diff --git a/src/libaevol/7/ExpManager_7.cpp b/src/libaevol/7/ExpManager_7.cpp
index 35ec34b7fad5e46dae01bc5bebde001b2a9f03ef..4caee8f9e29c15181c4c38542389264da96d9873 100644
--- a/src/libaevol/7/ExpManager_7.cpp
+++ b/src/libaevol/7/ExpManager_7.cpp
@@ -26,7 +26,7 @@
#include "ExpManager_7.h"
-#include "7/fuzzy/AbstractFuzzy_7.h"
+#include "7/fuzzy/AbstractFuzzy.h"
#include "7/Stats_7.h"
#include "DnaMutator.h"
#include "legacy/ExpManager.h"
@@ -4028,8 +4028,8 @@ void ExpManager_7::compute_phenotype(Individual_7* indiv) {
compute_protein_start_[indiv->indiv_id]= runtime_start.time_since_epoch().count();
#endif
- AbstractFuzzy_7* activ_phenotype = fuzzy_factory_->get_fuzzy();
- AbstractFuzzy_7* inhib_phenotype = fuzzy_factory_->get_fuzzy();
+ AbstractFuzzy* activ_phenotype = fuzzy_factory_->get_fuzzy();
+ AbstractFuzzy* inhib_phenotype = fuzzy_factory_->get_fuzzy();
std::vector<Protein_7*> protein_vector;
@@ -4101,8 +4101,8 @@ void ExpManager_7::compute_phenotype(Individual_7* indiv) {
// inhib_phenotype->print();
// }
- activ_phenotype->clip(AbstractFuzzy_7::max, Y_MAX);
- inhib_phenotype->clip(AbstractFuzzy_7::min, - Y_MAX);
+ activ_phenotype->clip(AbstractFuzzy::max, Y_MAX);
+ inhib_phenotype->clip(AbstractFuzzy::min, - Y_MAX);
activ_phenotype->simplify();
inhib_phenotype->simplify();
@@ -4116,7 +4116,7 @@ void ExpManager_7::compute_phenotype(Individual_7* indiv) {
indiv->phenotype = fuzzy_factory_->get_fuzzy();
indiv->phenotype->copy(activ_phenotype);
indiv->phenotype->add(inhib_phenotype);
- indiv->phenotype->clip(AbstractFuzzy_7::min, Y_MIN);
+ indiv->phenotype->clip(AbstractFuzzy::min, Y_MIN);
indiv->phenotype->simplify();
// if (indiv->indiv_id==205) {
@@ -4167,7 +4167,7 @@ void ExpManager_7::compute_fitness(Individual_7* indiv,
compute_fitness_start_[indiv->indiv_id] = runtime_start.time_since_epoch().count();
#endif
#ifdef __REGUL
- AbstractFuzzy_7* delta = fuzzy_factory_->get_fuzzy();
+ AbstractFuzzy* delta = fuzzy_factory_->get_fuzzy();
delta->copy(indiv->phenotype);
// if (indiv->indiv_id==0) printf("SIMD -- Step A -- Delta %lf\n",delta->get_geometric_area());
@@ -4248,7 +4248,7 @@ void ExpManager_7::compute_fitness(Individual_7* indiv,
-selection_pressure *
((double) indiv->metaerror_by_env_id_[env_id]));
#else
- AbstractFuzzy_7* delta = fuzzy_factory_->get_fuzzy();
+ AbstractFuzzy* delta = fuzzy_factory_->get_fuzzy();
// printf("%d -- Phenotype %lf : %p (%p)\n",indiv_id,current_individuals[indiv_id]->phenotype->get_geometric_area(),
// current_individuals[indiv_id]->phenotype,delta);
diff --git a/src/libaevol/7/ExpManager_7.h b/src/libaevol/7/ExpManager_7.h
index 384dea905c3b1d044a99a4522b19a19014cd3b4a..c14e6a93b23d52607b3358df3847098ae8a993f0 100644
--- a/src/libaevol/7/ExpManager_7.h
+++ b/src/libaevol/7/ExpManager_7.h
@@ -223,7 +223,7 @@ void Fetch_Remote_Individual();
#ifdef __REGUL
SIMD_PhenotypicTargetHandler_R* phenotypic_target_handler_;
#else
- AbstractFuzzy_7* target;
+ AbstractFuzzy* target;
#endif
int32_t grid_width_;
diff --git a/src/libaevol/7/Individual_7.h b/src/libaevol/7/Individual_7.h
index 146fcf288e5a5d04f56f02aff2b3aaebde3a37ed..533cd3f4e7a3f9b1193385aed2603898cd243bd8 100644
--- a/src/libaevol/7/Individual_7.h
+++ b/src/libaevol/7/Individual_7.h
@@ -79,8 +79,8 @@ class Individual_7 : public Observable {
double phenotype[PHENOTYPE_VECTOR_SIZE];
double delta[PHENOTYPE_VECTOR_SIZE];
#else
- AbstractFuzzy_7* phenotype = nullptr;
- AbstractFuzzy_7* delta = nullptr;
+ AbstractFuzzy* phenotype = nullptr;
+ AbstractFuzzy* delta = nullptr;
#endif
double fitness;
double metaerror;
diff --git a/src/libaevol/7/fuzzy/AbstractFuzzy_7.h b/src/libaevol/7/fuzzy/AbstractFuzzy.h
similarity index 89%
rename from src/libaevol/7/fuzzy/AbstractFuzzy_7.h
rename to src/libaevol/7/fuzzy/AbstractFuzzy.h
index 6938517195e0dac25bb25808caa3db67b30f85d5..46306048a73a96ef69373c652a4e5b49ea734626 100644
--- a/src/libaevol/7/fuzzy/AbstractFuzzy_7.h
+++ b/src/libaevol/7/fuzzy/AbstractFuzzy.h
@@ -25,8 +25,8 @@
// ****************************************************************************
-#ifndef AEVOL_ABSTRACTFUZZY_7_H
-#define AEVOL_ABSTRACTFUZZY_7_H
+#ifndef AEVOL_ABSTRACT_FUZZY_H
+#define AEVOL_ABSTRACT_FUZZY_H
#include <list>
@@ -37,8 +37,7 @@
namespace aevol {
-class AbstractFuzzy_7
-{
+class AbstractFuzzy {
public:
// ==========================================================================
// Constructors
@@ -47,7 +46,7 @@ class AbstractFuzzy_7
// ==========================================================================
// Destructor
// ==========================================================================
- virtual ~AbstractFuzzy_7() {};
+ virtual ~AbstractFuzzy() {};
// ==========================================================================
// Public Methods
@@ -55,10 +54,10 @@ class AbstractFuzzy_7
virtual void reset() = 0;
virtual void simplify() = 0;
virtual void add_triangle(ProteinConcentration mean, ProteinConcentration width, ProteinConcentration height, bool verbose = false) = 0;
-
- virtual void add(const AbstractFuzzy_7* f, bool verbose = false) = 0;
- virtual void sub(const AbstractFuzzy_7* f, bool verbose = false) = 0;
- virtual void copy(const AbstractFuzzy_7* f, bool verbose = false) = 0;
+
+ virtual void add(const AbstractFuzzy* f, bool verbose = false) = 0;
+ virtual void sub(const AbstractFuzzy* f, bool verbose = false) = 0;
+ virtual void copy(const AbstractFuzzy* f, bool verbose = false) = 0;
virtual void copy(const Fuzzy* f, bool verbose = false) = 0;
virtual void add_point(ProteinConcentration x, ProteinConcentration y) = 0;
@@ -74,7 +73,7 @@ class AbstractFuzzy_7
virtual ProteinConcentration get_geometric_area(bool verbose = false) const = 0;
virtual ProteinConcentration get_geometric_area(ProteinConcentration start_segment, ProteinConcentration end_segment) const = 0;
- virtual bool is_identical_to(const AbstractFuzzy_7& fs, ProteinConcentration tolerance) const = 0;
+ virtual bool is_identical_to(const AbstractFuzzy& fs, ProteinConcentration tolerance) const = 0;
virtual void print() const = 0;
@@ -103,4 +102,4 @@ class AbstractFuzzy_7
} // namespace aevol
-#endif //AEVOL_AbstractFuzzy_7_H
+#endif //AEVOL_ABSTRACT_FUZZY_H
diff --git a/src/libaevol/7/fuzzy/Discrete_Double_Fuzzy.cpp b/src/libaevol/7/fuzzy/Discrete_Double_Fuzzy.cpp
index 1dfad8705c4e483945e883e2c953c5abbce93455..9c33ec7a2fdaff9f520cd91274d34739994e683e 100644
--- a/src/libaevol/7/fuzzy/Discrete_Double_Fuzzy.cpp
+++ b/src/libaevol/7/fuzzy/Discrete_Double_Fuzzy.cpp
@@ -145,7 +145,7 @@ void Discrete_Double_Fuzzy::add_triangle(ProteinConcentration mean,
/// Semantically speaking, we deal with fuzzy sets over the same
/// range. So adding two fuzzy sets sums up to adding the probability
/// functions.
-void Discrete_Double_Fuzzy::add(const AbstractFuzzy_7* f, bool) {
+void Discrete_Double_Fuzzy::add(const AbstractFuzzy* f, bool) {
Discrete_Double_Fuzzy* fs = (Discrete_Double_Fuzzy*)(f);
#if defined(__INTEL_COMPILER)
__declspec(align(fs->points_));
@@ -163,7 +163,7 @@ void Discrete_Double_Fuzzy::add(const AbstractFuzzy_7* f, bool) {
/// Substract to the current fuzzy set.
///
/// TODO: Dumb version (?), to be completed.
-void Discrete_Double_Fuzzy::sub(const AbstractFuzzy_7* f, bool) {
+void Discrete_Double_Fuzzy::sub(const AbstractFuzzy* f, bool) {
Discrete_Double_Fuzzy* fs = (Discrete_Double_Fuzzy*)(f);
#if defined(__INTEL_COMPILER)
__declspec(align(fs->points_));
@@ -179,7 +179,7 @@ void Discrete_Double_Fuzzy::sub(const AbstractFuzzy_7* f, bool) {
}
-void Discrete_Double_Fuzzy::copy(const AbstractFuzzy_7* f, bool) {
+void Discrete_Double_Fuzzy::copy(const AbstractFuzzy* f, bool) {
Discrete_Double_Fuzzy* fs = (Discrete_Double_Fuzzy*)(f);
#if defined(__INTEL_COMPILER)
__declspec(align(fs->points_));
@@ -253,9 +253,9 @@ void Discrete_Double_Fuzzy::clip(clipping_direction direction,
#endif
for (int i = 0; i < length_; i++) {
- if ((direction == AbstractFuzzy_7::clipping_direction::min and
+ if ((direction == AbstractFuzzy::clipping_direction::min and
points_[i] < bound) or
- (direction == AbstractFuzzy_7::clipping_direction::max and
+ (direction == AbstractFuzzy::clipping_direction::max and
points_[i] > bound))
points_[i] = bound;
}
@@ -264,7 +264,7 @@ void Discrete_Double_Fuzzy::clip(clipping_direction direction,
}
bool Discrete_Double_Fuzzy::is_identical_to(
- const AbstractFuzzy_7&, ProteinConcentration) const {
+ const AbstractFuzzy&, ProteinConcentration) const {
assert(false);
}
diff --git a/src/libaevol/7/fuzzy/Discrete_Double_Fuzzy.h b/src/libaevol/7/fuzzy/Discrete_Double_Fuzzy.h
index bcc011ac8f446281a23c803c57ccc65c08151470..e0d57dfdc8b4cae4ae066077416d52ea598941f4 100644
--- a/src/libaevol/7/fuzzy/Discrete_Double_Fuzzy.h
+++ b/src/libaevol/7/fuzzy/Discrete_Double_Fuzzy.h
@@ -31,7 +31,7 @@
#include "macros.h"
#include "Point.h"
-#include "AbstractFuzzy_7.h"
+#include "AbstractFuzzy.h"
#include "FuzzyFactory_7.h"
#include "legacy/phenotype/fuzzy/Fuzzy.h"
namespace aevol {
@@ -75,8 +75,7 @@ namespace aevol {
/// \invariant{`points_.begin()->x == X_MIN`}
/// \invariant{`prev(points_.end())->x == X_MAX`}
/// \invariant{`is_increasing()`}
-class Discrete_Double_Fuzzy : public AbstractFuzzy_7
-{
+class Discrete_Double_Fuzzy : public AbstractFuzzy {
public:
// ==========================================================================
// Constructors
@@ -98,9 +97,9 @@ class Discrete_Double_Fuzzy : public AbstractFuzzy_7
ProteinConcentration width,
ProteinConcentration height,
bool verbose = false) override;
- void add(const AbstractFuzzy_7* f, bool verbose = false) override;
- void sub(const AbstractFuzzy_7* f, bool verbose = false) override;
- void copy(const AbstractFuzzy_7* f, bool verbose = false) override;
+ void add(const AbstractFuzzy* f, bool verbose = false) override;
+ void sub(const AbstractFuzzy* f, bool verbose = false) override;
+ void copy(const AbstractFuzzy* f, bool verbose = false) override;
void copy(const Fuzzy* f, bool verbose = false) override;
void add_point(ProteinConcentration x, ProteinConcentration y) override;
void add_point(int32_t x, ProteinConcentration y);
@@ -112,7 +111,7 @@ class Discrete_Double_Fuzzy : public AbstractFuzzy_7
ProteinConcentration get_geometric_area(bool verbose = false) const override;
ProteinConcentration get_geometric_area(ProteinConcentration start_segment,
ProteinConcentration end_segment) const override;
- bool is_identical_to(const AbstractFuzzy_7& fs, ProteinConcentration tolerance) const override;
+ bool is_identical_to(const AbstractFuzzy& fs, ProteinConcentration tolerance) const override;
void print() const override;
void clear() override;
double* points() { return points_; };
diff --git a/src/libaevol/7/fuzzy/FuzzyFactory_7.cpp b/src/libaevol/7/fuzzy/FuzzyFactory_7.cpp
index 5163fcf14bae28e62e6c52cfaa3cc212ee8a712f..e8436762c8a2dc52f77fa2ca69cf6b932c571dee 100644
--- a/src/libaevol/7/fuzzy/FuzzyFactory_7.cpp
+++ b/src/libaevol/7/fuzzy/FuzzyFactory_7.cpp
@@ -25,7 +25,7 @@
// ****************************************************************************
#include "FuzzyFactory_7.h"
-#include "AbstractFuzzy_7.h"
+#include "AbstractFuzzy.h"
#include <list>
#include <omp.h>
#include "Vector_Fuzzy.h"
@@ -54,8 +54,8 @@ FuzzyFactory_7::~FuzzyFactory_7() {
list_unused_fuzzy_.clear();
}
- AbstractFuzzy_7* FuzzyFactory_7::createFuzzy() {
- AbstractFuzzy_7* fuzz = nullptr;
+AbstractFuzzy* FuzzyFactory_7::createFuzzy() {
+ AbstractFuzzy* fuzz = nullptr;
switch (flavor_)
{
case FuzzyFlavor::VECTOR:
@@ -107,8 +107,8 @@ void FuzzyFactory_7::stats() {
total_length_);
}
- AbstractFuzzy_7 *FuzzyFactory_7::get_fuzzy() {
- AbstractFuzzy_7 *pop = nullptr;
+AbstractFuzzy* FuzzyFactory_7::get_fuzzy() {
+ AbstractFuzzy* pop = nullptr;
#ifdef _OPENMP
if (local_list_unused_fuzzy_[omp_get_thread_num()].empty()) {
@@ -143,7 +143,7 @@ void FuzzyFactory_7::stats() {
return pop;
}
-void FuzzyFactory_7::give_back(AbstractFuzzy_7 *fuzz) {
+void FuzzyFactory_7::give_back(AbstractFuzzy* fuzz) {
fuzz->clear();
#ifdef _OPENMP
if (local_list_unused_fuzzy_[omp_get_thread_num()].size() == local_pool_size_) {
@@ -151,7 +151,7 @@ void FuzzyFactory_7::give_back(AbstractFuzzy_7 *fuzz) {
// #pragma omp atomic
// free_space_local++;
- AbstractFuzzy_7* pop = local_list_unused_fuzzy_[omp_get_thread_num()].back();
+ AbstractFuzzy* pop = local_list_unused_fuzzy_[omp_get_thread_num()].back();
local_list_unused_fuzzy_[omp_get_thread_num()].pop_back();
#pragma omp critical(pop_fuzzy)
diff --git a/src/libaevol/7/fuzzy/FuzzyFactory_7.h b/src/libaevol/7/fuzzy/FuzzyFactory_7.h
index 753003af6dfeb0ccaa19d04922f1315202a84601..4ea6dc24c062efde63ba86d8b6b454a43024db76 100644
--- a/src/libaevol/7/fuzzy/FuzzyFactory_7.h
+++ b/src/libaevol/7/fuzzy/FuzzyFactory_7.h
@@ -27,7 +27,7 @@
#ifndef AEVOL_FUZZYFACTORY_H
#define AEVOL_FUZZYFACTORY_H
-#include "AbstractFuzzy_7.h"
+#include "AbstractFuzzy.h"
namespace aevol {
@@ -60,14 +60,14 @@ class FuzzyFactory_7 {
void init(int pop_size);
void stats();
- AbstractFuzzy_7 *get_fuzzy();
- void give_back(AbstractFuzzy_7 *fuzzy);
+ AbstractFuzzy* get_fuzzy();
+ void give_back(AbstractFuzzy* fuzzy);
private:
- AbstractFuzzy_7* createFuzzy();
+ AbstractFuzzy* createFuzzy();
- std::list<AbstractFuzzy_7 *> list_unused_fuzzy_;
- std::vector<std::list<AbstractFuzzy_7 *>> local_list_unused_fuzzy_;
+ std::list<AbstractFuzzy*> list_unused_fuzzy_;
+ std::vector<std::list<AbstractFuzzy*>> local_list_unused_fuzzy_;
FuzzyFlavor flavor_;
size_t pool_size_;
diff --git a/src/libaevol/7/fuzzy/Vector_Fuzzy.cpp b/src/libaevol/7/fuzzy/Vector_Fuzzy.cpp
index 5073ba68a2ff5f8034ee3e05ea5bc6304f8e2e60..39ea35efd1b1c24e34a4f13ec75232171f6d728e 100644
--- a/src/libaevol/7/fuzzy/Vector_Fuzzy.cpp
+++ b/src/libaevol/7/fuzzy/Vector_Fuzzy.cpp
@@ -256,7 +256,7 @@ void Vector_Fuzzy::add_triangle(ProteinConcentration mean, ProteinConcentration
/// Semantically speaking, we deal with fuzzy sets over the same
/// range. So adding two fuzzy sets sums up to adding the probability
/// functions.
-void Vector_Fuzzy::add(const AbstractFuzzy_7* f, bool) {
+void Vector_Fuzzy::add(const AbstractFuzzy* f, bool) {
Vector_Fuzzy* fs = (Vector_Fuzzy*)(f);
// assert(invariant());
@@ -277,7 +277,7 @@ void Vector_Fuzzy::add(const AbstractFuzzy_7* f, bool) {
/// Substract to the current fuzzy set.
///
/// TODO: Dumb version (?), to be completed.
-void Vector_Fuzzy::sub(const AbstractFuzzy_7* f, bool) {
+void Vector_Fuzzy::sub(const AbstractFuzzy* f, bool) {
Vector_Fuzzy* fs = (Vector_Fuzzy*)(f);
// assert(invariant());
@@ -298,7 +298,7 @@ void Vector_Fuzzy::sub(const AbstractFuzzy_7* f, bool) {
// assert(invariant());
}
-void Vector_Fuzzy::copy(const AbstractFuzzy_7* f, bool) {
+void Vector_Fuzzy::copy(const AbstractFuzzy* f, bool) {
Vector_Fuzzy* fs = (Vector_Fuzzy*)(f);
points_.clear();
@@ -390,8 +390,8 @@ void Vector_Fuzzy::clip(clipping_direction direction, ProteinConcentration bound
bound));
// could now fast forward over created point... TODO?
}
- if ((direction == AbstractFuzzy_7::clipping_direction::min and p->y < bound) or
- (direction == AbstractFuzzy_7::clipping_direction::max and p->y > bound))
+ if ((direction == AbstractFuzzy::clipping_direction::min and p->y < bound) or
+ (direction == AbstractFuzzy::clipping_direction::max and p->y > bound))
p->y = bound;
}
@@ -399,7 +399,7 @@ void Vector_Fuzzy::clip(clipping_direction direction, ProteinConcentration bound
}
-bool Vector_Fuzzy::is_identical_to(const AbstractFuzzy_7& f, ProteinConcentration tolerance ) const {
+bool Vector_Fuzzy::is_identical_to(const AbstractFuzzy& f, ProteinConcentration tolerance ) const {
const Vector_Fuzzy fs = (Vector_Fuzzy&)(f);
// Since set::size() has constant complexity since C++ 11, checking
// size is an inexpensive first step.
diff --git a/src/libaevol/7/fuzzy/Vector_Fuzzy.h b/src/libaevol/7/fuzzy/Vector_Fuzzy.h
index fb75f69cd112f16bb1fb0d98fcdf903739ff7d07..c667e6ed2abc557a63732030998f11075386f903 100644
--- a/src/libaevol/7/fuzzy/Vector_Fuzzy.h
+++ b/src/libaevol/7/fuzzy/Vector_Fuzzy.h
@@ -31,7 +31,7 @@
#include "macros.h"
#include "Point.h"
-#include "AbstractFuzzy_7.h"
+#include "AbstractFuzzy.h"
#include "legacy/phenotype/fuzzy/Fuzzy.h"
namespace aevol {
@@ -74,8 +74,7 @@ namespace aevol {
/// \invariant{`points_.begin()->x == X_MIN`}
/// \invariant{`prev(points_.end())->x == X_MAX`}
/// \invariant{`is_increasing()`}
-class Vector_Fuzzy : public AbstractFuzzy_7
-{
+class Vector_Fuzzy : public AbstractFuzzy {
public:
// ==========================================================================
// Constructors
@@ -97,9 +96,9 @@ class Vector_Fuzzy : public AbstractFuzzy_7
ProteinConcentration width,
ProteinConcentration height,
bool verbose = false) override;
- void add(const AbstractFuzzy_7* f, bool verbose = false) override;
- void sub(const AbstractFuzzy_7* f, bool verbose = false) override;
- void copy(const AbstractFuzzy_7* f, bool verbose = false) override;
+ void add(const AbstractFuzzy* f, bool verbose = false) override;
+ void sub(const AbstractFuzzy* f, bool verbose = false) override;
+ void copy(const AbstractFuzzy* f, bool verbose = false) override;
void copy(const Fuzzy* f, bool verbose = false) override;
void add_point(ProteinConcentration x, ProteinConcentration y) override;
@@ -121,7 +120,7 @@ class Vector_Fuzzy : public AbstractFuzzy_7
ProteinConcentration y(ProteinConcentration x, bool verbose = false) const;
// get_x should be moved out of fuzzy class as it really applies to pair of points
ProteinConcentration x(const Point& left, const Point& right, ProteinConcentration y) const;
- bool is_identical_to(const AbstractFuzzy_7& fs, ProteinConcentration tolerance) const override;
+ bool is_identical_to(const AbstractFuzzy& fs, ProteinConcentration tolerance) const override;
void print() const override;
void clear() override;
// ==========================================================================
diff --git a/src/libaevol/CMakeLists.txt b/src/libaevol/CMakeLists.txt
index 247c7fefbd40cfa3737b14f00d7c15e14c995990..f90ef847a82d2ceb56b2f2400d857a01231c0da6 100644
--- a/src/libaevol/CMakeLists.txt
+++ b/src/libaevol/CMakeLists.txt
@@ -123,7 +123,7 @@ set(libaevol_sources
7/Promoter.h
7/PromoterList.cpp
7/PromoterList.h
- 7/fuzzy/AbstractFuzzy_7.h
+ 7/fuzzy/AbstractFuzzy.h
7/fuzzy/FuzzyFactory_7.cpp
7/fuzzy/FuzzyFactory_7.h
7/fuzzy/Discrete_Double_Fuzzy.cpp
diff --git a/src/libaevol/raevol/SIMD_PhenotypicTargetHandler_R.cpp b/src/libaevol/raevol/SIMD_PhenotypicTargetHandler_R.cpp
index 4d228decb2df813dfe91493e63ebe53761e5b4f7..77d6d8c8a02c8de867e5f41d357408e815212db8 100644
--- a/src/libaevol/raevol/SIMD_PhenotypicTargetHandler_R.cpp
+++ b/src/libaevol/raevol/SIMD_PhenotypicTargetHandler_R.cpp
@@ -81,7 +81,7 @@ SIMD_PhenotypicTargetHandler_R::SIMD_PhenotypicTargetHandler_R(
sampling_ = handler->sampling();
- targets_fuzzy_by_id_ = new AbstractFuzzy_7*[nb_env_];
+ targets_fuzzy_by_id_ = new AbstractFuzzy*[nb_env_];
for (int env_id = 0; env_id < nb_env_; env_id++) {
targets_fuzzy_by_id_[env_id] = fuzzy_factory_->get_fuzzy();
@@ -103,8 +103,8 @@ SIMD_PhenotypicTargetHandler_R::SIMD_PhenotypicTargetHandler_R(
}
}
// Add lower and upper bounds
- targets_fuzzy_by_id_[env_id]->clip(AbstractFuzzy_7::min, Y_MIN);
- targets_fuzzy_by_id_[env_id]->clip(AbstractFuzzy_7::max, Y_MAX);
+ targets_fuzzy_by_id_[env_id]->clip(AbstractFuzzy::min, Y_MIN);
+ targets_fuzzy_by_id_[env_id]->clip(AbstractFuzzy::max, Y_MAX);
// Simplify (get rid of useless points)
targets_fuzzy_by_id_[env_id]->simplify();
@@ -113,7 +113,7 @@ SIMD_PhenotypicTargetHandler_R::SIMD_PhenotypicTargetHandler_R(
}
if (var_method_ == SWITCH_IN_A_LIST) {
- targets_fuzzy_ = new AbstractFuzzy_7*[nb_indiv_age_];
+ targets_fuzzy_ = new AbstractFuzzy*[nb_indiv_age_];
list_env_id_ = new int16_t[nb_indiv_age_];
if (nb_env_ <= 1) {
@@ -209,7 +209,7 @@ int32_t i = 0;
sampling_ = handler->sampling_;
- targets_fuzzy_by_id_ = new AbstractFuzzy_7*[nb_env_];
+ targets_fuzzy_by_id_ = new AbstractFuzzy*[nb_env_];
for (int env_id = 0; env_id < nb_env_; env_id++) {
targets_fuzzy_by_id_[env_id] = fuzzy_factory_->get_fuzzy();
@@ -217,7 +217,7 @@ int32_t i = 0;
}
if (var_method_ == SWITCH_IN_A_LIST) {
- targets_fuzzy_ = new AbstractFuzzy_7*[nb_indiv_age_];
+ targets_fuzzy_ = new AbstractFuzzy*[nb_indiv_age_];
list_env_id_ = new int16_t[nb_indiv_age_];
diff --git a/src/libaevol/raevol/SIMD_PhenotypicTargetHandler_R.h b/src/libaevol/raevol/SIMD_PhenotypicTargetHandler_R.h
index 55d9a0b96ac952b73791f3469330615c9f2eb2e4..dba46e283734d91b588ac748bdffce31a188bf9a 100644
--- a/src/libaevol/raevol/SIMD_PhenotypicTargetHandler_R.h
+++ b/src/libaevol/raevol/SIMD_PhenotypicTargetHandler_R.h
@@ -31,7 +31,7 @@
#include "PhenotypicTargetHandler_R.h"
#include "phenotype/Gaussian.h"
#include "legacy/raevol/Protein_R.h"
-#include "7/fuzzy/AbstractFuzzy_7.h"
+#include "7/fuzzy/AbstractFuzzy.h"
#include "7/fuzzy/FuzzyFactory_7.h"
#include <list>
#include <vector>
@@ -56,8 +56,8 @@ class SIMD_PhenotypicTargetHandler_R {
std::vector<Protein_7*> signals_models_;
std::vector<std::list<int16_t>> env_signals_list_;
- AbstractFuzzy_7** targets_fuzzy_;
- AbstractFuzzy_7** targets_fuzzy_by_id_;
+ AbstractFuzzy** targets_fuzzy_;
+ AbstractFuzzy** targets_fuzzy_by_id_;
PhenotypicTargetVariationMethod var_method_;
diff --git a/src/post_treatments/aevol_post_create_csv_7.cpp b/src/post_treatments/aevol_post_create_csv_7.cpp
index 46e89ea49374787e4f37dcee88bdf792a8648054..6ad223c62b11a36b3c24d83d8fada9e237853918 100644
--- a/src/post_treatments/aevol_post_create_csv_7.cpp
+++ b/src/post_treatments/aevol_post_create_csv_7.cpp
@@ -43,7 +43,7 @@
#include "aevol.h"
#include "Rna_7.h"
#include "Protein_7.h"
-#include "7/fuzzy/AbstractFuzzy_7.h"
+#include "7/fuzzy/AbstractFuzzy.h"
#include "7/fuzzy/Discrete_Double_Fuzzy.h"
#include "List_Metadata.h"
#include "7/fuzzy/Vector_Fuzzy.h"
@@ -80,7 +80,7 @@ void draw_triangles(Individual_7* indiv,
// lifetime.
#ifdef __REGUL
void draw_phenotype(Individual_7* indiv,
- AbstractFuzzy_7* target,
+ AbstractFuzzy* target,
char* directoryName,
int32_t timestep,
int32_t env_id = -1,
@@ -91,7 +91,7 @@ void draw_phenotype(Individual_7* indiv,
DnaFactory* dna_factory = nullptr);
#else
void draw_phenotype(Individual_7* indiv,
- AbstractFuzzy_7* target,
+ AbstractFuzzy* target,
char* directoryName,
int32_t timestep,
int32_t env_id = -1,
@@ -441,7 +441,7 @@ void draw_triangles(Individual_7* indiv,
#ifdef __REGUL
void draw_phenotype(Individual_7* indiv,
- AbstractFuzzy_7* target,
+ AbstractFuzzy* target,
char* directoryName,
int32_t timestep,
int32_t env_id,
@@ -452,7 +452,7 @@ void draw_phenotype(Individual_7* indiv,
DnaFactory* dna_factory) {
#else
void draw_phenotype(Individual_7* indiv,
- AbstractFuzzy_7* target,
+ AbstractFuzzy* target,
char* directoryName,
int32_t timestep,
int32_t env_id,
diff --git a/src/post_treatments/aevol_post_create_eps_7.cpp b/src/post_treatments/aevol_post_create_eps_7.cpp
index 39d53aa99a6e1e3b8a10fb06c4e9f3a3af2ae403..abc039be7817cf64c09c693a6e6e063cf0e1fe9e 100644
--- a/src/post_treatments/aevol_post_create_eps_7.cpp
+++ b/src/post_treatments/aevol_post_create_eps_7.cpp
@@ -43,7 +43,7 @@
#include "Rna_7.h"
#include "Protein_7.h"
#include "List_Metadata.h"
-#include "7/fuzzy/AbstractFuzzy_7.h"
+#include "7/fuzzy/AbstractFuzzy.h"
#include "7/fuzzy/Discrete_Double_Fuzzy.h"
#include "7/fuzzy/Vector_Fuzzy.h"
using namespace aevol;
@@ -77,7 +77,7 @@ void draw_triangles(Individual_7* indiv,
// In the case of Raevol, the phenotype is drawn using the final concentrations
// of the proteins, i.e. the ones reached after all the time steps of the
// lifetime.
-void draw_phenotype(Individual_7* indiv, AbstractFuzzy_7* target,
+void draw_phenotype(Individual_7* indiv, AbstractFuzzy* target,
char* directoryName);
@@ -338,7 +338,7 @@ void draw_triangles(Individual_7* indiv,
}
-void draw_phenotype(Individual_7* indiv, AbstractFuzzy_7* target,
+void draw_phenotype(Individual_7* indiv, AbstractFuzzy* target,
char* directoryName) {
const uint8_t bbsize = 200; // a4 paper: 595*842
double margin = 0.1;