From 3bcc57b054c9a78d2524212ff9f2af4be29dd5f5 Mon Sep 17 00:00:00 2001
From: Jonathan Rouzaud-Cornabas <jonathan.rouzaud-cornabas@inria.fr>
Date: Thu, 6 Aug 2015 16:38:45 +0200
Subject: [PATCH] start to fix X11 raevol bug (still unable to display
concentrations)
---
src/libaevol/AbstractFuzzy.h | 2 +-
src/libaevol/ExpManager_X11.cpp | 6 ++--
src/libaevol/Fuzzy.cpp | 2 +-
src/libaevol/Fuzzy.h | 2 +-
src/libaevol/FuzzyFactory.cpp | 4 +++
src/libaevol/FuzzyFactory.h | 2 +-
src/libaevol/HybridFuzzy.cpp | 2 +-
src/libaevol/HybridFuzzy.h | 2 +-
src/libaevol/PhenotypicTargetHandler.cpp | 42 +++++++++++++++++++++---
src/libaevol/raevol/Individual_R_X11.cpp | 13 ++------
src/libaevol/raevol/Protein_R.cpp | 3 ++
11 files changed, 57 insertions(+), 23 deletions(-)
diff --git a/src/libaevol/AbstractFuzzy.h b/src/libaevol/AbstractFuzzy.h
index 5f282587d..1013085c6 100644
--- a/src/libaevol/AbstractFuzzy.h
+++ b/src/libaevol/AbstractFuzzy.h
@@ -53,7 +53,7 @@ class AbstractFuzzy
virtual bool is_identical_to(const AbstractFuzzy& fs, double tolerance) const = 0;
- virtual void print() = 0;
+ virtual void print() const = 0;
virtual void clear() = 0;
diff --git a/src/libaevol/ExpManager_X11.cpp b/src/libaevol/ExpManager_X11.cpp
index 03c964751..490397107 100644
--- a/src/libaevol/ExpManager_X11.cpp
+++ b/src/libaevol/ExpManager_X11.cpp
@@ -462,6 +462,7 @@ void ExpManager_X11::display(X11Window * win,
} else {
const HybridFuzzy fuzzy = (HybridFuzzy&)(fuzz);
double hi,hi1;
+
for (int i = 0; i < fuzzy.get_pheno_size() - 1; i++) {
hi= (((double)i) / fuzzy.get_pheno_size());
hi1= (((double)i+1) / fuzzy.get_pheno_size());
@@ -471,7 +472,6 @@ void ExpManager_X11::display(X11Window * win,
next_x = ( ((hi1) - X_MIN) / delta_x ) * win->get_width();
next_y = ( 1 - ((fuzzy.get_points()[i+1] - y_min) / delta_y) ) * win->get_height();
-
if (fuzzy.get_points()[i] >= 0 && fuzzy.get_points()[i+1] >= 0) {
win->draw_line( cur_x, cur_y, next_x, next_y, color, bold );
@@ -483,6 +483,7 @@ void ExpManager_X11::display(X11Window * win,
fill_color = X11Window::get_color( ((double)i / win->get_width()) * (X_MAX - X_MIN) );
win->draw_line( i, ( 1 - ((0 - y_min) / delta_y) ) * win->get_height(),
i, cur_y + (((i - cur_x) * (next_y - cur_y)) / (next_x - cur_x)) , fill_color );
+
delete [] fill_color;
}
}
@@ -497,6 +498,7 @@ void ExpManager_X11::display(X11Window * win,
fill_color = X11Window::get_color( ((double)i / win->get_width()) * (X_MAX - X_MIN) );
win->draw_line( i, ( 1 - ((0 - y_min) / delta_y) ) * win->get_height(),
i, cur_y + (((i - cur_x) * (next_y - cur_y)) / (next_x - cur_x)) , fill_color );
+
delete [] fill_color;
}
}
@@ -509,8 +511,6 @@ void ExpManager_X11::display(X11Window * win,
else if (fuzzy.get_points()[i+1] == 0.0) x_at_0 = hi1;
else x_at_0 = ( (- d1) / p1 );
-// if (color == RED) printf("S1 %d %d %d %d\n",cur_x, cur_y, x_at_0, 0);
-// if (color == RED) printf("S2 %d %d %d %d\n",x_at_0, 0, next_x, next_y);
win->draw_line( cur_x, cur_y, x_at_0, 0, color, bold );
if ( fill )
diff --git a/src/libaevol/Fuzzy.cpp b/src/libaevol/Fuzzy.cpp
index ff87ccb43..4d87c3f41 100644
--- a/src/libaevol/Fuzzy.cpp
+++ b/src/libaevol/Fuzzy.cpp
@@ -430,7 +430,7 @@ void Fuzzy::add_point(double x, double y)
}
}
-void Fuzzy::print()
+void Fuzzy::print() const
{
for (const Point& p : points)
printf("[%f : %f] ",p.x,p.y);
diff --git a/src/libaevol/Fuzzy.h b/src/libaevol/Fuzzy.h
index 5e314cd22..ca51bd839 100644
--- a/src/libaevol/Fuzzy.h
+++ b/src/libaevol/Fuzzy.h
@@ -114,7 +114,7 @@ class Fuzzy : public AbstractFuzzy
// get_x should be moved out of fuzzy class as it really applies to pair of points
double get_x(const Point& left, const Point& right, double y) const;
bool is_identical_to(const AbstractFuzzy& fs, double tolerance) const;
- void print();
+ void print() const;
void clear();
// ==========================================================================
// Setters
diff --git a/src/libaevol/FuzzyFactory.cpp b/src/libaevol/FuzzyFactory.cpp
index a9aaed6dc..4820637d5 100644
--- a/src/libaevol/FuzzyFactory.cpp
+++ b/src/libaevol/FuzzyFactory.cpp
@@ -140,6 +140,10 @@ AbstractFuzzy* FuzzyFactory::create_fuzzy(const gzFile backup)
return fuzzy;
}
+int FuzzyFactory::get_fuzzy_flavor()
+{
+ return _exp_s->get_fuzzy_flavor();
+}
// ============================================================================
// Non inline accessors
// ============================================================================
diff --git a/src/libaevol/FuzzyFactory.h b/src/libaevol/FuzzyFactory.h
index 3605c4f4d..76d2311a2 100644
--- a/src/libaevol/FuzzyFactory.h
+++ b/src/libaevol/FuzzyFactory.h
@@ -62,7 +62,7 @@ class FuzzyFactory
// ==========================================================================
// Getters
// ==========================================================================
-
+ int get_fuzzy_flavor();
// ==========================================================================
// Setters
// ==========================================================================
diff --git a/src/libaevol/HybridFuzzy.cpp b/src/libaevol/HybridFuzzy.cpp
index bf6a2447c..04a5077cb 100644
--- a/src/libaevol/HybridFuzzy.cpp
+++ b/src/libaevol/HybridFuzzy.cpp
@@ -217,7 +217,7 @@ double HybridFuzzy::get_y( double x ) const
return retValue;
}
-void HybridFuzzy::print()
+void HybridFuzzy::print() const
{
for (int i = 0; i < _pheno_size; i++)
printf("[%d : %f] ",i,_points[i]);
diff --git a/src/libaevol/HybridFuzzy.h b/src/libaevol/HybridFuzzy.h
index 99fc5e1a4..3ce5195be 100644
--- a/src/libaevol/HybridFuzzy.h
+++ b/src/libaevol/HybridFuzzy.h
@@ -61,7 +61,7 @@ class HybridFuzzy : public AbstractFuzzy
int get_pheno_size() const { return _pheno_size; };
- void print();
+ void print() const;
inline void clear() {reset();};
// ==========================================================================
// Setters
diff --git a/src/libaevol/PhenotypicTargetHandler.cpp b/src/libaevol/PhenotypicTargetHandler.cpp
index 61ec93c4c..0f6a43d56 100644
--- a/src/libaevol/PhenotypicTargetHandler.cpp
+++ b/src/libaevol/PhenotypicTargetHandler.cpp
@@ -32,6 +32,7 @@
// ============================================================================
#include "PhenotypicTargetHandler.h"
#include "ExpSetup.h"
+#include "HybridFuzzy.h"
#include <iostream>
@@ -126,14 +127,47 @@ void PhenotypicTargetHandler::build_phenotypic_target() {
phenotypic_target_->fuzzy()->reset();
// Generate sample points from gaussians
- if (not current_gaussians_.empty())
- for (int16_t i = 0 ; i <= sampling_ ; i++) {
- Point new_point = Point(X_MIN + (double)i * (X_MAX - X_MIN) / (double)sampling_, 0.0);
- for (const Gaussian & g: current_gaussians_)
+ if (not current_gaussians_.empty()) {
+ for (int16_t i = 0; i <= sampling_; i++) {
+ Point new_point = Point(
+ X_MIN + (double) i * (X_MAX - X_MIN) / (double) sampling_, 0.0);
+ for (const Gaussian& g: current_gaussians_)
new_point.y += g.compute_y(new_point.x);
phenotypic_target_->fuzzy()->add_point(new_point.x, new_point.y);
}
+ if (FuzzyFactory::fuzzyFactory->get_fuzzy_flavor() == 1) {
+ HybridFuzzy* fuz = (HybridFuzzy*) phenotypic_target_->fuzzy();
+
+ for (int i = 1; i < fuz->get_pheno_size(); i++) {
+ if (fuz->get_points()[i] == 0.0) {
+ int minL = i - 1;
+ int maxL = i + 1;
+ int dist = 1;
+
+ while (fuz->get_points()[maxL] == 0.0) {
+ maxL++;
+ dist++;
+ }
+ double inc = 0.0;
+ if (fuz->get_points()[maxL] > fuz->get_points()[minL]) {
+ inc = (fuz->get_points()[maxL] - fuz->get_points()[minL]) / dist;
+ } else {
+ inc = (fuz->get_points()[minL] - fuz->get_points()[maxL]) / dist;
+ minL = maxL;
+ }
+
+ for (int j = i; j < maxL; j++) {
+ fuz->get_points()[j] = fuz->get_points()[minL] + inc;
+ inc += inc;
+ }
+
+ }
+ }
+ }
+ }
+
+
// Add lower and upper bounds
phenotypic_target_->fuzzy()->clip(AbstractFuzzy::min, Y_MIN);
phenotypic_target_->fuzzy()->clip(AbstractFuzzy::max, Y_MAX);
diff --git a/src/libaevol/raevol/Individual_R_X11.cpp b/src/libaevol/raevol/Individual_R_X11.cpp
index 6b4702474..ff22bca84 100644
--- a/src/libaevol/raevol/Individual_R_X11.cpp
+++ b/src/libaevol/raevol/Individual_R_X11.cpp
@@ -160,11 +160,7 @@ void Individual_R_X11::display_concentrations( X11Window* win )
double x_step = 0.8 * win->get_width() / (double)(life_time * _exp_m->get_exp_s()->get_degradation_step());
double y_step = 0.7 * win->get_height();
- for(int16_t indiv_age = 0 ; indiv_age < life_time ; indiv_age+=0 )
- {
- //Updating the concentrations in order to respect the degradation step.
- for( int16_t i = 0; i < 1/_exp_m->get_exp_s()->get_degradation_step(); i++ )
- {
+ for (int indiv_age = 1; indiv_age <= get_exp_m()->get_exp_s()->get_nb_indiv_age(); indiv_age++) {
update_concentrations();
//affichage des points n+1 dans la concentration
@@ -183,18 +179,15 @@ void Individual_R_X11::display_concentrations( X11Window* win )
strcpy( color2, "#FFFFFF" );
}
- win->draw_line( (int16_t)((win->get_width() / 10) + (((indiv_age/_exp_m->get_exp_s()->get_degradation_step())+i)*x_step)) ,
+ win->draw_line( (int16_t)((win->get_width() / 10) + (((indiv_age/_exp_m->get_exp_s()->get_nb_indiv_age())+i)*x_step)) ,
(int16_t)(( 9 * win->get_height() / 10)-(concentrations[proti]*y_step)) ,
- (int16_t)((win->get_width() / 10) + ((((indiv_age / _exp_m->get_exp_s()->get_degradation_step())+i) + 1) * x_step)) ,
+ (int16_t)((win->get_width() / 10) + ((((indiv_age / _exp_m->get_exp_s()->get_nb_indiv_age())+i) + 1) * x_step)) ,
(int16_t)((9 * win->get_height() / 10)-(((Protein_R*)prot)->get_concentration()*y_step)) ,color2);
concentrations[proti]=((Protein_R*)prot)->get_concentration();
delete[] color2;
proti++;
}
-
- }
- indiv_age+=1;
}
_protein_list.clear();
diff --git a/src/libaevol/raevol/Protein_R.cpp b/src/libaevol/raevol/Protein_R.cpp
index 2f7710940..e3bc13397 100644
--- a/src/libaevol/raevol/Protein_R.cpp
+++ b/src/libaevol/raevol/Protein_R.cpp
@@ -143,6 +143,8 @@ Protein_R::Protein_R( gzFile backup_file ) : Protein::Protein( backup_file )
Protein_R::~Protein_R( void )
{
_rna_R_list.clear();
+
+ delete [] _cod_tab;
}
// =================================================================
@@ -151,6 +153,7 @@ Protein_R::~Protein_R( void )
void Protein_R::compute_delta_concentration( void )
{
_delta_concentration = 0;
+
if( _signal == false )
{
for (auto& rna: _rna_R_list)
--
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