diff --git a/src/libaevol/SIMD_Individual.cpp b/src/libaevol/SIMD_Individual.cpp
index 257e7bc805f9f74c08b2462493993362bf156294..872e1afbcf33f67e05911e673cc128190ddae5a0 100644
--- a/src/libaevol/SIMD_Individual.cpp
+++ b/src/libaevol/SIMD_Individual.cpp
@@ -4749,7 +4749,7 @@ void SIMD_Individual::run_a_step(double w_max, double selection_pressure,bool op
exp_m_->output_m()->write_tree(AeTime::time());
}
- if (standalone_ && AeTime::time() % exp_m_->backup_step() == 0 && !exp_m_->record_light_tree()) {
+ if (standalone_ && AeTime::time() % exp_m_->backup_step() == 0) {
for (int indiv_id = 0; indiv_id < (int) exp_m_->nb_indivs(); indiv_id++) {
int x = indiv_id / exp_m_->world()->height();
diff --git a/src/post_treatments/ancestor_stats.cpp b/src/post_treatments/ancestor_stats.cpp
index 096aaf18bcfca73f3fc169e175c105c8f76c871d..23c1221836dc84569c48b026ee72c4bdbddd9b64 100644
--- a/src/post_treatments/ancestor_stats.cpp
+++ b/src/post_treatments/ancestor_stats.cpp
@@ -96,6 +96,7 @@ int main(int argc, char* argv[]) {
gzread(lineage_file, &t0, sizeof(t0));
gzread(lineage_file, &t_end, sizeof(t_end));
gzread(lineage_file, &final_indiv_index, sizeof(final_indiv_index));
+ gzread(lineage_file, &final_indiv_rank, sizeof(final_indiv_rank));
if (verbose) {
printf("\n\n""===============================================================================\n");
@@ -112,8 +113,6 @@ int main(int argc, char* argv[]) {
// =============================
ExpManager* exp_manager = new ExpManager();
exp_manager->load(t0, true, false);
- exp_manager->exp_s()->set_fuzzy_flavor(1);
- FuzzyFactory::fuzzyFactory = new FuzzyFactory(exp_manager->exp_s());
// The current version doesn't allow for phenotypic variation nor for
// different phenotypic targets among the grid
@@ -143,8 +142,8 @@ int main(int argc, char* argv[]) {
auto prefix = "ancestor_stats/ancestor_stats";
char postfix[255];
snprintf(postfix, 255,
- "-b" TIMESTEP_FORMAT "-e" TIMESTEP_FORMAT "-i%" PRId32 "-r%" PRId32,
- t0, t_end, final_indiv_index, final_indiv_rank);
+ "-b" TIMESTEP_FORMAT "-e" TIMESTEP_FORMAT "-i%" PRId32 "-r%" PRId32,
+ t0, t_end, final_indiv_index, final_indiv_rank);
bool best_indiv_only = true;
bool addition_old_stats = false;
bool delete_old_stats = true;
@@ -208,12 +207,14 @@ int main(int argc, char* argv[]) {
// ==================================================
// Prepare the initial ancestor and write its stats
// ==================================================
- Individual* indiv = new Individual(exp_manager, lineage_file);
- //auto* indiv = grid_cell->individual();
- indiv->EvaluateInContext(exp_manager->world()->grid(0,0)->habitat());
+ GridCell* grid_cell = new GridCell(lineage_file, exp_manager, nullptr);
+ auto* indiv = grid_cell->individual();
+ indiv->Evaluate();
indiv->compute_statistical_data();
indiv->compute_non_coding();
+ mystats->write_statistics_of_this_indiv(t0,indiv, nullptr);
+
// Additional outputs
write_environment_stats(t0, phenotypicTargetHandler, env_output_file);
write_terminators_stats(t0, indiv, term_output_file);
@@ -255,7 +256,7 @@ int main(int argc, char* argv[]) {
printf("Rebuilding ancestor at generation %" PRId64
" (index %" PRId32 ")...", time(), index);
- indiv->ReevaluateInContext(exp_manager->world()->grid(0,0)->habitat());
+ indiv->Reevaluate();
// 2) Replay replication (create current individual's child)
GeneticUnit& gen_unit = indiv->genetic_unit_nonconst(0);
@@ -377,7 +378,7 @@ int main(int argc, char* argv[]) {
}
// 3) All the mutations have been replayed, we can now evaluate the new individual
- indiv->ReevaluateInContext(exp_manager->world()->grid(0,0)->habitat());
+ indiv->Reevaluate();
indiv->compute_statistical_data();
indiv->compute_non_coding();
@@ -426,7 +427,7 @@ int main(int argc, char* argv[]) {
FILE* open_environment_stat_file(const char* prefix, const char* postfix) {
// Open file
- char* env_output_file_name = new char[80];
+ char* env_output_file_name = new char[120];
sprintf(env_output_file_name, "stats/%s_envir%s.out", prefix, postfix);
FILE* env_output_file = fopen(env_output_file_name, "w");
delete env_output_file_name;
@@ -458,7 +459,7 @@ void write_environment_stats(int64_t t, const PhenotypicTargetHandler* pth,
FILE* open_terminators_stat_file(const char* prefix, const char* postfix) {
- char* term_output_file_name = new char[80];
+ char* term_output_file_name = new char[120];
sprintf(term_output_file_name, "stats/%s_nb_term%s.out", prefix, postfix);
FILE* term_output_file = fopen(term_output_file_name, "w");
delete [] term_output_file_name;
@@ -485,7 +486,7 @@ void write_terminators_stats(int64_t t, Individual* indiv,
FILE* open_zones_stat_file(const char* prefix, const char* postfix) {
// Open file
- char* zones_output_file_name = new char[80];
+ char* zones_output_file_name = new char[120];
sprintf(zones_output_file_name, "stats/%s_zones%s.out", prefix, postfix);
FILE* zones_output_file = fopen(zones_output_file_name, "w");
delete [] zones_output_file_name;
@@ -606,7 +607,7 @@ void write_zones_stats(int64_t t,
FILE* open_operons_stat_file(const char* prefix, const char* postfix) {
- char* operons_output_file_name = new char[80];
+ char* operons_output_file_name = new char[120];
sprintf(operons_output_file_name, "stats/%s_operons%s.out", prefix, postfix);
FILE* operons_output_file = fopen(operons_output_file_name, "w");
delete [] operons_output_file_name,
diff --git a/src/post_treatments/soft_lineage.cpp b/src/post_treatments/soft_lineage.cpp
index 9f02187f86358003fd3e02ae20ff8cb04eb8ba07..22a0acb5b4c0b95ceaef088f0b42a790ad968ba5 100644
--- a/src/post_treatments/soft_lineage.cpp
+++ b/src/post_treatments/soft_lineage.cpp
@@ -82,15 +82,27 @@ int main(int argc, char** argv) {
printf("OK\n");
printf("====================================\n");
- //Find the best indiv
int32_t best_id = 0;
int32_t best_rank = 0;
+
+ // Specify the index of indiv
+ int final_indiv_index = 0;
+
for(auto rep : replics[last_gen]) {
- if(rep.second->rank() > best_rank) {
+ if (rep.first == final_indiv_index) {
best_rank = rep.second->rank();
best_id = rep.first;
}
}
+
+ //Find the best indiv
+
+ /*for(auto rep : replics[last_gen]) {
+ if(rep.second->rank() > best_rank) {
+ best_rank = rep.second->rank();
+ best_id = rep.first;
+ }
+ }*/
//His rank have to be the number of indivs
std::cout << "Best indiv is : " << best_id << " with rank : " << best_rank << '\n';
int32_t anc_id = best_id;
@@ -115,12 +127,15 @@ int main(int argc, char** argv) {
exit(EXIT_FAILURE);
}
+ //printf("Luca is %d\n",luca_time);
for(int64_t gen = 1 ; gen < luca_time ; ) {
+ //printf("Searching at gen %d\n",gen);
c = gzgetc(trunc_file);
if(c < 0) {
gzclose(trunc_file);
current_gen += backup_step;
if(current_gen > last_gen) {
+ //printf("Current gen %d -- %d\n",current_gen,last_gen);
break;
}
sprintf(input_file_name, "lightTree/tree_trunc" TIMESTEP_FORMAT ".ae", current_gen);
@@ -133,8 +148,8 @@ int main(int argc, char** argv) {
}
gzungetc(c, trunc_file);
ReplicationReport* rep = new ReplicationReport(trunc_file, nullptr);
- //printf("Getting the replication report for the ancestor at generation %" PRId64 "\n", gen);
reports[gen] = rep;
+ //printf("Getting TRUNC the replication report for the ancestor at generation %" PRId64 " => %d (%d)\n", gen,rep->id(),rep->parent_id());
gen++;
}
printf("OK\n");
@@ -158,6 +173,8 @@ int main(int argc, char** argv) {
exit(EXIT_FAILURE);
}
+ printf("Loading individual %d\n",reports[1]->parent_id());
+
const Individual& initial_ancestor = *(exp_manager->indiv_by_id(reports[1]->parent_id()));
// Write file "header"