coding_rnas_;
int32_t nb_non_coding_rnas_;
double av_size_coding_rnas_; // NOT including promoter but including terminator
double av_size_non_coding_rnas_; // NOT including promoter but including terminator
int32_t nb_functional_genes_;
int32_t nb_non_functional_genes_;
double av_size_functional_gene_; // NOT including START and STOP codons
double av_size_non_functional_gene_; // NOT including START and STOP codons
int32_t nb_mut_;
int32_t nb_rear_;
int32_t nb_switch_;
int32_t nb_indels_;
int32_t nb_dupl_;
int32_t nb_del_;
int32_t nb_trans_;
int32_t nb_inv_;
double dupl_rate_;
double del_rate_;
double trans_rate_;
double inv_rate_;
double mean_align_score_;
int32_t nb_bases_in_0_CDS_;
int32_t nb_bases_in_0_functional_CDS_;
int32_t nb_bases_in_0_non_functional_CDS_;
int32_t nb_bases_in_0_RNA_;
int32_t nb_bases_in_0_coding_RNA_;
int32_t nb_bases_in_0_non_coding_RNA_;
int32_t nb_bases_non_essential_;
int32_t nb_bases_non_essential_including_nf_genes_;
int32_t pop_size_ = 0.0;
double fitness_ = 0.0;
double metabolic_error_ = 0.0;
double parent_metabolic_error_ = 0.0;
double metabolic_fitness_ = 0.0;
double secretion_error_ = 0.0;
double parent_secretion_error_ = 0.0;
double secretion_fitness_ = 0.0;
double compound_amount_ = 0.0;
int32_t amount_of_dna_ = 0.0;
int32_t nb_coding_rnas_ = 0.0;
int32_t nb_non_coding_rnas_ = 0.0;
// NOT including promoter but including terminator
double av_size_coding_rnas_ = 0.0;
double av_size_non_coding_rnas_ = 0.0;
int32_t nb_functional_genes_ = 0.0;
int32_t nb_non_functional_genes_ = 0.0;
// NOT including START and STOP codons
double av_size_functional_gene_ = 0.0;
double av_size_non_functional_gene_ = 0.0;
int32_t nb_mut_ = 0.0;
int32_t nb_rear_ = 0.0;
int32_t nb_switch_ = 0.0;
int32_t nb_indels_ = 0.0;
int32_t nb_dupl_ = 0.0;
int32_t nb_del_ = 0.0;
int32_t nb_trans_ = 0.0;
int32_t nb_inv_ = 0.0;
double dupl_rate_ = 0.0;
double del_rate_ = 0.0;
double trans_rate_ = 0.0;
double inv_rate_ = 0.0;
double mean_align_score_ = 0.0;
int32_t nb_bases_in_0_CDS_ = 0.0;
int32_t nb_bases_in_0_functional_CDS_ = 0.0;
int32_t nb_bases_in_0_non_functional_CDS_ = 0.0;
int32_t nb_bases_in_0_RNA_ = 0.0;
int32_t nb_bases_in_0_coding_RNA_ = 0.0;
int32_t nb_bases_in_0_non_coding_RNA_ = 0.0;
int32_t nb_bases_non_essential_ = 0.0;
int32_t nb_bases_non_essential_including_nf_genes_ = 0.0;
#ifdef __REGUL
int32_t nb_influences_;
int32_t nb_enhancing_influences_;
int32_t nb_operating_influences_;
double av_value_influences_;
double av_value_enhancing_influences_;
double av_value_operating_influences_;
int32_t nb_influences_ = 0.0;
int32_t nb_enhancing_influences_ = 0.0;
int32_t nb_operating_influences_ = 0.0;
double av_value_influences_ = 0.0;
double av_value_enhancing_influences_ = 0.0;
double av_value_operating_influences_ = 0.0;
double nb_TF_;
double nb_pure_TF_;
#endif
......
src/libaevol/Stats.cpp
View file @ 7ffdc5fd
......@@ -82,12 +82,12 @@ Stats::Stats(ExpManager * exp_m,
write_headers();
}
/*!
Create a stat manager to append existing stats
/**
* Create a stat manager to append to existing stats
*/
Stats::Stats(ExpManager * exp_m,
int64_t time,
bool best_indiv_only,
bool best_indiv_only/* = false */,
const char * prefix /* = "stat" */,
bool addition_old_stats /* = true */,
bool delete_old_stats /* = true */) {
......@@ -476,6 +476,12 @@ void Stats::write_headers(bool ancstats_stats /* = false */)
void Stats::write_current_generation_statistics()
{
StatRecord** stat_records;
Individual* best_indiv = exp_m_->best_indiv();
ReplicationReport* best_replic_report = exp_m_->tree() ?
exp_m_->tree()->report_by_index(AeTime::time(), best_indiv->id()) :
nullptr;
std::list<std::pair<Individual*, ReplicationReport*>> annotated_indivs =
exp_m_->indivs_annotated();
for (int8_t chrom_or_GU = 0 ; chrom_or_GU < NB_CHROM_OR_GU ; chrom_or_GU++)
{
......@@ -484,18 +490,21 @@ void Stats::write_current_generation_statistics()
stat_records = new StatRecord* [NB_BEST_OR_GLOB];
stat_records[BEST] = new StatRecord(exp_m_,
exp_m_->best_indiv(),
// WARNING: stat_record initialization order matters: SKEW computation
// relies on SDEV being computed
stat_records[BEST] = new StatRecord(exp_m_->exp_s(),
best_indiv,
best_replic_report,
(chrom_or_gen_unit) chrom_or_GU);
stat_records[GLOB] = new StatRecord(exp_m_,
exp_m_->indivs(),
stat_records[GLOB] = new StatRecord(exp_m_->exp_s(),
annotated_indivs,
(chrom_or_gen_unit) chrom_or_GU);
stat_records[SDEV] = new StatRecord(exp_m_,
exp_m_->indivs(),
stat_records[SDEV] = new StatRecord(exp_m_->exp_s(),
annotated_indivs,
stat_records[GLOB],
(chrom_or_gen_unit) chrom_or_GU);
stat_records[SKEW] = new StatRecord(exp_m_,
exp_m_->indivs(),
stat_records[SKEW] = new StatRecord(exp_m_->exp_s(),
annotated_indivs,
stat_records[GLOB],
stat_records[SDEV],
(chrom_or_gen_unit) chrom_or_GU);
......@@ -506,7 +515,9 @@ void Stats::write_current_generation_statistics()
{
if (stat_files_names_[chrom_or_GU][best_or_glob][stat_type] != NULL)
{
stat_records[best_or_glob]->write_to_file(stat_files_[chrom_or_GU][best_or_glob][stat_type], (stats_type) stat_type);
stat_records[best_or_glob]->
write_to_file(stat_files_[chrom_or_GU][best_or_glob][stat_type],
(stats_type) stat_type);
}
}
......@@ -517,13 +528,15 @@ void Stats::write_current_generation_statistics()
}
}
void Stats::write_statistics_of_this_indiv(Individual * indiv)
void Stats::write_statistics_of_this_indiv(Individual * indiv,
ReplicationReport* replic_report)
{
StatRecord * stat_record;
for (int8_t chrom_or_GU = 0 ; chrom_or_GU < NB_CHROM_OR_GU ; chrom_or_GU++)
{
stat_record = new StatRecord(exp_m_, indiv, (chrom_or_gen_unit) chrom_or_GU, true);
stat_record = new StatRecord(exp_m_->exp_s(), indiv, replic_report,
(chrom_or_gen_unit) chrom_or_GU, true);
for (int8_t stat_type = 0 ; stat_type < NB_STATS_TYPES ; stat_type++)
{
......@@ -606,11 +619,11 @@ void Stats::set_file_names(const char* prefix,
}
const char* chrom_or_gu_name[NB_CHROM_OR_GU] =
{"", "chromosome_", "plasmids_"};
{"", "_chromosome", "_plasmids"};
const char* best_or_glob_name[NB_BEST_OR_GLOB] =
{"best_", "glob_", "sdev_", "skew_"};
{"_best", "_glob", "_sdev", "_skew"};
const char* stat_type_name[NB_STATS_TYPES] =
{"fitness_", "mutation_", "genes_", "bp_", "rear_"};
{"_fitness" ,"_mutation", "_genes", "_bp", "_rear"};
for (int8_t chrom_or_GU = 0 ; chrom_or_GU < NB_CHROM_OR_GU ; chrom_or_GU++) {
// If plasmids are not allowed, don't issue "chromosome" and
......@@ -720,9 +733,6 @@ void Stats::CreateTmpFiles(int64_t time) {
}
// Copy stats until time (included)
if (fgets(line, 500, old_file) == NULL) {
// TODO check for error
}
while ((int64_t)atol(line) <= time && !feof(old_file)) {
fputs(line, new_file);
if (fgets(line, 500, old_file)) {
......
src/libaevol/Stats.h
View file @ 7ffdc5fd
......@@ -50,6 +50,7 @@
#include <stdlib.h>
#include <assert.h>
#include "Individual.h"
#include "ReplicationReport.h"
namespace aevol {
......@@ -65,84 +66,84 @@ class ExpManager;
class Stats
{
public :
// =================================================================
// Constructors
// =================================================================
Stats() = delete;
Stats(const Stats &) = delete;
Stats(ExpManager * exp_m,
bool best_indiv_only = false,
const char* prefix = "stat",
bool with_plasmids = false,
bool compute_phen_contrib_by_GU = false);
Stats(ExpManager * exp_m,
int64_t time,
bool best_indiv_only = false,
const char * prefix = "stat",
bool addition_old_stats = true,
bool delete_old_stats = true);
// =================================================================
// Destructors
// =================================================================
virtual ~Stats();
// =================================================================
// Accessors: getters
// =================================================================
// =================================================================
// Accessors: setters
// =================================================================
inline void set_exp_m(ExpManager * exp_m);
// =================================================================
// Public Methods
// =================================================================
void write_current_generation_statistics();
void write_statistics_of_this_indiv(Individual * indiv);
void flush();
void write_headers(bool ancstats_stats = false);
void CreateTmpFiles(int64_t time);
void MoveTmpFiles(const std::string& destdir);
void PromoteTmpFiles();
class Stats {
public :
// =================================================================
// Constructors
// =================================================================
Stats() = delete;
Stats(const Stats&) = delete;
Stats(ExpManager* exp_m,
bool best_indiv_only = false,
const char* prefix = "stat",
bool with_plasmids = false,
bool compute_phen_contrib_by_GU = false);
Stats(ExpManager* exp_m,
int64_t time,
bool best_indiv_only = false,
const char * prefix = "stat",
bool addition_old_stats = true,
bool delete_old_stats = true);
// =================================================================
// Destructors
// =================================================================
virtual ~Stats();
// =================================================================
// Accessors: getters
// =================================================================
// =================================================================
// Accessors: setters
// =================================================================
inline void set_exp_m(ExpManager * exp_m);
// =================================================================
// Public Methods
// =================================================================
void write_current_generation_statistics();
void write_statistics_of_this_indiv(Individual* indiv,
ReplicationReport* replic_report);
void flush();
void write_headers(bool ancstats_stats = false);
void CreateTmpFiles(int64_t time);
void MoveTmpFiles(const std::string& destdir);
void PromoteTmpFiles();
protected :
// =================================================================
// Protected Methods
// =================================================================
void init_data();
void set_file_names(const char* prefix,
bool one_lambda_indiv_only,
bool with_plasmids = false,
bool compute_phen_contrib_by_GU = false);
void open_files();
inline void write_header(FILE* file_name, const char* header);
inline void write_header(FILE* file_name, const char* header, int8_t key);
// =================================================================
// Protected Attributes
// =================================================================
ExpManager * exp_m_;
// 3D tables of stat files (FILE*) and their names (char*)
// Dimensions are given by:
// * genetic unit (ALL_GU, CHROM or PLASMIDS)
// * BEST or GLOB
// * stat type (FITNESS_STATS, MUTATION_STATS, GENES_STATS, BP_STATS or REAR_STATS)
// Files that are not wanted MUST have their name set to NULL.
// The files themselves are also NULL because we don't fopen() them.
FILE**** stat_files_;
char**** stat_files_names_;
// =================================================================
// Protected Methods
// =================================================================
void init_data();
void set_file_names(const char* prefix,
bool one_lambda_indiv_only,
bool with_plasmids = false,
bool compute_phen_contrib_by_GU = false);
void open_files();
inline void write_header(FILE* file_name, const char* header);
inline void write_header(FILE* file_name, const char* header, int8_t key);
// =================================================================
// Protected Attributes
// =================================================================
ExpManager * exp_m_;
// 3D tables of stat files (FILE*) and their names (char*)
// Dimensions are given by:
// * genetic unit (ALL_GU, CHROM or PLASMIDS)
// * BEST or GLOB
// * stat type (FITNESS_STATS, MUTATION_STATS, GENES_STATS, BP_STATS or REAR_STATS)
// Files that are not wanted MUST have their name set to NULL.
// The files themselves are also NULL because we don't fopen() them.
FILE**** stat_files_;
char**** stat_files_names_;
};
......
src/libaevol/Tree.cpp
View file @ 7ffdc5fd
......@@ -179,13 +179,21 @@ void Tree::write_to_tree_file(gzFile tree_file) {
}
}
/**
* This method is called whenever an observed object calls notifyObservers
*
* \param o the observable that has called notifyObservers
* \param e type of event triggered
* \param arg array containing a pointer to the new indiv and its parent
*/
void Tree::update(Observable& o, ObservableEvent e, void* arg) {
switch (e) {
case NEW_INDIV : {
// Initialize the replication report corresponding to the new individual
auto indivs = reinterpret_cast<Individual**>(arg);
report_by_index(AeTime::time(), indivs[0]->id())->
init(indivs[0], indivs[1]);
Individual* new_indiv = indivs[0];
Individual* parent = indivs[1];
report_by_index(AeTime::time(), new_indiv->id())->init(new_indiv, parent);
break;
}
case END_GENERATION :
......
src/libaevol/World.h
View file @ 7ffdc5fd
......@@ -80,9 +80,9 @@ class World
std::shared_ptr<JumpingMT> mut_prng() const;
std::shared_ptr<JumpingMT> stoch_prng() const;
std::list<Individual *> indivs() const;
std::list<Individual*> indivs() const;
inline int32_t nb_indivs() const;
inline Individual * best_indiv() const;
inline Individual* best_indiv() const;
int16_t width() const {return width_;};
int16_t height() const {return height_;};
inline int32_t partial_mix_nb_permutations() const;
......
src/libaevol/aevol.h
View file @ 7ffdc5fd
......@@ -37,7 +37,6 @@
#include "DnaReplicationReport.h"
#include "Dump.h"
#include "ExpManager.h"
#include "ExpManager_X11.h"
#include "ExpSetup.h"
#include "ParameterLine.h"
#include "Fuzzy.h"
......@@ -47,7 +46,6 @@
#include "Habitat.h"
#include "IndividualFactory.h"
#include "Individual.h"
#include "Individual_X11.h"
#include "Metrics.h"
#include "JumpingMT.h"
#include "JumpPoly.h"
......@@ -80,6 +78,11 @@
#include "Tree.h"
#include "VisAVis.h"
#include "World.h"
#include "X11Window.h"
#ifdef __X11
#include "ExpManager_X11.h"
#include "Individual_X11.h"
#include "X11Window.h"
#endif
#endif // AEVOL_AEVOL_H_
src/libaevol/raevol/Habitat_R.h
View file @ 7ffdc5fd
......@@ -91,6 +91,7 @@ class Habitat_R : public virtual Habitat
// ==========================================================================
virtual const PhenotypicTarget& phenotypic_target() const {
Utils::ExitWithDevMsg("You should not call a phenotypic target without age id in RAevol", __FILE__, __LINE__);
return *(new PhenotypicTarget()); // suppress warning
}
const PhenotypicTarget_R& phenotypic_target( int8_t age ) const {
......
src/libaevol/raevol/Individual_R.cpp
View file @ 7ffdc5fd
......@@ -264,7 +264,7 @@ void Individual_R::one_step( void )
// fitnesses
//----------------------------------------------------------------------------
update_concentrations();
if (exp_m_->regul_or_not()) update_concentrations();
}
void Individual_R::eval_step( const Habitat_R& habitat, int8_t age ) {
......
src/libaevol/tests/Makefile.am deleted 100644 → 0
View file @ 5d97e536
if WITH_CPPUNIT
############################################
# Set a few variables #
############################################
AM_CPPFLAGS = $(AEVOLCPPFLAGS) $(CPPUNIT_CFLAGS)
AM_CXXFLAGS = $(AEVOLCXXFLAGS)
AM_LDFLAGS = $(AEVOLLDFLAGS)
AM_CPPFLAGS += -I$(top_srcdir)/src/libaevol
AM_LDFLAGS += -L$(top_srcdir)/src/libaevol
############################################
# Set aevol library to use #
############################################
LDADD = $(top_srcdir)/src/libaevol/libaevol.a
LDADD += $(top_srcdir)/src/libaevol/SFMT-src-1.4/libsfmt.a $(CPPUNIT_LIBS)
############################################
# C99 exact-width integer specific support #
############################################
# __STDC_FORMAT_MACROS allows us to use exact-width integer format specifiers e.g. PRId32 (for printf etc)
# __STDC_CONSTANT_MACROS allows us to define exact-width integer macros with e.g. INT32_C( <value> )
# __STDC_LIMIT_MACROS allows us to use exact-width integer limit macros with e.g. INT32_MAX
AM_CPPFLAGS += -D__STDC_FORMAT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS
############################################
# Set programs to build #
############################################
check_PROGRAMS = run_tests
CLEANFILES = $(check_PROGRAMS)
TESTS = $(check_PROGRAMS)
# The target_CPPFLAGS for each target may look useless, it is here to force automake to create
# prefixed object files so that we don't use an object file built for another set of macrodefinitions
# e.g. We don't want to use an object file created with NO_X when building the X11 lib
run_tests_SOURCES = \
run_tests.cpp \
Test_JumpingMT.h \
Test_JumpingMT.cpp
run_tests_CPPFLAGS = $(AM_CPPFLAGS)
endif
src/libaevol/tests/Test_JumpingMT.cpp deleted 100644 → 0
View file @ 5d97e536
// ****************************************************************************
//
// Aevol - An in silico experimental evolution platform
//
// ****************************************************************************
//
// Copyright: See the AUTHORS file provided with the package or <www.aevol.fr>
// Web: http://www.aevol.fr/
// E-mail: See <http://www.aevol.fr/contact/>
// Original Authors : Guillaume Beslon, Carole Knibbe, David Parsons
//
// This program is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 2 of the License, or
// (at your option) any later version.
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program. If not, see <http://www.gnu.org/licenses/>.
//
//*****************************************************************************
// =================================================================
// Libraries
// =================================================================
// =================================================================
// Project Files
// =================================================================
#include "Test_JumpingMT.h"
namespace aevol {
// ===========================================================================
// Declare Used Namespaces
// ===========================================================================
//############################################################################
// #
// Class Test_JumpingMT #
// #
//############################################################################
CPPUNIT_TEST_SUITE_REGISTRATION(Test_JumpingMT);
// ===========================================================================
// Static attributes
// ===========================================================================
// ===========================================================================
// Constructors
// ===========================================================================
Test_JumpingMT::Test_JumpingMT(void)
{
}
// ===========================================================================
// Destructors
// ===========================================================================
Test_JumpingMT::~Test_JumpingMT(void)
{
}
// ===========================================================================
// Operators
// ===========================================================================
// ===========================================================================
// Public Methods
// ===========================================================================
void Test_JumpingMT::setUp(void)
{
obj1 = new JumpingMT(56873);
obj2 = new JumpingMT(*obj1);
}
void Test_JumpingMT::tearDown(void)
{
delete obj1;
delete obj2;
}
void Test_JumpingMT::test1(void)
{
for (int i = 0 ; i < 10 ; i++)
{
obj1->random();
obj2->random();
}
CPPUNIT_ASSERT(obj1->random() == obj2->random());
CPPUNIT_ASSERT(obj1->random((int8_t) INT8_MAX) == obj2->random((int8_t) INT8_MAX));
CPPUNIT_ASSERT(obj1->random((int16_t) INT16_MAX) == obj2->random((int16_t) INT16_MAX));
CPPUNIT_ASSERT(obj1->random((int32_t) INT32_MAX) == obj2->random((int32_t) INT32_MAX));
CPPUNIT_ASSERT(obj1->random((int64_t) INT64_MAX) == obj2->random((int64_t) INT64_MAX));
CPPUNIT_ASSERT(obj1->binomial_random(435, 0.5) == obj2->binomial_random(435, 0.5));
CPPUNIT_ASSERT(obj1->gaussian_random() == obj2->gaussian_random());
}
void Test_JumpingMT::test2(void)
{
CPPUNIT_ASSERT(true);
}
// ===========================================================================
// Protected Methods
// ===========================================================================
// ===========================================================================
// Non inline accessors
// ===========================================================================
} // namespace aevol
src/libaevol/tests/Test_JumpingMT.h deleted 100644 → 0
View file @ 5d97e536
// ****************************************************************************
//
// Aevol - An in silico experimental evolution platform
//
// ****************************************************************************
//
// Copyright: See the AUTHORS file provided with the package or <www.aevol.fr>
// Web: http://www.aevol.fr/
// E-mail: See <http://www.aevol.fr/contact/>
// Original Authors : Guillaume Beslon, Carole Knibbe, David Parsons
//
// This program is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 2 of the License, or
// (at your option) any later version.
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program. If not, see <http://www.gnu.org/licenses/>.
//
//*****************************************************************************
#ifndef TEST_AE_JUMPING_MT
#define TEST_AE_JUMPING_MT
// =================================================================
// Libraries
// =================================================================
#include <cstdio>
#include <cstdlib>
#include <cppunit/TestCase.h>
#include <cppunit/extensions/HelperMacros.h>
// =================================================================
// Project Files
// =================================================================
#include "JumpingMT.h"
namespace aevol {
// ===========================================================================
// Declare Used Namespaces
// ===========================================================================
using namespace CppUnit;
using namespace std;
class Test_JumpingMT : public TestFixture
{
CPPUNIT_TEST_SUITE(Test_JumpingMT);
CPPUNIT_TEST(test1);
CPPUNIT_TEST(test2);
CPPUNIT_TEST_SUITE_END();
public :
// =======================================================================
// Enums
// =======================================================================
// =======================================================================
// Constructors
// =======================================================================
Test_JumpingMT(void);
// =======================================================================
// Destructors
// =======================================================================
virtual ~Test_JumpingMT(void);
// =======================================================================
// Accessors: getters
// =======================================================================
// =======================================================================
// Accessors: setters
// =======================================================================
// =======================================================================
// Operators
// =======================================================================
// =======================================================================
// Public Methods
// =======================================================================
void setUp(void);
void tearDown(void);
void test1(void);
void test2(void);
// =======================================================================
// Public Attributes
// =======================================================================
protected :
// =======================================================================
// Forbidden Constructors
// =======================================================================
/*Test_JumpingMT(void)
{
printf("%s:%d: error: call to forbidden constructor.\n", __FILE__, __LINE__);
exit(EXIT_FAILURE);
};
Test_JumpingMT(const Test_JumpingMT &model)
{
printf("%s:%d: error: call to forbidden constructor.\n", __FILE__, __LINE__);
exit(EXIT_FAILURE);
};*/
// =======================================================================
// Protected Methods
// =======================================================================
// =======================================================================
// Protected Attributes
// =======================================================================
JumpingMT* obj1;
JumpingMT* obj2;
};
// ===========================================================================
// Getters' definitions
// ===========================================================================
// ===========================================================================
// Setters' definitions
// ===========================================================================
// ===========================================================================
// Inline Operators' definitions
// ===========================================================================
// ===========================================================================
// Inline functions' definition
// ===========================================================================
} // namespace aevol
#endif // TEST_AE_JUMPING_MT