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cellule.cpp
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/*
* Copyright (C) 2005-2011 Hervé Rouault <[email protected]>
*
* This file is part of Genherite.
*
* Genherite 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 3 of the License, or
* (at your option) any later version.
*
* Genherite 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 Genherite. If not, see <http://www.gnu.org/licenses/>.
*/
#include <iostream>
#include <iomanip>
#include <cmath>
#include <string>
#include <fstream>
#include <sstream>
#include <vector>
#include <algorithm>
#include <gsl/gsl_math.h>
#include <gsl/gsl_rng.h>
#include "cmdline.h"
#include "evolution.hpp"
#include "composants.hpp"
#include "cellule.hpp"
#include "integr.hpp"
unsigned int nb_promoters_max = 5;
unsigned int nb_proteins_max = 15;
Cellule::Cellule()
: score(0)
{
}
Cellule::~Cellule()
{
vector < Gene * >::iterator igene;
vector < Arn * >::iterator iarn;
vector < Protein * >::iterator iprot;
vector < Promoter * >::iterator ipromo;
vector < Reaction * >::iterator ireact;
for (igene = genes.begin(); igene != genes.end(); igene++) {
delete *igene;
}
for (iarn = arns.begin(); iarn != arns.end(); iarn++) {
delete *iarn;
}
for (iprot = proteins.begin(); iprot != proteins.end(); iprot++) {
delete *iprot;
}
for (ipromo = promoters.begin(); ipromo != promoters.end(); ipromo++) {
delete *ipromo;
}
for (ireact = reactions.begin(); ireact != reactions.end(); ireact++) {
delete *ireact;
}
}
Protein *Cellule::existe(Protein * prot)
{
vector < Protein * >::iterator iprot;
for (iprot = proteins.begin(); iprot != proteins.end(); iprot++) {
if (prot->eqprot(*iprot)) {
return *iprot;
}
}
return NULL;
}
Protein *Cellule::searchcopyprot(Protein * prot)
{
vector < Protein * >::iterator iprot;
for (iprot = proteins.begin(); iprot != proteins.end(); iprot++) {
if ((static_cast < Protein * >(*iprot)->copie) == prot)
return *iprot;
}
return NULL;
}
string Cellule::especestring(Espece * pesp)
{
if (pesp == NULL)
return "NULL";
vector < Gene * >::iterator igene;
vector < Arn * >::iterator iarn;
vector < Protein * >::iterator iprot;
vector < Promoter * >::iterator ipromo;
int i = 0;
for (igene = genes.begin(); igene != genes.end(); igene++) {
if (pesp == *igene) {
stringstream sgene;
sgene << "cell->genes[" << i << "]";
return sgene.str();
}
i++;
}
i = 0;
for (iarn = arns.begin(); iarn != arns.end(); iarn++) {
if (pesp == *iarn) {
stringstream sarn;
sarn << "cell->arns[" << i << "]";
return sarn.str();
}
i++;
}
i = 0;
for (iprot = proteins.begin(); iprot != proteins.end(); iprot++) {
if (pesp == *iprot) {
stringstream sprot;
sprot << "cell->proteins[" << i << "]";
return sprot.str();
}
i++;
}
i = 0;
for (ipromo = promoters.begin(); ipromo != promoters.end(); ipromo++) {
if (pesp == *ipromo) {
stringstream spromo;
spromo << "cell->promoters[" << i << "]";
return spromo.str();
}
i++;
}
cout << "Erreur : espèce introuvable!\n";
return "-1";
}
void Cellule::copygene(Gene * gene)
{
Gene *cgene;
Protein *cprot;
Espece *react1, *react2, *prod1, *prod2;
Reaction *react;
vector < Gene * >::iterator igene;
vector < Protein * >::iterator iprot;
vector < Promoter * >::iterator ipromo;
vector < Composant * >::iterator icomp;
vector < Reaction * >::iterator ireact;
for (ireact = reactions.begin(); ireact != reactions.end(); ireact++) {
(*ireact)->copie = 0;
}
for (iprot = proteins.begin(); iprot != proteins.end(); iprot++) {
(*iprot)->copie = (*iprot);
}
char lastgene = 'a';
for (igene = genes.begin(); igene != genes.end(); igene++) {
lastgene++;
}
cgene = addgene();
cgene->copie = gene;
gene->copie = cgene;
cgene->label = lastgene;
cgene->transrate = gene->transrate;
gene->arn->copie = cgene->arn;
cgene->arn->copie = gene->arn;
cgene->arn->qtite = gene->arn->qtite;
cgene->arn->cste = gene->arn->cste;
cgene->arn->label = lastgene;
gene->arn->protein->copie = cgene->arn->protein;
cgene->arn->protein->copie = gene->arn->protein;
cgene->arn->protein->cste = gene->arn->protein->cste;
cgene->arn->protein->qtite = gene->arn->protein->qtite;
cgene->arn->protein->label = toupper(lastgene);
cgene->arn->translation->cste = gene->arn->translation->cste;
gene->arn->translation->copie = cgene->arn->translation;
cgene->transrate = gene->transrate;
cgene->arn->translation->copie = cgene->arn->translation;
cprot = cgene->arn->protein;
vector < Protein * >tempprotvec;
for (iprot = proteins.begin(); iprot != proteins.end(); iprot++) {
for (icomp = (*iprot)->composants.begin();
icomp != (*iprot)->composants.end(); icomp++) {
if ((*icomp)->protein == gene->arn->protein) {
Protein *cpprot = (*iprot)->copyprot();
cpprot->copie = *iprot;
(*iprot)->copie = cpprot;
tempprotvec.push_back(cpprot);
break;
}
}
}
for (iprot = tempprotvec.begin(); iprot != tempprotvec.end(); iprot++) {
Protein *prot = *iprot;
for (string::iterator istr = prot->label.begin();
istr != prot->label.end(); istr++) {
if (*istr == gene->arn->protein->label[0]) {
*istr = cgene->arn->protein->label[0];
}
}
proteins.push_back(*iprot);
}
vector < Promoter * >temppromovec;
for (ipromo = promoters.begin(); ipromo != promoters.end(); ipromo++) {
Protein *prot = (*ipromo)->protein;
if (prot->contain(gene->arn->protein)) {
temppromovec.push_back(*ipromo);
}
}
for (ipromo = temppromovec.begin(); ipromo != temppromovec.end(); ipromo++) {
addpromotion((*ipromo)->gene,
static_cast < Protein * >((*ipromo)->protein->copie),
(*ipromo)->eqcte, (*ipromo)->transrate);
}
vector < Promoter * >temppromovec2;
for (ipromo = promoters.begin(); ipromo != promoters.end(); ipromo++) {
if ((*ipromo)->gene == gene) {
temppromovec2.push_back(*ipromo);
}
}
for (ipromo = temppromovec2.begin(); ipromo != temppromovec2.end();
ipromo++) {
addpromotion(cgene, static_cast < Protein * >((*ipromo)->protein),
(*ipromo)->eqcte, (*ipromo)->transrate);
}
vector < Reaction * >tempreactvec;
for (ireact = reactions.begin(); ireact != reactions.end(); ireact++) {
if ((*ireact)->copie == 0) {
react = *ireact;
bool test = false;
if (react->reactif1->contain(gene->arn->protein, this)) {
react1 = react->reactif1->copie;
test = true;
} else
react1 = react->reactif1;
if (react->reactif2->contain(gene->arn->protein, this)) {
react2 = react->reactif2->copie;
test = true;
} else
react2 = react->reactif2;
if (react->produit1->contain(gene->arn->protein, this)) {
prod1 = react->produit1->copie;
test = true;
} else
prod1 = react->produit1;
if (react->produit2->contain(gene->arn->protein, this)) {
prod2 = react->produit2->copie;
test = true;
} else
prod2 = react->produit2;
if (test) {
Reaction *creact =
new Reaction(react1, react2, prod1, prod2,
(*ireact)->cste);
tempreactvec.push_back(creact);
creact->copie = react;
react->copie = creact;
}
}
}
for (ireact = tempreactvec.begin(); ireact != tempreactvec.end(); ireact++) {
reactions.push_back(*ireact);
}
}
int Cellule::reactionnum(Reaction * react)
{
if (react == NULL)
return 0;
vector < Reaction * >::iterator ireact;
int i = 1;
for (ireact = reactions.begin(); ireact != reactions.end(); ireact++) {
if (react == *ireact)
return i;
i++;
}
cout << "Erreur : réaction introuvable!\n";
return -1;
}
string Cellule::reactionstring(Reaction * react)
{
if (react == NULL)
return "NULL";
vector < Reaction * >::iterator ireact;
int i = 0;
for (ireact = reactions.begin(); ireact != reactions.end(); ireact++) {
if (react == *ireact) {
stringstream sreact;
sreact << "cell->reactions[" << i << "]";
return sreact.str();
}
i++;
}
cout << "Erreur : réaction introuvable!\n";
return "-1";
}
Cellule *Cellule::copycellule()
{
Cellule *cell = new Cellule();
Gene *gene;
Protein *prot;
Promoter *promo;
Espece *react1, *react2, *prod1, *prod2;
Reaction *react;
vector < Gene * >::iterator igene;
vector < Protein * >::iterator iprot;
vector < Promoter * >::iterator ipromo;
vector < Composant * >::iterator icomp;
vector < Reaction * >::iterator ireact;
for (ireact = reactions.begin(); ireact != reactions.end(); ireact++) {
(*ireact)->copie = 0;
}
for (igene = genes.begin(); igene != genes.end(); igene++) {
gene = cell->addgene();
(*igene)->copie = gene;
gene->copie = *igene;
gene->label = (*igene)->label;
(*igene)->arn->copie = gene->arn;
gene->arn->copie = (*igene)->arn;
gene->arn->qtite = (*igene)->arn->qtite;
gene->arn->label = (*igene)->arn->label;
gene->arn->cste = (*igene)->arn->cste;
(*igene)->arn->protein->copie = gene->arn->protein;
gene->arn->protein->copie = (*igene)->arn->protein;
gene->arn->protein->cste = (*igene)->arn->protein->cste;
gene->arn->protein->qtite = (*igene)->arn->protein->qtite;
gene->arn->protein->label = (*igene)->arn->protein->label;
gene->arn->translation->cste = (*igene)->arn->translation->cste;
(*igene)->arn->translation->copie = gene->arn->translation;
gene->transrate = (*igene)->transrate;
}
for (iprot = proteins.begin(); iprot != proteins.end(); iprot++) {
if (!((*iprot)->composants.empty())) {
prot = (*iprot)->copyprot();
cell->proteins.push_back(prot);
}
}
for (ipromo = promoters.begin(); ipromo != promoters.end(); ipromo++) {
promo = new Promoter(static_cast < Gene * >((*ipromo)->gene->copie),
static_cast <
Protein * >((*ipromo)->protein->copie));
cell->promoters.push_back(promo);
promo->label = (*ipromo)->label;
promo->eqcte = (*ipromo)->eqcte;
promo->transrate = (*ipromo)->transrate;
(*ipromo)->copie = promo;
promo->copie = *ipromo;
}
for (ireact = reactions.begin(); ireact != reactions.end(); ireact++) {
if ((*ireact)->copie == 0) {
react = *ireact;
(react->reactif1) ? react1 = react->reactif1->copie : react1 =
NULL;
(react->reactif2) ? react2 = react->reactif2->copie : react2 =
NULL;
(react->produit1) ? prod1 = react->produit1->copie : prod1 = NULL;
(react->produit2) ? prod2 = react->produit2->copie : prod2 = NULL;
Reaction *creact =
cell->addreaction(react1, react2, prod1, prod2,
(*ireact)->cste);
creact->copie = react;
react->copie = creact;
}
}
cell->score = score;
return cell;
}
int Cellule::especenum(Espece * pesp)
{
if (pesp == NULL)
return 0;
vector < Arn * >::iterator iarn;
vector < Protein * >::iterator iprot;
int narns = arns.size();
int i = 1;
for (iarn = arns.begin(); iarn != arns.end(); iarn++) {
if (pesp == *iarn)
return i;
i++;
}
i = 1 + narns;
for (iprot = proteins.begin(); iprot != proteins.end(); iprot++) {
if (pesp == *iprot)
return i;
i++;
}
cout << "Erreur : espèce introuvable (especenum)!" << pesp->label << endl;
return -1;
}
Protein *Cellule::addprotein(double c, double q)
{
//Rajoute une proteine exterieure dans le milieu
Protein *prot = new Protein(c, q);
proteins.push_back(prot);
return prot;
}
Protein *Cellule::fusion(Protein * prot1, Protein * prot2)
{
// rassemble des composants de i et j
Protein *prot = new Protein();
prot->addcomposant(prot1);
prot->addcomposant(prot2);
return prot;
}
Reaction *Cellule::adddimere(Protein * prot1, Protein * prot2, double c,
double q, double cdimerisation)
{
vector < Composant * >::iterator icomp;
Protein *prot = fusion(prot1, prot2);
prot->qtite = q;
prot->cste = c;
proteins.push_back(prot);
for (icomp = prot->composants.begin(); icomp != prot->composants.end();
icomp++) {
for (int i = 0; i < (*icomp)->nb; i++)
prot->label += (*icomp)->protein->label;
}
//Ajout de la réaction de dimérisation
return addreaction(prot1, prot2, prot, NULL, cdimerisation);
}
Reaction *Cellule::addrandactiv()
{
Protein *anchorprot = proteins[nb_genes];
Protein *prots;
Protein *protc;
if (anchorsignal) {
prots = proteins[(int) (proteins.size() * frand())];
protc = proteins[(int) (proteins.size() * frand())];
} else {
prots = anchorprot;
protc = anchorprot;
while (prots == anchorprot) {
prots = proteins[(int) (proteins.size() * frand())];
}
while (protc == anchorprot) {
protc = proteins[(int) (proteins.size() * frand())];
}
}
Protein *protp = protc->addphospho();
proteins.push_back(protp);
return addreaction(prots, protc, prots, protp);
}
Reaction *Cellule::addreaction(Espece * react1, Espece * react2,
Espece * prod1, Espece * prod2, double q)
{
Reaction *react = new Reaction(react1, react2, prod1, prod2, q);
reactions.push_back(react);
return react;
}
Reaction *Cellule::addrandreact()
{
Protein *randprot1, *randprot2, *anchorprot;
Reaction *react;
anchorprot = proteins[nb_genes];
randprot1 = randprot2 = anchorprot;
if (anchorsignal) {
randprot1 = proteins[(int) (frand() * proteins.size())];
randprot2 = proteins[(int) (frand() * proteins.size())];
} else {
randprot1 = randprot2 = anchorprot;
while (randprot1 == anchorprot) {
randprot1 = proteins[(int) (frand() * proteins.size())];
}
while (randprot2 == anchorprot) {
randprot2 = proteins[(int) (frand() * proteins.size())];
}
}
react = adddimere(randprot1, randprot2);
return react;
}
void Cellule::phosphorylation(Protein * prot)
{
Protein *protcible = prot->addphospho();
proteins.push_back(protcible);
addreaction(prot, NULL, protcible, NULL, 0.2 * frand2());
}
void Cellule::addphospho()
{
Protein *anchorprot = proteins[nb_genes];
Protein *prot = anchorprot;
if (anchorsignal) {
prot = proteins[(int) (frand() * proteins.size())];
} else {
while (prot == anchorprot) {
prot = proteins[(int) (frand() * proteins.size())];
}
}
Protein *protcible = prot->addphospho();
proteins.push_back(protcible);
addreaction(prot, NULL, protcible, NULL);
}
Gene *Cellule::addgene()
{
Gene *gene = new Gene();
genes.push_back(gene);
Arn *arn = gene->arn;
arns.push_back(arn);
proteins.push_back(arn->protein);
reactions.push_back(arn->translation);
return gene;
}
Promoter *Cellule::addpromotion(Gene * gene, Protein * prot, double e,
double t)
{
Promoter *promo = new Promoter(gene, prot);
promo->label = gene->label;
promo->transrate = t;
promo->eqcte = e;
promoters.push_back(promo);
return promo;
}
bool Cellule::addclivage()
{
int size = 0;
vector < Composant * >::iterator icomp;
Protein *protini, *prot;
Protein *prot1 = new Protein();
Protein *prot2 = new Protein();
if (!(proteins.size())) {
delete prot1;
delete prot2;
return false;
}
int i = (int) (frand() * proteins.size());
protini = proteins[i];
for (icomp = protini->composants.begin();
icomp != protini->composants.end(); icomp++) {
size += (*icomp)->nb;
}
if (size < 2) {
delete prot1;
delete prot2;
return false;
}
protini->clivage(*prot1, *prot2);
if (prot1->composants.empty() || prot2->composants.empty()) {
delete prot1;
delete prot2;
return false;
}
prot = existe(prot1);
if (prot) {
delete prot1;
prot1 = prot;
} else {
proteins.push_back(prot1);
}
prot = existe(prot2);
if (prot) {
delete prot2;
prot2 = prot;
} else {
proteins.push_back(prot2);
}
addreaction(protini, NULL, prot1, prot2);
return true;
}
bool Cellule::rmrandpromo()
{
if (promoters.size() == 0)
return false;
Promoter *promo;
int i = (int) (frand() * promoters.size());
promo = promoters[i];
promoters.erase(promoters.begin() + i);
delete promo;
return true;
}
bool Cellule::rmrandprot()
{
int i = (int) (proteins.size() * frand());
Protein *prot = proteins[i];
vector < Reaction * >reacts;
if (prot->composants.empty() && prot->phosphosite == NULL)
return false;
if (prot->label == "X")
return false;
vector < Reaction * >::iterator ireact;
for (ireact = reactions.begin(); ireact != reactions.end(); ireact++) {
if ((*ireact)->reactif1 == prot || (*ireact)->reactif2 == prot)
return false;
}
for (vector < Promoter * >::iterator ipromo = promoters.begin();
ipromo != promoters.end(); ipromo++) {
if ((*ipromo)->protein == prot)
return false;
}
for (ireact = reactions.begin(); ireact != reactions.end(); ireact++) {
if ((*ireact)->produit1 == prot || (*ireact)->produit2 == prot) {
reacts.push_back(*ireact);
}
}
for (unsigned int j = 0; j < reacts.size(); j++) {
rmreaction(reacts.back());
reacts.pop_back();
}
proteins.erase(proteins.begin() + i);
delete prot;
return true;
}
void Cellule::rmreaction(Reaction * r)
{
reactions.erase(find(reactions.begin(), reactions.end(), r));
delete r;
}
bool Cellule::evolution_modifq()
{
const double sommetaux =
t_mod_r + t_mod_pro + t_mod_qtite + t_rmreact + t_mod_qpromo;
const double taux[] =
{ t_mod_r, t_mod_pro, t_mod_qtite, t_rmreact, t_mod_qpromo };
/* Sélection de la modification */
double r = frand() * sommetaux;
double inf = 0;
int i = 0;
do {
inf += taux[i];
i++;
} while (r > inf);
i--;
switch (i) {
case 0:
//Modif réaction
reactions[(int) (frand() * reactions.size())]->modifcinetique();
return true;
break;
case 1:
//Modif dégradation
if (frand() < 0.8)
proteins[(int) (frand() * proteins.size())]->modifdegrad();
else
arns[(int) (frand() * arns.size())]->modifdegrad();
return true;
break;
case 2:
//Modif quantités
if (frand() < 0.2)
arns[(int) (frand() * arns.size())]->modifqtite();
else
proteins[(int) (frand() * proteins.size())]->modifqtite();
return true;
break;
case 3:
//Suppression de réactions
if (frand() < 0.5) {
if (rmrandpromo())
return true;
} else {
if (rmrandprot())
return true;
}
break;
case 4:
//Modification des quantités de promoteurs
if (promoters.size()) {
promoters[(int) (frand() * promoters.size())]->modifeq();
return true;
}
break;
}
return false;
}
bool Cellule::evolution_ajout()
{
//procedure d'evolution
const double sommetaux = t_new_r + t_new_promo + t_clivage + t_phospho;
const double taux[] = { t_new_r, t_new_promo, t_clivage, t_phospho };
Gene *randgene;
Protein *randprot;
/* Sélection de la modification */
double r = frand() * sommetaux;
double inf = 0;
int i = 0;
do {
inf += taux[i];
i++;
} while (r > inf);
i--;
switch (i) {
case 0:
//Dimérisation
if (reactions.size() < nb_reactions_max
&& proteins.size() < nb_proteins_max) {
addrandreact();
return true;
}
break;
case 1:
//Ajout d'une promotion
if (reactions.size() < nb_reactions_max - 2
&& promoters.size() < nb_promoters_max) {
randgene = genes[(int) (frand() * genes.size())];
randprot = proteins[(int) (frand() * proteins.size())];
addpromotion(randgene, randprot);
return true;
}
break;
case 2:
//Clivage d'une protéïne
if (reactions.size() < nb_reactions_max
&& proteins.size() < nb_proteins_max - 1) {
addclivage();
return true;
}
break;
case 3:
//Ajout d'une phosphorylation
if (reactions.size() < nb_reactions_max
&& proteins.size() < nb_proteins_max) {
if (frand() < 0.5)
addphospho();
else
addrandactiv();
return true;
}
break;
}
return false;
}
void Cellule::evolution()
{
//procedure d'evolution
const double sommetaux = t_new_r + t_mod_r + t_mod_pro + t_mod_qtite
+ t_new_promo + t_clivage + t_rmreact + t_phospho + t_mod_qpromo +
t_dupgene + t_mutdir;
const double taux[] = { t_new_r, t_mod_r, t_mod_pro, t_mod_qtite,
t_new_promo, t_clivage, t_rmreact, t_phospho, t_mod_qpromo, t_dupgene,
t_mutdir
};
Gene *randgene;
Protein *randprot;
/* Sélection de la modification */
int j = 1;
while (j) {
double r = frand() * sommetaux;
double inf = 0;
int i = 0;
do {
inf += taux[i];
i++;
} while (r > inf);
i--;
switch (i) {
case 0:
//Dimérisation
if (reactions.size() < nb_reactions_max
&& proteins.size() < nb_proteins_max) {
addrandreact();
j = 0;
}
break;
case 1:
//Modif réaction
reactions[(int) (frand() * reactions.size())]->modifcinetique();
j = 0;
break;
case 2:
//Modif dégradation
if (frand() < 0.8)
proteins[(int) (frand() * proteins.size())]->modifdegrad();
else
arns[(int) (frand() * arns.size())]->modifdegrad();
j = 0;
break;
case 3:
//Modif quantités
if (frand() < 0.2)
arns[(int) (frand() * arns.size())]->modifqtite();
else
proteins[(int) (frand() * proteins.size())]->modifqtite();
j = 0;
break;
case 4:
//Ajout d'une promotion
if (reactions.size() < nb_reactions_max - 2
&& promoters.size() < nb_promoters_max) {
// cout << "addpromo" << endl;
randgene = genes[(int) (frand() * genes.size())];
randprot = proteins[(int) (frand() * proteins.size())];
addpromotion(randgene, randprot);
j = 0;
}
break;
case 5:
//Clivage d'une protéïne
if (reactions.size() < nb_reactions_max
&& proteins.size() < nb_proteins_max - 1) {
addclivage();
j = 0;
}
break;
case 6:
//Suppression de réactions
if (frand() < 0.5) {
if (rmrandpromo())
j = 0;
} else {
if (rmrandprot())
j = 0;
}
break;
case 7:
//Ajout d'une phosphorylation
if (reactions.size() < nb_reactions_max
&& proteins.size() < nb_proteins_max) {
if (frand() < 0.5)
addphospho();
else
addrandactiv();
j = 0;
}
break;
case 8:
//Modification des quantités de promoteurs
if (promoters.size()) {
if (frand() < 0.5) {
promoters[(int) (frand() * promoters.size())]->modifeq();
} else {
if (frand() < 0.5) {
promoters[(int) (frand() * promoters.size())]->
modiftrans();
} else
genes[(int) (frand() * genes.size())]->modiftrans();
}
j = 0;
}
break;
case 9:
//Duplication d'un gène
copygene(genes[(int) (frand() * genes.size())]);
j = 0;
break;
case 10:
//modification du sens des quantités initiales
proteins[(int) (frand() * proteins.size())]->mutinit();
j = 0;
break;
}
}
score = 0;
}
void Cellule::optievolution()
{
const double sommetaux =
t_mod_r_opti + t_mod_pro_opti + t_mod_qtite_opti + t_rmreact_opti;
const double taux[] =
{ t_mod_r_opti, t_mod_pro_opti, t_mod_qtite_opti, t_rmreact_opti };
/* Sélection de la modification */
int j = 1;
while (j) {
double r = frand() * sommetaux;
double inf = 0;
int i = 0;
do {
inf += taux[i];
i++;
} while (r > inf);
i--;
switch (i) {
case 0:
//Modif réaction
reactions[(int) (frand() * reactions.size())]->
modifcinetique(ampli_opti);
j = 0;
break;
case 1:
//Modif dégradation
if (frand() < 0.5) {
proteins[(int) (frand() * proteins.size())]->
modifdegrad(ampli_opti);
} else {
arns[(int) (frand() * arns.size())]->modifdegrad(ampli_opti);
}
j = 0;
break;
case 2:
//Modif quantités
if (frand() < 0.3) {
arns[(int) (frand() * arns.size())]->modifqtite(ampli_opti);
} else {
proteins[(int) (frand() * proteins.size())]->
modifqtite(ampli_opti);
}
j = 0;
break;
case 3:
//Suppression de réactions
if (frand() < 0.3) {
if (rmrandpromo())
j = 0;
} else {
if (rmrandprot())
j = 0;
}
break;
}
}
score = 0;
}
void Cellule::printgraph(ostream & out)
{
printinternpart(out);
printproperties(out);
}
void Cellule::printinternpart(ostream & out)
{
vector < Gene * >::iterator igene;
vector < Arn * >::iterator iarn;
vector < Protein * >::iterator iprot;
vector < Promoter * >::iterator ipromo;
vector < Reaction * >::iterator ireact;
out << "digraph network {" << endl;
out << "fontname=\"Helvetica\"" << endl;
out << "node [fontname=\"Helvetica\"];" << endl;
out << "edge [fontname=\"Helvetica\"]" << endl;
out << "{ rank=same; node [shape=box,color=red];" << endl;
for (iarn = arns.begin(); iarn != arns.end(); iarn++) {
out << "\"" << *iarn << "\" [label=\"" << (*iarn)->
label << "\\nρ=" << setprecision(2) << (*iarn)->gene->
transrate << ", δ=" << (*iarn)->cste << ", α=" << (*iarn)->
translation->cste << "\"]; ";
}
out << "}" << endl;
out << "{" << endl;
for (iprot = proteins.begin(); iprot != proteins.end(); iprot++) {
out << "\"" << *iprot << "\" [label=\"" << (*iprot)->
label << ", δ=" << setprecision(2) << (*iprot)->cste << "\"]; ";
}
out << "}" << endl;
out << "node [shape=plaintext];" << endl;
for (iarn = arns.begin(); iarn != arns.end(); iarn++) {
out << "\"" << *iarn << "\" -> \"" << (*iarn)->protein << "\"; ";
}
for (ipromo = promoters.begin(); ipromo != promoters.end(); ipromo++) {
out << "\"" << (*ipromo)->protein << "\" -> \"" << (*ipromo)->gene->
arn << "\" [color=red, decorate=true, label=\"K=" <<
setprecision(2) << (*ipromo)->eqcte << "\\nρ=" << (*ipromo)->
transrate << "\"";
if ((*ipromo)->transrate > (*ipromo)->gene->transrate) {
out << "];";
} else {
out << ", arrowhead=\"tee\"];";
}
}
for (ireact = reactions.begin(); ireact != reactions.end(); ireact++)
(*ireact)->copie = NULL;
for (igene = genes.begin(); igene != genes.end(); igene++) {
(*igene)->arn->translation->copie = (*igene)->arn->translation;
}
for (ireact = reactions.begin(); ireact != reactions.end(); ireact++) {
if ((*ireact)->reactif1 && (*ireact)->reactif2 && (*ireact)->produit1
&& (*ireact)->produit2
&& (*ireact)->reactif1 == (*ireact)->produit1) {
out << "\"" << *ireact << "\" [label=\"" << setprecision(2) <<
(*ireact)->cste << "\"];";
out << "\"" << (*ireact)->
reactif2 << "\" -> \"" << *ireact << "\"; ";
out << "\"" << *ireact << "\" -> \"" << (*ireact)->
produit2 << "\"; ";
out << "\"" << (*ireact)->
reactif1 << "\" -> \"" << *ireact << "\" [style=dashed]; ";
(*ireact)->copie = *ireact;
}
}
for (ireact = reactions.begin(); ireact != reactions.end(); ireact++) {
if ((*ireact)->copie == NULL) {
out << "\"" << *ireact << "\" [label=\"" << setprecision(2) <<
(*ireact)->cste << "\"];";
if ((*ireact)->reactif1) {
out << "\"" << (*ireact)->
reactif1 << "\" -> \"" << *ireact << "\"; ";
}
if ((*ireact)->reactif2) {
out << "\"" << (*ireact)->
reactif2 << "\" -> \"" << *ireact << "\"; ";
}
if ((*ireact)->produit1) {